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Ytterbium in PDB 1sk6: Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate

Enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate

All present enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate, PDB code: 1sk6 was solved by Q.Guo, Y.Shen, N.L.Zhukovskaya, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.870, 166.453, 342.393, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 30.7

Other elements in 1sk6:

The structure of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate (pdb code 1sk6). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 9 binding sites of Ytterbium where determined in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate, PDB code: 1sk6:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Ytterbium binding site 1 out of 9 in 1sk6

Go back to Ytterbium Binding Sites List in 1sk6
Ytterbium binding site 1 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb901

b:50.0
occ:0.20
 YB A:YB907 1.7 50.0 0.8
OD2 A:ASP493 1.9 28.8 1.0
NE2 A:HIS577 2.2 20.5 1.0
O1P A:CMP289 2.4 13.0 1.0
CG A:ASP493 2.5 27.0 1.0
CE1 A:HIS577 2.6 20.3 1.0
OD1 A:ASP493 2.7 28.4 1.0
CD2 A:HIS577 2.8 19.4 1.0
ND1 A:HIS577 3.3 18.9 1.0
CG A:HIS577 3.4 17.8 1.0
P A:CMP289 3.7 14.5 1.0
CB A:ASP493 3.8 24.9 1.0
C5' A:CMP289 3.8 14.9 1.0
YB A:YB904 3.9 42.9 0.2
OD2 A:ASP491 4.0 10.0 1.0
O5' A:CMP289 4.1 14.8 1.0
OD1 A:ASP491 4.1 13.0 1.0
CA A:ASP493 4.3 18.9 1.0
CG A:ASP491 4.5 10.7 1.0
C3' A:CMP289 4.5 18.4 1.0
O3' A:CMP289 4.6 14.2 1.0
CB A:HIS577 4.7 17.5 1.0
C4' A:CMP289 4.7 15.4 1.0
O2P A:CMP289 4.8 12.0 1.0
O A:TYR492 4.8 21.4 1.0

Ytterbium binding site 2 out of 9 in 1sk6

Go back to Ytterbium Binding Sites List in 1sk6
Ytterbium binding site 2 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb904

b:42.9
occ:0.20
 OD1 A:ASP491 2.1 13.0 1.0
YB A:YB907 2.2 50.0 0.8
OD2 A:ASP491 2.3 10.0 1.0
CG A:ASP491 2.4 10.7 1.0
O3 A:POP893 3.0 0.8 1.0
O1P A:CMP289 3.3 13.0 1.0
CG A:LYS346 3.4 10.4 1.0
CD A:LYS346 3.5 10.0 1.0
CB A:ASP491 3.7 10.0 1.0
OD2 A:ASP493 3.7 28.8 1.0
O2P A:CMP289 3.8 12.0 1.0
CE A:LYS346 3.8 10.0 1.0
N A:ASP491 3.8 12.6 1.0
P1 A:POP893 3.8 96.7 1.0
YB A:YB901 3.9 50.0 0.2
O1 A:POP893 4.0 0.4 1.0
OD1 A:ASP493 4.1 28.4 1.0
O2 A:POP893 4.1 98.9 1.0
P A:CMP289 4.1 14.5 1.0
O A:LYS346 4.1 10.0 1.0
CG A:ASP493 4.2 27.0 1.0
CA A:ASP491 4.3 14.1 1.0
NZ A:LYS346 4.5 15.0 1.0
O A:GLY347 4.7 46.7 1.0
C A:ASP491 4.7 17.0 1.0
CB A:LYS346 4.8 18.2 1.0
O5' A:CMP289 4.8 14.8 1.0
C A:LYS346 4.9 10.0 1.0
C A:ALA490 4.9 12.7 1.0
O A:ASP491 5.0 18.4 1.0

Ytterbium binding site 3 out of 9 in 1sk6

Go back to Ytterbium Binding Sites List in 1sk6
Ytterbium binding site 3 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb907

b:50.0
occ:0.80
 YB A:YB901 1.7 50.0 0.2
O1P A:CMP289 2.2 13.0 1.0
YB A:YB904 2.2 42.9 0.2
OD2 A:ASP493 2.2 28.8 1.0
OD2 A:ASP491 2.4 10.0 1.0
OD1 A:ASP491 2.8 13.0 1.0
CG A:ASP491 3.0 10.7 1.0
CG A:ASP493 3.1 27.0 1.0
OD1 A:ASP493 3.2 28.4 1.0
P A:CMP289 3.6 14.5 1.0
NE2 A:HIS577 3.6 20.5 1.0
CD2 A:HIS577 3.6 19.4 1.0
O2P A:CMP289 4.1 12.0 1.0
CE1 A:HIS577 4.1 20.3 1.0
CG A:HIS577 4.1 17.8 1.0
O5' A:CMP289 4.3 14.8 1.0
ND1 A:HIS577 4.3 18.9 1.0
CB A:ASP491 4.5 10.0 1.0
CB A:ASP493 4.5 24.9 1.0
C5' A:CMP289 4.7 14.9 1.0
O3 A:POP893 4.7 0.8 1.0
O A:TYR492 4.7 21.4 1.0
O3' A:CMP289 4.7 14.2 1.0
O A:GLY347 4.8 46.7 1.0
ND2 A:ASN576 4.9 15.1 1.0
CA A:ASP493 4.9 18.9 1.0
O A:LYS346 4.9 10.0 1.0
CB A:HIS577 5.0 17.5 1.0

Ytterbium binding site 4 out of 9 in 1sk6

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Ytterbium binding site 4 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb902

b:0.1
occ:0.20
 YB B:YB908 2.0 50.0 0.8
O1 B:POP894 3.0 51.1 1.0
CE B:LYS346 3.0 27.1 1.0
O1P B:CMP290 3.0 17.0 1.0
OD1 B:ASP491 3.0 10.0 1.0
OD2 B:ASP491 3.1 10.0 1.0
CG B:ASP491 3.3 10.0 1.0
OD1 B:ASP493 3.5 18.0 1.0
CD B:LYS346 3.5 26.8 1.0
P1 B:POP894 3.6 53.9 1.0
O3 B:POP894 3.6 52.7 1.0
YB B:YB905 3.7 31.9 0.2
O2 B:POP894 4.0 55.2 1.0
P B:CMP290 4.1 25.5 1.0
CG B:ASP493 4.1 15.3 1.0
OD2 B:ASP493 4.1 16.0 1.0
NZ B:LYS346 4.2 24.4 1.0
O5' B:CMP290 4.3 24.5 1.0
O2P B:CMP290 4.3 25.2 1.0
N B:ASP491 4.5 20.5 1.0
NE2 B:HIS577 4.6 33.7 1.0
CB B:ASP491 4.7 10.0 1.0
C5' B:CMP290 4.8 25.1 1.0
O B:LYS346 4.8 19.3 1.0
CG B:LYS346 4.9 26.8 1.0

Ytterbium binding site 5 out of 9 in 1sk6

Go back to Ytterbium Binding Sites List in 1sk6
Ytterbium binding site 5 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb905

b:31.9
occ:0.20
 O1P B:CMP290 2.0 17.0 1.0
NE2 B:HIS577 2.3 33.7 1.0
YB B:YB908 2.5 50.0 0.8
CD2 B:HIS577 2.8 34.1 1.0
P B:CMP290 3.2 25.5 1.0
CE1 B:HIS577 3.2 33.1 1.0
C5' B:CMP290 3.4 25.1 1.0
C3' B:CMP290 3.5 22.0 1.0
O5' B:CMP290 3.7 24.5 1.0
YB B:YB902 3.7 0.1 0.2
O3' B:CMP290 3.7 16.1 1.0
CG B:HIS577 3.9 31.5 1.0
C4' B:CMP290 4.0 22.6 1.0
OD1 B:ASP493 4.0 18.0 1.0
ND1 B:HIS577 4.0 32.6 1.0
OD2 B:ASP491 4.1 10.0 1.0
OD2 B:ASP493 4.1 16.0 1.0
O B:GLY347 4.3 40.0 1.0
O2P B:CMP290 4.4 25.2 1.0
CG B:ASP493 4.4 15.3 1.0
O4' B:CMP290 4.5 24.9 1.0
C1' B:CMP290 4.5 21.9 1.0
CG B:LEU348 4.5 21.6 1.0
C2' B:CMP290 4.6 25.5 1.0
CD1 B:LEU348 4.9 19.2 1.0
CD B:LYS346 5.0 26.8 1.0
CA B:LEU348 5.0 19.1 1.0

Ytterbium binding site 6 out of 9 in 1sk6

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Ytterbium binding site 6 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb908

b:50.0
occ:0.80
 YB B:YB902 2.0 0.1 0.2
OD2 B:ASP491 2.3 10.0 1.0
OD2 B:ASP493 2.5 16.0 1.0
YB B:YB905 2.5 31.9 0.2
OD1 B:ASP491 2.6 10.0 1.0
NE2 B:HIS577 2.7 33.7 1.0
OD1 B:ASP493 2.7 18.0 1.0
CG B:ASP491 2.8 10.0 1.0
CG B:ASP493 2.9 15.3 1.0
O1P B:CMP290 3.1 17.0 1.0
CD2 B:HIS577 3.6 34.1 1.0
CE1 B:HIS577 3.7 33.1 1.0
CB B:ASP491 4.4 10.0 1.0
CB B:ASP493 4.4 10.2 1.0
P B:CMP290 4.4 25.5 1.0
C5' B:CMP290 4.5 25.1 1.0
CD B:LYS346 4.6 26.8 1.0
O5' B:CMP290 4.6 24.5 1.0
CE B:LYS346 4.6 27.1 1.0
O B:GLY347 4.6 40.0 1.0
O B:LYS346 4.8 19.3 1.0
CG B:HIS577 4.8 31.5 1.0
ND1 B:HIS577 4.8 32.6 1.0
O B:TYR492 4.9 20.7 1.0
O1 B:POP894 4.9 51.1 1.0

