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Zinc in PDB 2a5v: Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form

Enzymatic activity of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form

All present enzymatic activity of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form, PDB code: 2a5v was solved by A.S.Covarrubias, T.Bergfors, T.A.Jones, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.884, 70.302, 84.361, 90.00, 93.41, 90.00
R / Rfree (%) 16.2 / 21.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form (pdb code 2a5v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form, PDB code: 2a5v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 2a5v

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Zinc binding site 1 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:33.9
occ:1.00
 N A:SCN501 1.9 42.9 1.0
NE2 A:HIS104 2.1 29.0 1.0
SG A:CYS107 2.3 33.4 1.0
SG A:CYS51 2.4 42.5 1.0
C A:SCN501 2.6 45.0 1.0
CE1 A:HIS104 3.1 26.9 1.0
CD2 A:HIS104 3.1 28.2 1.0
CB A:CYS107 3.2 32.6 1.0
CB A:CYS51 3.3 33.9 1.0
CA A:CYS107 3.6 33.3 1.0
CB A:ASP53 4.0 27.7 1.0
ND1 A:HIS104 4.2 30.8 1.0
S A:SCN501 4.2 45.0 1.0
O A:HOH562 4.2 45.5 1.0
CG A:HIS104 4.2 31.4 1.0
N A:GLY108 4.2 32.3 1.0
N A:GLY76 4.3 31.0 1.0
C A:CYS107 4.3 33.6 1.0
CA A:GLY76 4.4 31.2 1.0
OD2 A:ASP53 4.4 29.6 1.0
CA A:CYS51 4.7 33.9 1.0
CG A:ASP53 4.7 27.9 1.0
N A:CYS107 4.8 34.1 1.0
N A:ALA109 4.9 32.4 1.0
N A:ASP53 5.0 29.0 1.0

Zinc binding site 2 out of 11 in 2a5v

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Zinc binding site 2 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:33.3
occ:1.00
 NE2 A:HIS0 2.0 28.2 1.0
ND1 A:HIS-3 2.1 31.4 1.0
CE1 A:HIS0 2.9 29.6 1.0
CG A:HIS-3 3.0 31.7 1.0
CD2 A:HIS0 3.1 30.6 1.0
CE1 A:HIS-3 3.1 31.1 1.0
CB A:HIS-3 3.2 32.2 1.0
ND1 A:HIS0 4.0 33.2 1.0
CD2 A:HIS-3 4.1 31.2 1.0
CG A:HIS0 4.1 32.3 1.0
NE2 A:HIS-3 4.1 32.1 1.0
CE1 A:HIS-1 4.2 28.1 1.0
NE2 A:HIS-1 4.5 29.3 1.0
CA A:HIS-3 4.8 32.4 1.0

Zinc binding site 3 out of 11 in 2a5v

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Zinc binding site 3 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:46.7
occ:0.50
 ND1 A:HIS158 1.8 34.5 1.0
OD2 A:ASP198 2.1 49.0 1.0
CE1 A:HIS158 2.7 34.9 1.0
CG A:ASP198 2.8 45.9 1.0
CG A:HIS158 3.0 33.7 1.0
OD1 A:ASP198 3.1 50.8 1.0
CB A:HIS158 3.5 32.1 1.0
NE2 A:HIS158 3.9 36.8 1.0
CD2 A:HIS158 4.0 36.9 1.0
CA A:HIS158 4.0 31.8 1.0
CB A:ASP198 4.1 42.9 1.0
O A:HIS158 4.4 32.0 1.0
O A:HOH590 4.5 49.9 1.0
C A:HIS158 4.6 31.8 1.0

Zinc binding site 4 out of 11 in 2a5v

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Zinc binding site 4 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:29.7
occ:1.00
 ND1 A:HIS-4 2.0 32.5 1.0
NE2 A:HIS-2 2.0 36.3 1.0
CG A:HIS-4 3.0 34.3 1.0
CE1 A:HIS-2 3.0 36.2 1.0
CE1 A:HIS-4 3.0 33.2 1.0
CD2 A:HIS-2 3.0 32.6 1.0
CB A:HIS-4 3.2 36.7 1.0
ND1 A:HIS-2 4.1 35.5 1.0
NE2 A:HIS-4 4.1 33.6 1.0
CD2 A:HIS-4 4.1 33.5 1.0
CG A:HIS-2 4.1 33.9 1.0
O A:HOH548 4.3 41.2 1.0
CA A:HIS-4 4.7 37.2 1.0

Zinc binding site 5 out of 11 in 2a5v

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Zinc binding site 5 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:29.1
occ:1.00
 NE2 B:HIS104 2.2 21.8 1.0
SG B:CYS51 2.3 35.0 1.0
SG B:CYS107 2.3 30.8 1.0
N B:SCN502 2.7 56.6 1.0
CD2 B:HIS104 3.1 23.8 1.0
C B:SCN502 3.1 57.2 1.0
CE1 B:HIS104 3.1 23.3 1.0
CB B:CYS51 3.2 27.6 1.0
CB B:CYS107 3.3 28.5 1.0
CA B:CYS107 3.6 29.2 1.0
CB B:ASP53 4.1 26.3 1.0
O B:HOH522 4.1 34.3 1.0
N B:GLY76 4.2 27.2 1.0
S B:SCN502 4.2 55.5 1.0
ND1 B:HIS104 4.2 26.7 1.0
CG B:HIS104 4.3 28.5 1.0
N B:GLY108 4.3 28.9 1.0
C B:CYS107 4.3 29.2 1.0
CA B:GLY76 4.4 27.9 1.0
OD2 B:ASP53 4.4 24.3 1.0
CA B:CYS51 4.6 27.2 1.0
N B:CYS107 4.8 30.6 1.0
CG B:ASP53 4.8 25.3 1.0
N B:ASP53 5.0 25.9 1.0

Zinc binding site 6 out of 11 in 2a5v

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Zinc binding site 6 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn408

b:77.1
occ:1.00
 NE2 B:HIS0 2.3 65.9 1.0
ND1 B:HIS-2 2.5 71.8 1.0
CE1 B:HIS-2 3.1 72.3 1.0
CE1 B:HIS0 3.1 66.1 1.0
CD2 B:HIS0 3.3 66.1 1.0
CG B:HIS-2 3.7 71.1 1.0
CB B:HIS-2 4.3 69.6 1.0
ND1 B:HIS0 4.3 66.5 1.0
NE2 B:HIS-2 4.3 73.1 1.0
CG B:HIS0 4.4 66.5 1.0
CD2 B:HIS-2 4.7 72.2 1.0
O B:HIS-2 4.8 69.2 1.0

Zinc binding site 7 out of 11 in 2a5v

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Zinc binding site 7 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:41.0
occ:1.00
 N C:SCN503 2.0 48.8 1.0
NE2 C:HIS104 2.3 33.4 1.0
SG C:CYS107 2.3 41.8 1.0
SG C:CYS51 2.3 46.3 1.0
C C:SCN503 2.7 50.5 1.0
CD2 C:HIS104 3.1 33.8 1.0
CE1 C:HIS104 3.3 33.8 1.0
CB C:CYS107 3.3 40.9 1.0
CB C:CYS51 3.3 41.0 1.0
CA C:CYS107 3.6 41.3 1.0
CB C:ASP53 4.1 39.8 1.0
S C:SCN503 4.2 50.5 1.0
N C:GLY76 4.2 39.4 1.0
N C:GLY108 4.3 39.7 1.0
OD2 C:ASP53 4.3 42.0 1.0
CG C:HIS104 4.3 39.2 1.0
CA C:GLY76 4.3 39.3 1.0
ND1 C:HIS104 4.3 38.3 1.0
C C:CYS107 4.3 40.6 1.0
CA C:CYS51 4.7 40.8 1.0
CG C:ASP53 4.7 41.6 1.0
N C:CYS107 4.8 42.8 1.0
N C:ASP53 4.9 38.8 1.0
N C:ALA109 5.0 38.9 1.0

