Chlorine 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:

Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Vim-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products, PDB code: 6y6j:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6y6j

Go back to Chlorine Binding Sites List in 6y6j
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl706

b:15.8
occ:1.00
ZN A:ZN705 2.2 13.7 1.0
O A:HOH819 3.1 21.2 1.0
O A:HOH996 3.1 21.8 0.5
O A:HOH996 3.4 20.3 0.5
NE2 A:HIS153 3.6 13.1 1.0
CB A:ALA132 3.7 12.7 1.0
CL A:CL707 3.7 15.9 1.0
CE1 A:HIS153 3.9 17.3 1.0
OH A:TYR134 4.6 18.1 1.0
CD2 A:HIS153 4.6 12.7 1.0
O A:HOH988 4.7 30.7 1.0
CA A:ALA132 5.0 11.8 1.0

Chlorine binding site 2 out of 3 in 6y6j

Go back to Chlorine Binding Sites List in 6y6j
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl707

b:15.9
occ:1.00
ZN A:ZN705 2.2 13.7 1.0
O A:HOH965 3.1 19.6 1.0
NE2 A:HIS153 3.3 13.1 1.0
CB A:ALA132 3.6 12.7 1.0
CA A:ALA132 3.7 11.8 1.0
CL A:CL706 3.7 15.8 1.0
CD2 A:HIS153 3.8 12.7 1.0
O A:HOH873 4.1 13.2 1.0
O A:HOH882 4.4 18.4 1.0
CG2 A:THR152 4.5 12.4 1.0
CE1 A:HIS153 4.5 17.3 1.0
N A:ALA132 4.6 11.4 1.0
O A:VAL131 4.7 13.6 1.0
C A:ALA132 4.8 11.4 1.0
N A:THR133 4.8 9.2 1.0
CB A:THR152 4.9 12.6 1.0

Chlorine binding site 3 out of 3 in 6y6j

Go back to Chlorine Binding Sites List in 6y6j
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl708

b:17.1
occ:1.00
O A:HOH967 3.0 39.8 1.0
N A:ASP117 3.2 9.4 1.0
ND2 A:ASN148 3.3 13.2 1.0
CA A:HIS116 3.6 8.9 1.0
OD2 A:ASP117 3.6 34.4 1.0
CD2 A:HIS116 3.7 12.3 1.0
CB A:HIS116 3.7 10.2 1.0
O A:HOH804 3.7 41.8 1.0
CG A:ASP117 3.8 25.3 1.0
O A:HOH803 3.8 31.7 1.0
CG A:HIS116 3.9 9.6 1.0
C A:HIS116 3.9 9.2 1.0
CB A:ASP117 3.9 12.8 1.0
CA A:ASP117 4.2 9.8 1.0
C12 A:OEN701 4.2 9.6 0.5
C12 A:OEQ702 4.2 17.8 0.5
CG A:ASN148 4.3 13.6 1.0
OD1 A:ASN148 4.4 16.4 1.0
C13 A:OEQ702 4.4 18.0 0.5
OD1 A:ASP117 4.5 25.3 1.0
C13 A:OEN701 4.5 9.6 0.5
O1 A:OEQ702 4.6 17.8 0.5
O1 A:OEN701 4.6 9.3 0.5
CG A:GLU146 4.6 18.6 1.0
NE2 A:HIS116 4.8 15.2 1.0
OE2 A:GLU146 4.9 36.4 1.0
N A:HIS116 4.9 8.6 1.0

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 14:18:46 2021

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