Ytterbium binding site 7 out of 9 in 1sk6

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Ytterbium binding site 7 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Yb903

b:72.6
occ:0.20
 YB C:YB909 2.0 72.5 0.8
OD2 C:ASP491 2.4 28.2 1.0
O5 C:POP895 2.5 62.0 1.0
OD1 C:ASP493 3.1 10.0 1.0
O1P C:CMP910 3.4 15.4 1.0
CE C:LYS346 3.4 10.0 1.0
CG C:ASP491 3.5 27.2 1.0
OD2 C:ASP493 3.6 10.0 1.0
CG C:ASP493 3.6 10.0 1.0
P2 C:POP895 3.6 56.4 1.0
YB C:YB906 3.7 31.2 0.2
O6 C:POP895 3.8 56.8 1.0
OD1 C:ASP491 4.0 27.3 1.0
O4 C:POP895 4.0 62.6 1.0
CG C:LYS346 4.2 10.0 1.0
N C:ASP491 4.3 22.4 1.0
CD C:LYS346 4.4 10.0 1.0
NZ C:LYS346 4.5 10.0 1.0
CB C:ASP491 4.6 27.4 1.0
O C:ASP491 4.6 25.1 1.0
O C:LYS346 4.7 11.4 1.0
P C:CMP910 4.7 22.0 1.0
CA C:ASP491 4.9 22.3 1.0
O C:POP895 4.9 52.8 1.0
CB C:ASP493 4.9 10.0 1.0
C C:ASP491 5.0 23.6 1.0
O2P C:CMP910 5.0 15.3 1.0

Ytterbium binding site 8 out of 9 in 1sk6

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Ytterbium binding site 8 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Yb906

b:31.2
occ:0.20
 OD1 C:ASP493 2.0 10.0 1.0
NE2 C:HIS577 2.3 24.7 1.0
YB C:YB909 2.5 72.5 0.8
O1P C:CMP910 2.5 15.4 1.0
CG C:ASP493 2.8 10.0 1.0
CE1 C:HIS577 2.8 25.7 1.0
C5' C:CMP910 3.1 17.2 1.0
OD2 C:ASP493 3.3 10.0 1.0
CD2 C:HIS577 3.5 24.4 1.0
P C:CMP910 3.5 22.0 1.0
O5' C:CMP910 3.6 17.1 1.0
YB C:YB903 3.7 72.6 0.2
C3' C:CMP910 3.7 22.2 1.0
C4' C:CMP910 3.9 19.1 1.0
CB C:ASP493 4.0 10.0 1.0
O3' C:CMP910 4.1 21.9 1.0
ND1 C:HIS577 4.1 26.5 1.0
O4' C:CMP910 4.4 19.1 1.0
CG C:HIS577 4.4 24.6 1.0
C1' C:CMP910 4.6 20.3 1.0
N3 C:CMP910 4.7 38.7 1.0
OD2 C:ASP491 4.8 28.2 1.0
O2P C:CMP910 4.8 15.3 1.0
C2' C:CMP910 4.9 20.7 1.0
OD1 C:ASP491 5.0 27.3 1.0

Ytterbium binding site 9 out of 9 in 1sk6

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Ytterbium binding site 9 out of 9 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 9 of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Yb909

b:72.5
occ:0.80
 YB C:YB903 2.0 72.6 0.2
YB C:YB906 2.5 31.2 0.2
OD2 C:ASP493 2.5 10.0 1.0
OD2 C:ASP491 2.6 28.2 1.0
OD1 C:ASP493 2.6 10.0 1.0
OD1 C:ASP491 2.9 27.3 1.0
CG C:ASP493 2.9 10.0 1.0
CG C:ASP491 3.0 27.2 1.0
O1P C:CMP910 3.1 15.4 1.0
NE2 C:HIS577 3.1 24.7 1.0
CD2 C:HIS577 3.8 24.4 1.0
CE1 C:HIS577 4.1 25.7 1.0
O C:LYS346 4.2 11.4 1.0
CB C:ASP493 4.4 10.0 1.0
O5 C:POP895 4.5 62.0 1.0
CB C:ASP491 4.5 27.4 1.0
P C:CMP910 4.6 22.0 1.0
CE C:LYS346 4.8 10.0 1.0
CG C:LYS346 5.0 10.0 1.0

Reference:

Q.Guo, Y.Shen, N.L.Zhukovskaya, J.Florian, W.J.Tang. Structural and Kinetic Analyses of the Interaction of Anthrax Adenylyl Cyclase Toxin with Reaction Products Camp and Pyrophosphate. J.Biol.Chem. V. 279 29427 2004.
ISSN: ISSN 0021-9258
PubMed: 15131111
DOI: 10.1074/JBC.M402689200
Page generated: Sat Oct 12 20:57:09 2024

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