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Zinc in PDB 4c1d: Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril, PDB code: 4c1d was solved by D.Zollman, J.Brem, M.A.Mcdonough, S.S.Vanberkel, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.701 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.246, 79.402, 67.774, 90.00, 130.30, 90.00
R / Rfree (%) 14.27 / 17.22

Other elements in 4c1d:

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril (pdb code 4c1d). 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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril, PDB code: 4c1d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4c1d

Go back to Zinc Binding Sites List in 4c1d
Zinc binding site 1 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril


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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:9.7
occ:1.00
 NE2 A:HIS179 2.0 9.8 1.0
ND1 A:HIS116 2.0 11.0 1.0
NE2 A:HIS114 2.1 9.6 1.0
S A:X8Z350 2.3 8.5 0.8
CE1 A:HIS116 2.9 12.0 1.0
CD2 A:HIS179 3.0 8.9 1.0
CE1 A:HIS114 3.0 10.5 1.0
CE1 A:HIS179 3.0 9.6 1.0
CD2 A:HIS114 3.0 8.5 1.0
CG A:HIS116 3.1 10.9 1.0
C1 A:X8Z350 3.2 10.5 0.8
CB A:HIS116 3.5 10.9 1.0
ZN A:ZN502 3.7 10.5 1.0
NE2 A:HIS116 4.1 13.9 1.0
CB A:CYS198 4.1 11.2 1.0
ND1 A:HIS114 4.1 10.1 1.0
ND1 A:HIS179 4.1 10.4 1.0
CG A:HIS179 4.1 9.2 1.0
OD1 A:ASP118 4.1 10.6 1.0
CD2 A:HIS116 4.1 13.1 1.0
CG A:HIS114 4.1 8.9 1.0
SG A:CYS198 4.3 10.3 1.0
C2 A:X8Z350 4.6 12.9 0.8
OD2 A:ASP118 4.7 12.0 1.0
CG A:ASP118 4.9 10.5 1.0
CA A:HIS116 4.9 10.4 1.0
O1 A:X8Z350 4.9 17.1 0.8

Zinc binding site 2 out of 6 in 4c1d

Go back to Zinc Binding Sites List in 4c1d
Zinc binding site 2 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril


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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:10.5
occ:1.00
 OD2 A:ASP118 2.0 12.0 1.0
NE2 A:HIS240 2.0 9.9 1.0
SG A:CYS198 2.3 10.3 1.0
S A:X8Z350 2.3 8.5 0.8
CE1 A:HIS240 3.0 10.4 1.0
CG A:ASP118 3.0 10.5 1.0
CD2 A:HIS240 3.0 9.0 1.0
C1 A:X8Z350 3.3 10.5 0.8
OD1 A:ASP118 3.4 10.6 1.0
CB A:CYS198 3.4 11.2 1.0
NH2 A:ARG119 3.7 14.0 1.0
ZN A:ZN501 3.7 9.7 1.0
C2 A:X8Z350 3.8 12.9 0.8
NE A:ARG119 4.1 10.8 1.0
ND1 A:HIS240 4.1 11.0 1.0
CG A:HIS240 4.2 10.0 1.0
CE1 A:HIS114 4.2 10.5 1.0
CB A:ASP118 4.3 12.1 1.0
CZ A:ARG119 4.3 10.6 1.0
NE2 A:HIS114 4.5 9.6 1.0
NE2 A:HIS179 4.6 9.8 1.0
CA A:CYS198 4.6 9.0 1.0
O A:HOH2149 4.7 13.2 1.0
O A:HOH2053 4.8 20.0 1.0
C4 A:X8Z350 4.8 14.9 0.8
CE1 A:HIS179 4.9 9.6 1.0
C3 A:X8Z350 5.0 14.1 0.8

Zinc binding site 3 out of 6 in 4c1d

Go back to Zinc Binding Sites List in 4c1d
Zinc binding site 3 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril


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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:17.7
occ:1.00
 NE2 A:HIS153 2.0 16.5 1.0
O2 A:FMT401 2.2 21.9 1.0
O1 A:FMT400 2.3 17.9 1.0
O1 A:FMT401 2.6 23.9 1.0
C A:FMT401 2.8 23.9 1.0
CE1 A:HIS153 2.9 15.9 1.0
CD2 A:HIS153 3.1 14.1 1.0
C A:FMT400 3.2 21.9 1.0
O2 A:FMT400 3.5 20.9 1.0
ND1 A:HIS153 4.0 14.6 1.0
CG A:HIS153 4.2 13.4 1.0
CB A:ALA132 4.3 13.0 1.0
CG2 A:THR152 4.6 15.3 1.0
O A:HOH2096 4.7 26.4 1.0
CA A:ALA132 4.9 12.8 1.0

Zinc binding site 4 out of 6 in 4c1d

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Zinc binding site 4 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril


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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:10.6
occ:1.00
 NE2 B:HIS179 2.0 10.8 1.0
ND1 B:HIS116 2.0 12.0 1.0
NE2 B:HIS114 2.0 11.6 1.0
S B:X8Z350 2.3 9.8 0.8
CE1 B:HIS116 3.0 12.8 1.0
CD2 B:HIS179 3.0 10.3 1.0
CE1 B:HIS179 3.0 11.7 1.0
CE1 B:HIS114 3.0 11.2 1.0
CD2 B:HIS114 3.0 9.9 1.0
CG B:HIS116 3.0 12.2 1.0
C1 B:X8Z350 3.1 13.3 0.8
CB B:HIS116 3.4 11.3 1.0
ZN B:ZN502 3.7 11.1 1.0
CB B:CYS198 4.1 11.0 1.0
NE2 B:HIS116 4.1 14.7 1.0
ND1 B:HIS114 4.1 9.9 1.0
ND1 B:HIS179 4.1 10.2 1.0
OD1 B:ASP118 4.1 12.1 1.0
CG B:HIS114 4.1 10.0 1.0
CG B:HIS179 4.1 9.9 1.0
CD2 B:HIS116 4.1 14.4 1.0
SG B:CYS198 4.3 11.2 1.0
C2 B:X8Z350 4.5 16.8 0.8
OD2 B:ASP118 4.8 12.4 1.0
CA B:HIS116 4.9 10.7 1.0
CG B:ASP118 4.9 11.2 1.0
O1 B:X8Z350 4.9 19.4 0.8

Zinc binding site 5 out of 6 in 4c1d

Go back to Zinc Binding Sites List in 4c1d
Zinc binding site 5 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril


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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:11.1
occ:1.00
 OD2 B:ASP118 2.0 12.4 1.0
NE2 B:HIS240 2.1 11.0 1.0
SG B:CYS198 2.3 11.2 1.0
S B:X8Z350 2.3 9.8 0.8
CE1 B:HIS240 3.0 10.6 1.0
CG B:ASP118 3.0 11.2 1.0
CD2 B:HIS240 3.1 10.5 1.0
C1 B:X8Z350 3.3 13.3 0.8
OD1 B:ASP118 3.4 12.1 1.0
CB B:CYS198 3.4 11.0 1.0
NH2 B:ARG119 3.7 15.5 1.0
C2 B:X8Z350 3.7 16.8 0.8
ZN B:ZN501 3.7 10.6 1.0
NE B:ARG119 4.0 11.7 1.0
ND1 B:HIS240 4.1 10.8 1.0
CG B:HIS240 4.2 11.2 1.0
CE1 B:HIS114 4.2 11.2 1.0
CZ B:ARG119 4.3 13.9 1.0
CB B:ASP118 4.3 13.6 1.0
NE2 B:HIS114 4.4 11.6 1.0
CA B:CYS198 4.7 10.0 1.0
NE2 B:HIS179 4.7 10.8 1.0
O B:HOH2142 4.7 13.3 1.0
C4 B:X8Z350 4.8 17.9 0.8
O B:HOH2049 4.8 21.1 1.0
C3 B:X8Z350 4.9 19.4 0.8
CE1 B:HIS179 4.9 11.7 1.0

Zinc binding site 6 out of 6 in 4c1d

Go back to Zinc Binding Sites List in 4c1d
Zinc binding site 6 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with L-Captopril


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 the Metallo-Beta-Lactamase Vim-2 with L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:12.8
occ:1.00
 NE2 B:HIS153 2.0 14.1 1.0
O1 B:FMT400 2.1 14.8 1.0
O2 B:FMT401 2.1 14.9 1.0
O2 B:FMT400 2.7 16.6 1.0
C B:FMT400 2.8 14.9 1.0
CE1 B:HIS153 2.9 14.7 1.0
C B:FMT401 3.0 16.4 1.0
CD2 B:HIS153 3.1 13.5 1.0
O1 B:FMT401 3.2 16.4 1.0
ND1 B:HIS153 4.0 15.7 1.0
CG B:HIS153 4.2 12.1 1.0
CB B:ALA132 4.3 13.8 1.0
O B:HOH2083 4.9 26.5 1.0
CG2 B:THR152 4.9 14.7 1.0
CA B:ALA132 4.9 12.5 1.0

Reference:

J.Brem, S.S.Vanberkel, D.Zollman, C.J.Schofield. B1 Mbl Inhibitor Structures. To Be Published.
Page generated: Sat Oct 26 20:18:00 2024

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