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Ytterbium in PDB 1k90: Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp

Enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp

All present enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp:
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 and 3' Deoxy-Atp, PDB code: 1k90 was solved by C.L.Drum, S.-Z.Yan, J.Bard, Y.-Q.Shen, D.Lu, S.Soelaiman, Z.Grabarek, A.Bohm, W.-J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.099, 166.100, 343.330, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 28.6

Other elements in 1k90:

The structure of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp 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 and 3' Deoxy-Atp (pdb code 1k90). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp, PDB code: 1k90:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 1k90

Go back to Ytterbium Binding Sites List in 1k90
Ytterbium binding site 1 out of 3 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb901

b:38.1
occ:1.00
 OD1 A:ASP491 2.1 30.0 1.0
OD2 A:ASP493 2.2 35.6 1.0
OD1 A:ASP493 2.2 10.7 1.0
O1A A:3AT902 2.4 55.3 1.0
CG A:ASP493 2.5 40.5 1.0
OD2 A:ASP491 2.6 46.8 1.0
CG A:ASP491 2.7 55.9 1.0
NE2 A:HIS577 2.8 11.6 1.0
O2B A:3AT902 3.0 40.1 1.0
PB A:3AT902 3.5 36.1 1.0
PA A:3AT902 3.5 36.3 1.0
O1B A:3AT902 3.5 39.4 1.0
CD2 A:HIS577 3.5 31.9 1.0
O3A A:3AT902 3.6 44.1 1.0
O5' A:3AT902 3.8 44.4 1.0
CE1 A:HIS577 3.9 70.2 1.0
O A:ASP491 4.0 97.0 1.0
CB A:ASP493 4.0 27.8 1.0
CB A:ASP491 4.2 47.5 1.0
O A:LYS346 4.5 34.7 1.0
C A:ASP491 4.7 30.0 1.0
CG A:HIS577 4.8 33.8 1.0
NZ A:LYS346 4.8 10.5 1.0
N A:ASP491 4.8 43.2 1.0
O2A A:3AT902 4.8 55.5 1.0
CA A:ASP491 4.8 31.2 1.0
CA A:ASP493 4.9 38.7 1.0
ND1 A:HIS577 4.9 34.6 1.0
NH2 A:ARG329 5.0 53.2 1.0

Ytterbium binding site 2 out of 3 in 1k90

Go back to Ytterbium Binding Sites List in 1k90
Ytterbium binding site 2 out of 3 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb902

b:48.0
occ:1.00
 OD2 B:ASP493 2.2 42.8 1.0
O1A B:3AT903 2.2 65.6 1.0
OD2 B:ASP491 2.3 30.4 1.0
CE1 B:HIS577 2.4 21.6 1.0
OD1 B:ASP493 2.5 57.7 1.0
OD1 B:ASP491 2.6 53.0 1.0
CG B:ASP493 2.7 42.7 1.0
CG B:ASP491 2.8 34.5 1.0
NE2 B:HIS577 3.0 47.3 1.0
O2B B:3AT903 3.1 49.2 1.0
PA B:3AT903 3.3 49.1 1.0
PB B:3AT903 3.5 48.5 1.0
O1B B:3AT903 3.5 59.2 1.0
ND1 B:HIS577 3.5 65.5 1.0
O3A B:3AT903 3.6 49.4 1.0
O5' B:3AT903 3.7 58.4 1.0
CB B:ASP493 4.2 57.3 1.0
CD2 B:HIS577 4.3 55.0 1.0
CB B:ASP491 4.3 32.5 1.0
O B:LYS346 4.5 62.9 1.0
CG B:HIS577 4.6 38.1 1.0
O2A B:3AT903 4.7 61.6 1.0
CA B:ASP493 4.9 63.8 1.0

Ytterbium binding site 3 out of 3 in 1k90

Go back to Ytterbium Binding Sites List in 1k90
Ytterbium binding site 3 out of 3 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Yb903

b:38.0
occ:1.00
 OD1 C:ASP493 2.0 9.5 1.0
OD2 C:ASP493 2.2 9.7 1.0
OD1 C:ASP491 2.4 32.0 1.0
CG C:ASP493 2.4 9.7 1.0
OD2 C:ASP491 2.4 54.9 1.0
O1A C:3AT904 2.5 56.5 1.0
CG C:ASP491 2.7 38.6 1.0
CE1 C:HIS577 2.8 12.0 1.0
O2B C:3AT904 3.2 32.3 1.0
PA C:3AT904 3.5 28.4 1.0
O1B C:3AT904 3.5 29.5 1.0
PB C:3AT904 3.6 37.2 1.0
NE2 C:HIS577 3.7 31.2 1.0
O5' C:3AT904 3.7 41.2 1.0
O3A C:3AT904 3.7 35.9 1.0
ND1 C:HIS577 3.9 53.1 1.0
CB C:ASP493 4.0 10.1 1.0
CB C:ASP491 4.2 36.0 1.0
O C:LYS346 4.5 37.2 1.0
CA C:ASP493 4.8 14.5 1.0
O2A C:3AT904 4.9 53.6 1.0
CD2 C:HIS577 4.9 51.5 1.0
N C:ASP493 4.9 29.5 1.0

Reference:

C.L.Drum, S.-Z.Yan, J.Bard, Y.-Q.Shen, D.Lu, S.Soelaiman, Z.Grabarek, A.Bohm, W.-J.Tang. Structural Basis For the Activation of Anthrax Adenylyl Cyclase Exotoxin By Calmodulin. Nature V. 415 396 2002.
ISSN: ISSN 0028-0836
PubMed: 11807546
DOI: 10.1038/415396A
Page generated: Wed Dec 16 02:41:28 2020

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