Atomistry » Zinc » PDB 4bue-4c1c » 4bz3
Atomistry »
  Zinc »
    PDB 4bue-4c1c »
      4bz3 »

Zinc in PDB 4bz3: Crystal Structure of the Metallo-Beta-Lactamase Vim-2

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

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

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2, PDB code: 4bz3 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) 39.844 / 1.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.955, 79.689, 68.171, 90.00, 130.56, 90.00
R / Rfree (%) 11.26 / 13.75

Other elements in 4bz3:

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 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 (pdb code 4bz3). 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, PDB code: 4bz3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4bz3

Go back to Zinc Binding Sites List in 4bz3
Zinc binding site 1 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:7.4
occ:1.00
 O A:HOH2098 1.9 8.6 1.0
ND1 A:HIS116 2.0 8.0 1.0
NE2 A:HIS179 2.0 6.8 1.0
NE2 A:HIS114 2.1 6.6 1.0
CE1 A:HIS116 3.0 7.7 1.0
CE1 A:HIS114 3.0 6.4 1.0
CD2 A:HIS179 3.0 6.7 1.0
CE1 A:HIS179 3.0 7.0 1.0
CG A:HIS116 3.0 7.3 1.0
CD2 A:HIS114 3.1 6.3 1.0
CB A:HIS116 3.4 7.0 1.0
ZN A:ZN502 3.5 8.2 1.0
O A:HOH2208 3.6 27.0 1.0
OD1 A:ASP118 3.9 9.0 1.0
O A:HOH2182 3.9 24.8 0.5
O2 A:FMT402 3.9 4.2 0.5
NE2 A:HIS116 4.1 9.4 1.0
ND1 A:HIS114 4.1 6.3 1.0
ND1 A:HIS179 4.1 7.2 1.0
CB A:CYS198 4.1 6.6 1.0
CD2 A:HIS116 4.1 8.4 1.0
CG A:HIS179 4.2 6.5 1.0
CG A:HIS114 4.2 5.9 1.0
SG A:CYS198 4.2 7.2 1.0
OD2 A:ASP118 4.5 9.0 1.0
C A:FMT402 4.5 8.2 0.5
CG A:ASP118 4.6 7.7 1.0
CA A:HIS116 4.8 6.8 1.0
ND2 A:ASN210 4.9 23.7 1.0

Zinc binding site 2 out of 6 in 4bz3

Go back to Zinc Binding Sites List in 4bz3
Zinc binding site 2 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:8.2
occ:1.00
 O A:HOH2098 2.0 8.6 1.0
NE2 A:HIS240 2.1 7.0 1.0
O A:HOH2182 2.2 24.8 0.5
OD2 A:ASP118 2.2 9.0 1.0
O2 A:FMT402 2.2 4.2 0.5
SG A:CYS198 2.3 7.2 1.0
CD2 A:HIS240 3.0 7.0 1.0
C A:FMT402 3.1 8.2 0.5
CE1 A:HIS240 3.1 6.8 1.0
CG A:ASP118 3.2 7.7 1.0
CB A:CYS198 3.3 6.6 1.0
ZN A:ZN501 3.5 7.4 1.0
OD1 A:ASP118 3.6 9.0 1.0
NH2 A:ARG119 3.9 9.5 1.0
O A:HOH2208 4.2 27.0 1.0
CG A:HIS240 4.2 6.8 1.0
ND1 A:HIS240 4.2 6.8 1.0
NE2 A:HIS179 4.2 6.8 1.0
NE A:ARG119 4.3 7.7 1.0
O1 A:FMT402 4.3 12.5 0.5
CE1 A:HIS114 4.3 6.4 1.0
O A:HOH2190 4.4 10.0 1.0
O A:HOH2207 4.4 30.7 0.5
CE1 A:HIS179 4.4 7.0 1.0
NE2 A:HIS114 4.4 6.6 1.0
CZ A:ARG119 4.5 7.4 1.0
CB A:ASP118 4.6 8.6 1.0
CA A:CYS198 4.6 6.0 1.0

Zinc binding site 3 out of 6 in 4bz3

Go back to Zinc Binding Sites List in 4bz3
Zinc binding site 3 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:11.5
occ:1.00
 O1 A:FMT401 1.9 13.9 1.0
NE2 A:HIS153 2.0 9.5 1.0
O1 A:FMT400 2.1 13.1 1.0
C A:FMT401 2.7 15.0 1.0
O2 A:FMT401 2.8 15.4 1.0
CE1 A:HIS153 2.9 10.9 1.0
C A:FMT400 3.0 13.9 1.0
CD2 A:HIS153 3.1 8.9 1.0
O2 A:FMT400 3.2 13.6 1.0
ND1 A:HIS153 4.1 10.2 1.0
CG A:HIS153 4.2 8.4 1.0
CB A:ALA132 4.4 8.5 1.0
O A:HOH2122 4.6 24.9 1.0
CG2 A:THR152 4.6 10.4 1.0
CA A:ALA132 4.9 7.7 1.0

Zinc binding site 4 out of 6 in 4bz3

Go back to Zinc Binding Sites List in 4bz3
Zinc binding site 4 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:7.9
occ:1.00
 O B:HOH2085 1.9 8.4 1.0
NE2 B:HIS179 2.0 7.5 1.0
ND1 B:HIS116 2.0 9.2 1.0
NE2 B:HIS114 2.1 7.1 1.0
CE1 B:HIS116 3.0 9.2 1.0
CD2 B:HIS179 3.0 7.0 1.0
CE1 B:HIS114 3.0 6.7 1.0
CE1 B:HIS179 3.0 8.0 1.0
CG B:HIS116 3.0 7.8 1.0
CD2 B:HIS114 3.1 6.5 1.0
CB B:HIS116 3.4 7.9 1.0
ZN B:ZN502 3.5 9.2 1.0
O B:HOH2185 3.8 29.6 1.0
O B:HOH2159 3.8 9.9 1.0
OD1 B:ASP118 3.9 10.3 1.0
NE2 B:HIS116 4.1 9.7 1.0
CB B:CYS198 4.1 7.1 1.0
ND1 B:HIS179 4.1 7.8 1.0
ND1 B:HIS114 4.1 6.6 1.0
CG B:HIS179 4.1 7.1 1.0
CD2 B:HIS116 4.2 9.6 1.0
CG B:HIS114 4.2 6.4 1.0
SG B:CYS198 4.2 7.4 1.0
OD2 B:ASP118 4.4 9.7 1.0
CG B:ASP118 4.6 8.3 1.0
CA B:HIS116 4.8 7.7 1.0
ND2 B:ASN210 4.9 22.9 1.0

Zinc binding site 5 out of 6 in 4bz3

Go back to Zinc Binding Sites List in 4bz3
Zinc binding site 5 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:9.2
occ:1.00
 O B:HOH2085 2.0 8.4 1.0
NE2 B:HIS240 2.1 7.4 1.0
O B:HOH2159 2.2 9.9 1.0
OD2 B:ASP118 2.2 9.7 1.0
SG B:CYS198 2.3 7.4 1.0
CD2 B:HIS240 3.0 7.8 1.0
CE1 B:HIS240 3.1 7.5 1.0
CG B:ASP118 3.2 8.3 1.0
CB B:CYS198 3.3 7.1 1.0
ZN B:ZN501 3.5 7.9 1.0
OD1 B:ASP118 3.6 10.3 1.0
NH2 B:ARG119 3.9 10.7 1.0
O B:HOH2185 4.0 29.6 1.0
CG B:HIS240 4.2 7.9 1.0
ND1 B:HIS240 4.2 8.3 1.0
NE2 B:HIS179 4.2 7.5 1.0
NE B:ARG119 4.2 8.4 1.0
CE1 B:HIS114 4.3 6.7 1.0
O B:HOH2168 4.4 9.7 1.0
CE1 B:HIS179 4.4 8.0 1.0
NE2 B:HIS114 4.4 7.1 1.0
CZ B:ARG119 4.5 9.1 1.0
CB B:ASP118 4.5 10.3 1.0
CA B:CYS198 4.6 6.1 1.0
O B:HOH2184 4.6 29.2 1.0

Zinc binding site 6 out of 6 in 4bz3

Go back to Zinc Binding Sites List in 4bz3
Zinc binding site 6 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:8.3
occ:1.00
 O2 B:FMT400 1.9 8.8 1.0
O1 B:FMT401 2.0 9.5 1.0
NE2 B:HIS153 2.0 8.9 1.0
C B:FMT400 2.7 10.0 1.0
O1 B:FMT400 2.8 10.7 1.0
C B:FMT401 2.9 9.9 1.0
CE1 B:HIS153 2.9 10.3 1.0
O2 B:FMT401 3.1 10.0 1.0
CD2 B:HIS153 3.1 7.8 1.0
ND1 B:HIS153 4.1 10.6 1.0
CG B:HIS153 4.2 8.6 1.0
CB B:ALA132 4.3 8.7 1.0
CA B:ALA132 4.8 7.9 1.0
O B:HOH2099 4.9 17.4 1.0
CG2 B:THR152 4.9 10.6 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 20:10:07 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy