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Zinc in PDB 5cxk: Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae

Enzymatic activity of Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae

All present enzymatic activity of Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae, PDB code: 5cxk was solved by M.Ferraroni, C.Supuran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.53 / 1.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 84.087, 84.087, 316.378, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae (pdb code 5cxk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae, PDB code: 5cxk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5cxk

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Zinc binding site 1 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.2
occ:1.00
 SG A:CYS101 2.0 21.9 1.0
NE2 A:HIS98 2.1 15.8 1.0
SG A:CYS42 2.1 14.4 1.0
OD2 A:ASP44 2.3 20.3 1.0
CD2 A:HIS98 3.0 15.7 1.0
CE1 A:HIS98 3.1 15.0 1.0
CB A:CYS42 3.1 14.3 1.0
CG A:ASP44 3.2 18.2 1.0
CB A:CYS101 3.2 20.8 1.0
CB A:ASP44 3.5 18.0 1.0
O A:HOH497 3.6 21.4 1.0
CA A:CYS101 3.7 19.5 1.0
CG A:HIS98 4.1 15.6 1.0
O A:HOH410 4.2 15.6 1.0
ND1 A:HIS98 4.2 15.7 1.0
OD1 A:ASP44 4.3 19.6 1.0
C A:CYS101 4.4 19.1 1.0
N A:GLY102 4.4 18.8 1.0
N A:ALA67 4.5 14.1 1.0
CA A:CYS42 4.5 14.9 1.0
N A:ASP44 4.6 16.1 1.0
CA A:ALA67 4.6 13.9 1.0
CA A:ASP44 4.6 17.3 1.0
O A:HOH423 4.8 29.4 1.0
OD1 A:ASN68 4.9 12.9 1.0
N A:CYS101 5.0 19.7 1.0

Zinc binding site 2 out of 8 in 5cxk

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Zinc binding site 2 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:15.0
occ:1.00
 SG B:CYS101 2.0 17.5 1.0
NE2 B:HIS98 2.2 15.1 1.0
SG B:CYS42 2.2 18.1 1.0
OD2 B:ASP44 2.4 17.2 1.0
CE1 B:HIS98 3.0 14.7 1.0
CB B:CYS101 3.2 15.8 1.0
CD2 B:HIS98 3.2 14.6 1.0
CG B:ASP44 3.3 18.1 1.0
CB B:CYS42 3.4 17.1 1.0
O B:HOH451 3.5 18.9 1.0
CB B:ASP44 3.5 18.6 1.0
CA B:CYS101 3.7 16.7 1.0
O B:HOH466 3.9 9.5 1.0
ND1 B:HIS98 4.1 14.4 1.0
CG B:HIS98 4.3 15.0 1.0
OD1 B:ASP44 4.4 19.1 1.0
C B:CYS101 4.5 16.6 1.0
OD1 B:ASN68 4.5 12.2 1.0
N B:GLY102 4.5 15.8 1.0
CA B:ALA67 4.6 11.5 1.0
N B:ALA67 4.6 11.5 1.0
O B:HOH467 4.7 15.8 1.0
N B:ASP44 4.8 19.1 1.0
CA B:CYS42 4.8 17.3 1.0
CA B:ASP44 4.8 19.0 1.0
N B:CYS101 4.9 16.8 1.0
O B:HOH449 4.9 16.6 1.0

Zinc binding site 3 out of 8 in 5cxk

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Zinc binding site 3 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:20.0
occ:1.00
 OD2 H:ASP44 1.8 13.6 1.0
NE2 H:HIS98 1.9 17.2 1.0
SG H:CYS42 2.5 18.8 1.0
CE1 H:HIS98 2.6 16.7 1.0
SG H:CYS101 2.6 14.5 1.0
CG H:ASP44 2.8 14.2 1.0
CD2 H:HIS98 3.1 16.5 1.0
CB H:CYS42 3.1 15.6 1.0
CB H:CYS101 3.2 16.7 1.0
CB H:ASP44 3.3 15.0 1.0
CA H:CYS101 3.6 17.2 1.0
ND1 H:HIS98 3.8 17.7 1.0
O H:HOH445 3.9 13.0 1.0
OD1 H:ASP44 3.9 14.6 1.0
O H:HOH469 3.9 4.8 1.0
CG H:HIS98 4.1 17.3 1.0
C H:CYS101 4.5 17.7 1.0
O H:HOH472 4.5 17.8 1.0
N H:ASP44 4.5 15.1 1.0
CA H:ASP44 4.5 15.6 1.0
CA H:ALA67 4.6 13.7 1.0
CA H:CYS42 4.6 15.1 1.0
N H:GLY102 4.7 17.4 1.0
N H:CYS101 4.7 17.7 1.0
OD1 H:ASN68 4.8 15.5 1.0
N H:ALA67 4.8 12.4 1.0

Zinc binding site 4 out of 8 in 5cxk

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Zinc binding site 4 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:18.7
occ:1.00
 OD2 G:ASP44 1.8 11.5 1.0
NE2 G:HIS98 1.8 16.6 1.0
SG G:CYS42 2.4 12.5 1.0
CE1 G:HIS98 2.7 17.1 1.0
SG G:CYS101 2.7 17.8 1.0
CG G:ASP44 2.8 12.4 1.0
CD2 G:HIS98 2.9 16.8 1.0
CB G:ASP44 3.2 12.6 1.0
CB G:CYS42 3.2 12.3 1.0
CB G:CYS101 3.3 16.1 1.0
O G:HOH428 3.7 18.9 1.0
CA G:CYS101 3.8 15.9 1.0
ND1 G:HIS98 3.8 16.2 1.0
OD1 G:ASP44 3.9 13.1 1.0
CG G:HIS98 4.0 16.7 1.0
N G:ASP44 4.2 12.6 1.0
CA G:ASP44 4.3 13.6 1.0
O G:HOH435 4.3 16.1 1.0
C G:CYS101 4.6 14.9 1.0
CA G:CYS42 4.6 12.6 1.0
CA G:ALA67 4.7 11.4 1.0
N G:ALA67 4.7 11.7 1.0
N G:GLY102 4.9 14.3 1.0
O G:HOH444 4.9 18.2 1.0
C G:CYS42 4.9 12.9 1.0

Zinc binding site 5 out of 8 in 5cxk

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Zinc binding site 5 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:23.8
occ:1.00
 NE2 D:HIS98 1.9 16.5 1.0
OD2 D:ASP44 2.1 19.2 1.0
SG D:CYS42 2.3 18.1 1.0
CE1 D:HIS98 2.6 17.1 1.0
SG D:CYS101 2.7 19.4 1.0
CG D:ASP44 3.0 19.5 1.0
CD2 D:HIS98 3.1 16.3 1.0
CB D:CYS42 3.1 16.6 1.0
CB D:ASP44 3.3 19.2 1.0
CB D:CYS101 3.5 18.9 1.0
ND1 D:HIS98 3.8 16.3 1.0
CA D:CYS101 3.9 19.2 1.0
O D:HOH417 4.0 13.7 1.0
CG D:HIS98 4.0 16.9 1.0
OD1 D:ASP44 4.2 21.6 1.0
O D:HOH413 4.4 13.6 1.0
OD1 D:ASN68 4.5 15.6 1.0
N D:ASP44 4.5 19.6 1.0
CA D:ALA67 4.5 15.4 1.0
CA D:CYS42 4.5 17.1 1.0
N D:ALA67 4.5 15.0 1.0
CA D:ASP44 4.5 19.3 1.0
C D:CYS101 4.7 19.3 1.0
N D:GLY102 4.7 19.6 1.0
C D:CYS42 4.9 17.5 1.0

