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Ytterbium in PDB 1lvc: Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 2' Deoxy, 3' Anthraniloyl Atp

Enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 2' Deoxy, 3' Anthraniloyl Atp

All present enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 2' Deoxy, 3' Anthraniloyl 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 2' Deoxy, 3' Anthraniloyl Atp, PDB code: 1lvc was solved by Y.Shen, Y.-S.Lee, S.Soelaiman, P.Bergson, D.Lu, A.Chen, K.Beckingham, Z.Grabarek, M.Mrksich, W.-J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 3.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.924, 167.918, 341.743, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 30.7

Other elements in 1lvc:

The structure of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 2' Deoxy, 3' Anthraniloyl 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 2' Deoxy, 3' Anthraniloyl Atp (pdb code 1lvc). 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 2' Deoxy, 3' Anthraniloyl Atp, PDB code: 1lvc:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 1lvc

Go back to Ytterbium Binding Sites List in 1lvc
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 2' Deoxy, 3' Anthraniloyl 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 2' Deoxy, 3' Anthraniloyl Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb901

b:0.3
occ:1.00
 OD1 A:ASP491 2.1 47.8 1.0
NE2 A:HIS577 2.1 28.5 1.0
O1A A:DOT999 2.2 77.0 1.0
OD2 A:ASP491 2.4 48.5 1.0
CG A:ASP491 2.6 45.8 1.0
OD2 A:ASP493 2.9 39.2 1.0
OD1 A:ASP493 2.9 39.2 1.0
CE1 A:HIS577 3.1 29.9 1.0
CD2 A:HIS577 3.2 31.1 1.0
PA A:DOT999 3.2 77.3 1.0
CG A:ASP493 3.2 38.7 1.0
O2A A:DOT999 3.8 77.7 1.0
O3A A:DOT999 3.8 72.6 1.0
O2B A:DOT999 3.9 67.7 1.0
O A:LYS346 4.0 26.9 1.0
CB A:ASP491 4.0 40.6 1.0
ND1 A:HIS577 4.2 28.2 1.0
CG A:HIS577 4.3 28.7 1.0
O5' A:DOT999 4.5 75.7 1.0
CE A:LYS346 4.5 33.3 1.0
PB A:DOT999 4.6 69.2 1.0
O A:GLY347 4.6 38.2 1.0
CB A:ASP493 4.7 36.2 1.0
CG A:LYS346 4.8 34.6 1.0
O A:ASP491 4.9 36.2 1.0
CA A:ASP491 4.9 36.5 1.0
C A:ASP491 5.0 35.6 1.0

Ytterbium binding site 2 out of 3 in 1lvc

Go back to Ytterbium Binding Sites List in 1lvc
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 2' Deoxy, 3' Anthraniloyl 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 2' Deoxy, 3' Anthraniloyl Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb902

b:0.9
occ:1.00
 CE1 B:HIS577 1.8 36.9 1.0
OD1 B:ASP493 2.0 41.1 1.0
NE2 B:HIS577 2.3 37.4 1.0
OD1 B:ASP491 2.3 32.7 1.0
CG B:ASP493 2.7 39.2 1.0
OD2 B:ASP493 2.8 43.1 1.0
ND1 B:HIS577 3.0 39.0 1.0
CG B:ASP491 3.2 31.7 1.0
OD2 B:ASP491 3.3 31.5 1.0
CD2 B:HIS577 3.6 39.0 1.0
CG B:HIS577 3.9 38.7 1.0
CB B:ASP493 4.2 34.8 1.0
O B:LYS346 4.4 30.9 1.0
CB B:ASP491 4.6 30.5 1.0
CE B:LYS346 4.7 36.8 1.0
CA B:ASP493 4.9 31.7 1.0

Ytterbium binding site 3 out of 3 in 1lvc

Go back to Ytterbium Binding Sites List in 1lvc
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 2' Deoxy, 3' Anthraniloyl 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 2' Deoxy, 3' Anthraniloyl Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Yb903

b:0.6
occ:1.00
 NE2 C:HIS577 2.1 33.0 1.0
OD1 C:ASP491 2.2 47.9 1.0
OD2 C:ASP491 2.3 48.5 1.0
O1A C:DOT1999 2.5 69.8 1.0
CG C:ASP491 2.5 45.1 1.0
OD1 C:ASP493 2.6 43.4 1.0
OD2 C:ASP493 2.6 41.8 1.0
CE1 C:HIS577 2.9 33.2 1.0
CG C:ASP493 2.9 39.5 1.0
CD2 C:HIS577 3.2 33.7 1.0
PA C:DOT1999 3.9 68.2 1.0
CB C:ASP491 4.0 40.3 1.0
O2B C:DOT1999 4.1 55.1 1.0
ND1 C:HIS577 4.1 32.7 1.0
CG C:HIS577 4.3 32.4 1.0
O C:LYS346 4.3 29.1 1.0
CB C:ASP493 4.3 35.2 1.0
O3A C:DOT1999 4.5 62.0 1.0
CA C:ASP493 4.7 32.6 1.0
O2A C:DOT1999 4.7 68.4 1.0
O C:ASP491 4.7 36.4 1.0
C C:ASP491 4.8 35.0 1.0
CA C:ASP491 4.8 36.1 1.0
N C:ASP493 4.9 32.3 1.0
C5B C:DOT1999 4.9 74.7 1.0
O5' C:DOT1999 4.9 70.4 1.0

Reference:

Y.Shen, Y.-S.Lee, S.Soelaiman, P.Bergson, D.Lu, A.Chen, K.Beckingham, Z.Grabarek, M.Mrksich, W.-J.Tang. Physiological Calcium Concentrations Regulate Calmodulin Binding and Catalysis of Adenylyl Cyclase Exotoxins Embo J. V. 21 6721 2002.
ISSN: ISSN 0261-4189
PubMed: 12485993
DOI: 10.1093/EMBOJ/CDF681
Page generated: Sat Oct 12 20:55:03 2024

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