Zinc binding site 8 out of 11 in 2a5v

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Zinc binding site 8 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:38.8
occ:1.00
 SG D:CYS51 2.2 48.1 1.0
SG D:CYS107 2.3 41.7 1.0
NE2 D:HIS104 2.3 40.7 1.0
CD2 D:HIS104 3.2 39.5 1.0
CB D:CYS51 3.2 42.3 1.0
CE1 D:HIS104 3.3 40.4 1.0
CB D:CYS107 3.3 41.1 1.0
CA D:CYS107 3.7 41.2 1.0
CB D:ASP53 4.0 38.9 1.0
S C:SCN504 4.0 56.1 1.0
OD2 D:ASP53 4.2 40.0 1.0
C C:SCN504 4.2 56.8 1.0
CG D:HIS104 4.3 42.1 1.0
ND1 D:HIS104 4.3 42.4 1.0
N D:GLY108 4.3 41.1 1.0
C D:CYS107 4.4 41.4 1.0
N D:GLY76 4.4 39.1 1.0
CG D:ASP53 4.5 39.2 1.0
CA D:GLY76 4.6 38.1 1.0
CA D:CYS51 4.6 42.0 1.0
N C:SCN504 4.8 57.4 1.0
N D:ASP53 4.9 38.6 1.0
N D:ALA109 4.9 38.8 1.0
N D:CYS107 4.9 42.3 1.0
CA D:ASP53 5.0 38.7 1.0

Zinc binding site 9 out of 11 in 2a5v

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Zinc binding site 9 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn406

b:36.2
occ:0.50
 ND1 D:HIS-3 1.7 67.8 1.0
NE2 D:HIS-1 2.4 71.5 1.0
CE1 D:HIS-3 2.7 67.8 1.0
CG D:HIS-3 2.8 69.4 1.0
CD2 D:HIS-1 3.1 70.9 1.0
CB D:HIS-3 3.2 69.9 1.0
CE1 D:HIS-1 3.5 71.1 1.0
NE2 D:HIS-3 3.8 68.4 1.0
CD2 D:HIS-3 3.9 68.8 1.0
CG D:HIS-1 4.3 70.6 1.0
ND1 D:HIS-1 4.5 70.7 1.0
CA D:HIS-3 4.5 70.0 1.0

Zinc binding site 10 out of 11 in 2a5v

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Zinc binding site 10 out of 11 in the Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of M. Tuberculosis Beta Carbonic Anhydrase, RV3588C, Tetrameric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn407

b:64.8
occ:1.00
 NE2 D:HIS0 2.3 68.3 1.0
ND1 D:HIS-2 2.4 71.5 1.0
CE1 D:HIS0 3.1 68.8 1.0
CE1 D:HIS-2 3.3 71.9 1.0
CG D:HIS-2 3.3 71.2 1.0
CD2 D:HIS0 3.4 68.8 1.0
CB D:HIS-2 3.7 69.8 1.0
ND1 D:HIS0 4.3 69.8 1.0
NE2 D:HIS-2 4.3 72.4 1.0
O D:HIS-2 4.3 69.3 1.0
CD2 D:HIS-2 4.4 71.8 1.0
CG D:HIS0 4.4 69.4 1.0
C D:HIS-2 4.7 69.5 1.0
CA D:HIS-2 4.8 69.7 1.0

Reference:

A.S.Covarrubias, T.Bergfors, T.A.Jones, M.Hogbom. Structural Mechanics of the pH-Dependent Activity of Beta-Carbonic Anhydrase From Mycobacterium Tuberculosis J.Biol.Chem. V. 281 4993 2006.
ISSN: ISSN 0021-9258
PubMed: 16321983
DOI: 10.1074/JBC.M510756200
Page generated: Wed Oct 16 21:30:46 2024

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