Zinc binding site 6 out of 8 in 5cxk

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Zinc binding site 6 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:22.1
occ:1.00
 OD2 C:ASP44 2.0 23.0 1.0
NE2 C:HIS98 2.1 20.6 1.0
SG C:CYS42 2.3 20.5 1.0
SG C:CYS101 2.4 21.4 1.0
CE1 C:HIS98 2.8 20.4 1.0
CG C:ASP44 3.0 22.0 1.0
CB C:CYS42 3.2 17.7 1.0
CD2 C:HIS98 3.2 20.4 1.0
CB C:CYS101 3.3 23.8 1.0
CB C:ASP44 3.4 21.9 1.0
CA C:CYS101 3.8 25.1 1.0
ND1 C:HIS98 4.0 20.4 1.0
O C:HOH413 4.1 13.6 1.0
OD1 C:ASP44 4.2 22.9 1.0
CG C:HIS98 4.2 20.7 1.0
N C:ALA67 4.6 16.0 1.0
C C:CYS101 4.6 25.4 1.0
N C:ASP44 4.6 19.6 1.0
CA C:ALA67 4.6 15.9 1.0
CA C:CYS42 4.6 16.9 1.0
N C:GLY102 4.6 24.8 1.0
CA C:ASP44 4.6 21.5 1.0
OD1 C:ASN68 4.7 16.8 1.0

Zinc binding site 7 out of 8 in 5cxk

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Zinc binding site 7 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:16.6
occ:1.00
 SG F:CYS42 2.0 20.0 1.0
OD2 F:ASP44 2.1 18.2 1.0
NE2 F:HIS98 2.1 17.0 1.0
SG F:CYS101 2.1 26.6 1.0
CG F:ASP44 2.9 18.3 1.0
CE1 F:HIS98 3.0 17.2 1.0
CD2 F:HIS98 3.1 17.0 1.0
CB F:CYS42 3.2 18.2 1.0
CB F:ASP44 3.3 18.7 1.0
CB F:CYS101 3.3 23.9 1.0
O F:HOH427 3.4 8.8 1.0
CA F:CYS101 3.8 23.5 1.0
OD1 F:ASP44 4.0 18.8 1.0
O F:HOH461 4.1 20.5 1.0
ND1 F:HIS98 4.1 18.3 1.0
CG F:HIS98 4.2 17.9 1.0
CA F:ASP44 4.5 18.6 1.0
N F:ASP44 4.5 17.2 1.0
CA F:CYS42 4.6 17.9 1.0
C F:CYS101 4.6 22.3 1.0
CA F:ALA67 4.7 14.5 1.0
N F:ALA67 4.7 14.7 1.0
N F:GLY102 4.8 21.4 1.0
N F:CYS101 5.0 23.5 1.0

Zinc binding site 8 out of 8 in 5cxk

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Zinc binding site 8 out of 8 in the Crystal Structure of Beta Carbonic Anhydrase From Vibrio Cholerae


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 Beta Carbonic Anhydrase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:26.2
occ:1.00
 OD2 E:ASP44 1.9 17.5 1.0
NE2 E:HIS98 2.0 22.1 1.0
SG E:CYS101 2.1 27.9 1.0
SG E:CYS42 2.3 24.5 1.0
CG E:ASP44 2.9 19.6 1.0
CD2 E:HIS98 2.9 22.8 1.0
CE1 E:HIS98 3.1 23.8 1.0
CB E:CYS101 3.2 28.0 1.0
CB E:CYS42 3.3 21.9 1.0
CB E:ASP44 3.4 19.1 1.0
CA E:CYS101 3.5 27.8 1.0
OD1 E:ASP44 3.9 18.8 1.0
CG E:HIS98 4.1 23.3 1.0
ND1 E:HIS98 4.2 23.7 1.0
C E:CYS101 4.4 27.4 1.0
N E:ASP44 4.5 20.3 1.0
O E:HOH466 4.5 20.3 1.0
O E:HOH408 4.5 17.4 1.0
N E:GLY102 4.5 26.7 1.0
CA E:ASP44 4.5 21.2 1.0
CA E:CYS42 4.7 20.7 1.0
N E:CYS101 4.7 28.7 1.0
N E:ALA67 4.7 17.9 1.0
CA E:ALA67 4.7 19.1 1.0

Reference:

M.Ferraroni, S.Del Prete, D.Vullo, C.Capasso, C.T.Supuran. Crystal Structure and Kinetic Studies of A Tetrameric Type II Beta-Carbonic Anhydrase From the Pathogenic Bacterium Vibrio Cholerae. Acta Crystallogr.,Sect.D V. 71 2449 2015.
ISSN: ESSN 1399-0047
PubMed: 26627652
DOI: 10.1107/S1399004715018635
Page generated: Sun Oct 27 14:30:43 2024

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