Zinc in PDB 6y6j: Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products

Protein crystallography data

The structure of Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products, PDB code: 6y6j was solved by A.Lucic, C.J.Schofield, J.Brem, M.A.Mcdonough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.61 / 1.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 64.324, 74.02, 78.354, 90, 90, 90
R / Rfree (%) 12.9 / 15.7

Other elements in 6y6j:

The structure of Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products (pdb code 6y6j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products, PDB code: 6y6j:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6y6j

Go back to Zinc Binding Sites List in 6y6j
Zinc binding site 1 out of 3 in the Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:11.0
occ:1.00
O2 A:OEN701 1.9 10.3 0.5
NE2 A:HIS179 2.0 9.7 1.0
ND1 A:HIS116 2.0 11.8 1.0
O2 A:OEQ702 2.0 17.2 0.5
NE2 A:HIS114 2.1 9.7 1.0
C14 A:OEN701 2.6 10.2 0.5
C14 A:OEQ702 2.8 17.4 0.5
O3 A:OEN701 2.8 10.3 0.5
O3 A:OEQ702 2.9 17.2 0.5
CE1 A:HIS179 3.0 10.2 1.0
CD2 A:HIS179 3.0 10.5 1.0
CG A:HIS116 3.0 9.6 1.0
CE1 A:HIS116 3.0 13.0 1.0
CE1 A:HIS114 3.0 7.3 1.0
CD2 A:HIS114 3.0 10.2 1.0
CB A:HIS116 3.3 10.2 1.0
ND1 A:HIS179 4.1 10.6 1.0
CG A:HIS179 4.1 10.0 1.0
NE2 A:HIS116 4.1 15.2 1.0
ND1 A:HIS114 4.1 9.6 1.0
C11 A:OEN701 4.1 10.1 0.5
CD2 A:HIS116 4.1 12.3 1.0
CG A:HIS114 4.2 10.1 1.0
C11 A:OEQ702 4.2 17.8 0.5
OD1 A:ASP118 4.2 11.9 1.0
O1 A:OEQ702 4.2 17.8 0.5
N3 A:OEN701 4.3 10.7 0.5
ZN A:ZN704 4.3 10.8 1.0
O1 A:OEN701 4.3 9.3 0.5
SG A:CYS198 4.4 10.6 1.0
CB A:CYS198 4.4 8.9 1.0
C12 A:OEQ702 4.5 17.8 0.5
N3 A:OEQ702 4.5 18.2 0.5
C12 A:OEN701 4.5 9.6 0.5
CA A:HIS116 4.7 8.9 1.0
O4 A:OEN701 4.7 10.2 0.5
O A:OEQ702 4.8 17.4 0.5
C10 A:OEN701 4.9 10.6 0.5
O A:HOH902 4.9 18.6 1.0
N A:HIS116 5.0 8.6 1.0
CG A:ASP118 5.0 11.5 1.0
OD2 A:ASP118 5.0 10.7 1.0

Zinc binding site 2 out of 3 in 6y6j

Go back to Zinc Binding Sites List in 6y6j
Zinc binding site 2 out of 3 in the Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:10.8
occ:1.00
NE2 A:HIS240 2.1 9.7 1.0
N3 A:OEN701 2.1 10.7 0.5
OD2 A:ASP118 2.1 10.7 1.0
N3 A:OEQ702 2.2 18.2 0.5
O4 A:OEN701 2.2 10.2 0.5
SG A:CYS198 2.3 10.6 1.0
O A:OEQ702 2.4 17.4 0.5
C1 A:OEN701 2.7 11.2 0.5
C A:OEN701 2.8 10.7 0.5
C1 A:OEQ702 2.9 18.6 0.5
CE1 A:HIS240 3.0 9.4 1.0
C A:OEQ702 3.0 18.0 0.5
CD2 A:HIS240 3.1 10.9 1.0
CG A:ASP118 3.2 11.5 1.0
O2 A:OEQ702 3.2 17.2 0.5
C10 A:OEN701 3.3 10.6 0.5
O2 A:OEN701 3.3 10.3 0.5
C10 A:OEQ702 3.4 18.3 0.5
CB A:CYS198 3.5 8.9 1.0
OD1 A:ASP118 3.6 11.9 1.0
C14 A:OEQ702 3.6 17.4 0.5
C14 A:OEN701 3.8 10.2 0.5
NH2 A:ARG119 3.8 13.4 1.0
C2 A:OEN701 4.0 12.7 0.5
O A:OEN701 4.1 10.8 0.5
C11 A:OEN701 4.1 10.1 0.5
C2 A:OEQ702 4.1 19.7 0.5
C11 A:OEQ702 4.1 17.8 0.5
ND1 A:HIS240 4.1 9.9 1.0
C8 A:OEN701 4.2 11.6 0.5
CG A:HIS240 4.2 8.3 1.0
O3 A:OEQ702 4.3 17.2 0.5
O4 A:OEQ702 4.3 18.1 0.5
ZN A:ZN703 4.3 11.0 1.0
C8 A:OEQ702 4.4 18.9 0.5
NE A:ARG119 4.4 10.6 1.0
O1 A:OEQ702 4.4 17.8 0.5
O A:HOH841 4.4 11.8 1.0
CB A:ASP118 4.5 9.6 1.0
O1 A:OEN701 4.5 9.3 0.5
O3 A:OEN701 4.5 10.3 0.5
CZ A:ARG119 4.5 11.6 1.0
CE1 A:HIS179 4.5 10.2 1.0
CA A:CYS198 4.5 10.0 1.0
NE2 A:HIS179 4.6 9.7 1.0
S A:OEN701 4.7 15.2 0.5
CE1 A:HIS114 4.7 7.3 1.0
C12 A:OEN701 5.0 9.6 0.5
C12 A:OEQ702 5.0 17.8 0.5
NE2 A:HIS114 5.0 9.7 1.0

Zinc binding site 3 out of 3 in 6y6j

Go back to Zinc Binding Sites List in 6y6j
Zinc binding site 3 out of 3 in the Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn705

b:13.7
occ:1.00
NE2 A:HIS153 2.1 13.1 1.0
CL A:CL707 2.2 15.9 1.0
CL A:CL706 2.2 15.8 1.0
CE1 A:HIS153 2.9 17.3 1.0
CD2 A:HIS153 3.2 12.7 1.0
CB A:ALA132 3.9 12.7 1.0
ND1 A:HIS153 4.1 19.6 1.0
CG A:HIS153 4.3 14.0 1.0
O A:HOH819 4.6 21.2 1.0
CA A:ALA132 4.7 11.8 1.0
O A:HOH996 4.8 21.8 0.5

Reference:

A.Lucic, B.G.Saward, J.Brem, M.A.Mcdonough, K.Calvopina, C.J.Schofield. Structure of Metallo-Beta-Lactamase Vim-2 in Complex with the Imine and Enamine Form of Hydrolysed Biapenem To Be Published.
Page generated: Sat Apr 3 18:29:08 2021

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