Atomistry » Zinc » PDB 4c11-4c6m » 4c1d
Atomistry »
  Zinc »
    PDB 4c11-4c6m »
      4c1d »

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

Go back to Zinc Binding Sites List in 4c1d
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy