Zinc in PDB 8i52: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia

Enzymatic activity of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia

All present enzymatic activity of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia, PDB code: 8i52 was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.39 / 1.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.32, 79.25, 67.9, 90, 130.14, 90
R / Rfree (%) 14.7 / 17.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia (pdb code 8i52). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia, PDB code: 8i52:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8i52

Go back to Zinc Binding Sites List in 8i52
Zinc binding site 1 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia


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 Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.2
occ:1.00
 OD2 A:ASP118 2.0 8.1 1.0
NE2 A:HIS240 2.0 7.2 1.0
SG A:CYS198 2.3 6.4 1.0
CE1 A:HIS240 3.0 8.4 1.0
CG A:ASP118 3.0 7.8 1.0
CD2 A:HIS240 3.1 7.7 1.0
CB A:CYS198 3.3 5.5 1.0
OD1 A:ASP118 3.4 7.5 1.0
NH2 A:ARG119 3.7 8.3 1.0
ZN A:ZN302 3.7 6.8 1.0
NE A:ARG119 4.0 7.2 1.0
ND1 A:HIS240 4.1 7.9 1.0
CE1 A:HIS114 4.2 5.1 1.0
CG A:HIS240 4.2 7.5 1.0
CZ A:ARG119 4.3 7.6 1.0
CB A:ASP118 4.3 8.5 1.0
NE2 A:HIS114 4.4 5.0 1.0
NE2 A:HIS179 4.6 7.1 1.0
CA A:CYS198 4.6 5.6 1.0
O A:HOH491 4.6 8.6 1.0
O A:HOH642 4.8 16.7 1.0
CE1 A:HIS179 4.8 8.0 1.0

Zinc binding site 2 out of 6 in 8i52

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Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia


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 Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:6.8
occ:1.00
 ND1 A:HIS116 1.9 6.3 1.0
NE2 A:HIS114 2.0 5.0 1.0
NE2 A:HIS179 2.0 7.1 1.0
CE1 A:HIS116 2.9 6.5 1.0
CE1 A:HIS114 2.9 5.1 1.0
CG A:HIS116 3.0 6.2 1.0
CE1 A:HIS179 3.0 8.0 1.0
CD2 A:HIS179 3.0 7.0 1.0
CD2 A:HIS114 3.0 5.2 1.0
CB A:HIS116 3.3 6.5 1.0
ZN A:ZN301 3.7 8.2 1.0
OD1 A:ASP118 3.9 7.5 1.0
NE2 A:HIS116 4.1 6.9 1.0
ND1 A:HIS114 4.1 4.8 1.0
CD2 A:HIS116 4.1 6.5 1.0
ND1 A:HIS179 4.1 7.5 1.0
CB A:CYS198 4.1 5.5 1.0
CG A:HIS114 4.1 5.2 1.0
CG A:HIS179 4.2 6.9 1.0
SG A:CYS198 4.4 6.4 1.0
OD2 A:ASP118 4.7 8.1 1.0
CG A:ASP118 4.7 7.8 1.0
CA A:HIS116 4.8 6.7 1.0

Zinc binding site 3 out of 6 in 8i52

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Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia


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 Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:13.7
occ:1.00
 O2 A:FMT305 1.1 5.0 1.0
O2 A:FMT304 2.0 15.4 1.0
ND1 A:HIS251 2.1 8.8 1.0
O1 A:FMT304 2.2 22.5 1.0
C A:FMT304 2.4 12.4 1.0
C A:FMT305 2.5 10.9 1.0
CE1 A:HIS251 2.9 10.7 1.0
CG A:HIS251 3.2 10.0 1.0
O1 A:FMT305 3.3 25.6 1.0
CB A:HIS251 3.6 10.1 1.0
CA A:HIS251 3.8 9.4 1.0
NE2 A:HIS251 4.1 11.0 1.0
CD2 A:HIS251 4.2 9.2 1.0
O A:HIS251 4.4 11.2 1.0
C A:HIS251 4.6 9.5 1.0
ND2 A:ASN254 4.6 8.7 0.5
CD2 A:LEU203 4.9 12.5 1.0
O A:LEU203 4.9 15.1 1.0
N A:HIS251 5.0 9.0 1.0

Zinc binding site 4 out of 6 in 8i52

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Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia


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 Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:8.3
occ:1.00
 OD2 D:ASP118 2.0 9.1 1.0
NE2 D:HIS240 2.1 6.9 1.0
O1 D:OR6306 2.1 8.4 1.0
SG D:CYS198 2.3 6.7 1.0
O3 D:OR6306 2.3 11.7 1.0
C5 D:OR6306 2.8 11.3 1.0
CD2 D:HIS240 3.0 7.0 1.0
CE1 D:HIS240 3.1 7.1 1.0
CG D:ASP118 3.1 7.7 1.0
C2 D:OR6306 3.1 13.4 1.0
CB D:CYS198 3.3 6.8 1.0
C4 D:OR6306 3.4 12.1 1.0
OD1 D:ASP118 3.5 8.3 1.0
C1 D:OR6306 3.7 13.3 1.0
ZN D:ZN302 3.7 7.1 1.0
NH2 D:ARG119 3.8 9.3 1.0
O2 D:OR6306 3.9 15.3 1.0
NE D:ARG119 4.1 8.0 1.0
ND1 D:HIS240 4.2 6.5 1.0
CG D:HIS240 4.2 6.9 1.0
CE1 D:HIS114 4.2 5.7 1.0
CZ D:ARG119 4.4 8.4 1.0
CB D:ASP118 4.4 7.8 1.0
NE2 D:HIS114 4.4 5.5 1.0
O D:HOH542 4.4 7.8 1.0
C6 D:OR6306 4.4 14.2 1.0
CA D:CYS198 4.5 5.7 1.0
NE2 D:HIS179 4.5 6.7 1.0
C7 D:OR6306 4.6 16.9 1.0
O4 D:OR6306 4.7 12.3 1.0
CE1 D:HIS179 4.7 7.0 1.0
C3 D:OR6306 4.9 15.3 1.0

Zinc binding site 5 out of 6 in 8i52

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Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia


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 Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:7.1
occ:1.00
 ND1 D:HIS116 2.0 7.1 1.0
NE2 D:HIS114 2.0 5.5 1.0
O1 D:OR6306 2.0 8.4 1.0
NE2 D:HIS179 2.0 6.7 1.0
O2 D:OR6306 2.3 15.3 1.0
C5 D:OR6306 2.6 11.3 1.0
CE1 D:HIS116 2.9 6.5 1.0
CE1 D:HIS114 3.0 5.7 1.0
CD2 D:HIS114 3.0 5.8 1.0
CE1 D:HIS179 3.0 7.0 1.0
CD2 D:HIS179 3.0 6.7 1.0
CG D:HIS116 3.1 7.3 1.0
CB D:HIS116 3.4 7.2 1.0
ZN D:ZN301 3.7 8.3 1.0
OD1 D:ASP118 3.9 8.3 1.0
O3 D:OR6306 4.0 11.7 1.0
ND1 D:HIS114 4.1 5.8 1.0
NE2 D:HIS116 4.1 7.7 1.0
CB D:CYS198 4.1 6.8 1.0
ND1 D:HIS179 4.1 6.9 1.0
CG D:HIS114 4.1 5.5 1.0
CG D:HIS179 4.2 6.3 1.0
CD2 D:HIS116 4.2 6.9 1.0
C2 D:OR6306 4.2 13.4 1.0
SG D:CYS198 4.4 6.7 1.0
OD2 D:ASP118 4.5 9.1 1.0
CG D:ASP118 4.6 7.7 1.0
C4 D:OR6306 4.7 12.1 1.0
CA D:HIS116 4.8 7.1 1.0
C7 D:OR6306 4.8 16.9 1.0
C6 D:OR6306 4.9 14.2 1.0
ND2 D:ASN210 4.9 13.4 1.0

Zinc binding site 6 out of 6 in 8i52

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Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia


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 Vim-2 Metallo-Beta-Lactamase in Complex with 10- Hhia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:11.2
occ:1.00
 O2 D:FMT305 2.0 15.0 1.0
O2 D:FMT304 2.0 13.3 1.0
ND1 D:HIS251 2.0 7.2 1.0
C D:FMT304 2.7 11.0 1.0
O1 D:FMT304 2.8 11.8 1.0
C D:FMT305 2.9 16.6 1.0
CE1 D:HIS251 2.9 8.1 1.0
CG D:HIS251 3.1 8.7 1.0
O1 D:FMT305 3.1 16.8 1.0
CB D:HIS251 3.5 7.8 1.0
CA D:HIS251 3.8 7.8 1.0
NE2 D:HIS251 4.1 8.8 1.0
CD2 D:HIS251 4.1 7.5 1.0
ND2 D:ASN254 4.3 13.3 1.0
O D:HIS251 4.4 7.5 1.0
C D:HIS251 4.6 7.5 1.0
CD2 D:LEU203 4.6 13.3 1.0
N D:HIS251 4.9 8.1 1.0
CB D:ASN254 5.0 8.8 1.0

Reference:

J.Wachino, J.Wachino. N/A N/A.
Page generated: Thu Oct 31 07:39:01 2024

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