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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: Wed Dec 16 05:06:46 2020

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