Zinc in PDB 6v1p: Structure of Vim-2 Bound to QPX7728 at 1.20 A

Protein crystallography data

The structure of Structure of Vim-2 Bound to QPX7728 at 1.20 A, PDB code: 6v1p was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.20 / 1.20
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.670, 79.120, 77.110, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.8

Other elements in 6v1p:

The structure of Structure of Vim-2 Bound to QPX7728 at 1.20 A also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Vim-2 Bound to QPX7728 at 1.20 A (pdb code 6v1p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Vim-2 Bound to QPX7728 at 1.20 A, PDB code: 6v1p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6v1p

Go back to Zinc Binding Sites List in 6v1p
Zinc binding site 1 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:7.9
occ:1.00
O13 A:QNA401 1.9 7.3 1.0
ND1 A:HIS118 2.0 8.2 1.0
NE2 A:HIS196 2.0 7.3 1.0
NE2 A:HIS116 2.1 7.6 1.0
O14 A:QNA401 2.5 8.3 1.0
B12 A:QNA401 2.7 7.8 1.0
CG A:HIS118 2.9 8.4 1.0
CE1 A:HIS196 3.0 7.1 1.0
CD2 A:HIS196 3.0 7.3 1.0
CE1 A:HIS118 3.0 9.3 1.0
CE1 A:HIS116 3.0 7.4 1.0
CD2 A:HIS116 3.1 7.3 1.0
CB A:HIS118 3.2 8.2 1.0
O11 A:QNA401 3.8 7.7 1.0
C15 A:QNA401 4.0 9.9 1.0
CD2 A:HIS118 4.1 10.0 1.0
ND1 A:HIS196 4.1 6.9 1.0
NE2 A:HIS118 4.1 10.0 1.0
CG A:HIS196 4.1 6.6 1.0
ND1 A:HIS116 4.1 7.8 1.0
OD1 A:ASP120 4.1 7.7 1.0
CG A:HIS116 4.2 6.9 1.0
ZN A:ZN403 4.3 7.7 1.0
CB A:CYS221 4.4 6.8 1.0
SG A:CYS221 4.4 7.7 1.0
CA A:HIS118 4.7 8.3 1.0
O A:HOH629 4.7 10.3 1.0
O03 A:QNA401 4.9 7.3 1.0
C10 A:QNA401 4.9 7.8 1.0
OD2 A:ASP120 4.9 7.8 1.0
N A:HIS118 4.9 7.8 1.0
CG A:ASP120 5.0 7.3 1.0

Zinc binding site 2 out of 6 in 6v1p

Go back to Zinc Binding Sites List in 6v1p
Zinc binding site 2 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:7.7
occ:1.00
NE2 A:HIS263 2.1 7.5 1.0
O11 A:QNA401 2.1 7.7 1.0
O03 A:QNA401 2.2 7.3 1.0
OD2 A:ASP120 2.2 7.8 1.0
SG A:CYS221 2.3 7.7 1.0
C10 A:QNA401 2.9 7.8 1.0
O13 A:QNA401 3.0 7.3 1.0
CD2 A:HIS263 3.0 8.3 1.0
C02 A:QNA401 3.1 8.2 1.0
CE1 A:HIS263 3.1 8.2 1.0
B12 A:QNA401 3.2 7.8 1.0
CG A:ASP120 3.3 7.3 1.0
C04 A:QNA401 3.3 8.2 1.0
CB A:CYS221 3.4 6.8 1.0
OD1 A:ASP120 3.8 7.7 1.0
NH2 A:ARG121 4.0 12.9 1.0
C15 A:QNA401 4.1 9.9 1.0
O14 A:QNA401 4.1 8.3 1.0
C09 A:QNA401 4.2 8.9 1.0
ND1 A:HIS263 4.2 8.4 1.0
CG A:HIS263 4.2 8.0 1.0
O01 A:QNA401 4.3 8.2 1.0
O A:HOH556 4.3 8.5 1.0
ZN A:ZN402 4.3 7.9 1.0
CE1 A:HIS196 4.4 7.1 1.0
C16 A:QNA401 4.5 10.5 1.0
C17 A:QNA401 4.5 9.7 1.0
CA A:CYS221 4.5 6.8 1.0
CB A:ASP120 4.5 8.1 1.0
NE A:ARG121 4.6 7.9 1.0
NE2 A:HIS196 4.6 7.3 1.0
C05 A:QNA401 4.6 9.3 1.0
CZ A:ARG121 4.8 9.9 1.0
CE1 A:HIS116 4.9 7.4 1.0

Zinc binding site 3 out of 6 in 6v1p

Go back to Zinc Binding Sites List in 6v1p
Zinc binding site 3 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:14.5
occ:1.00
OXT A:ACT406 1.9 15.3 1.0
ND1 A:HIS285 2.0 10.3 1.0
OXT A:ACT405 2.0 15.8 1.0
O A:ACT406 2.6 16.2 1.0
C A:ACT406 2.6 16.1 1.0
CE1 A:HIS285 3.0 10.0 1.0
C A:ACT405 3.0 16.4 1.0
CG A:HIS285 3.1 8.9 1.0
O A:ACT405 3.3 17.1 1.0
CB A:HIS285 3.5 9.1 1.0
CA A:HIS285 3.8 9.5 1.0
CH3 A:ACT406 4.0 18.4 1.0
NE2 A:HIS285 4.1 9.6 1.0
CD2 A:HIS285 4.2 9.6 1.0
CH3 A:ACT405 4.4 17.2 1.0
ND2 A:ASN288 4.4 14.0 1.0
O A:HIS285 4.5 9.4 1.0
CD2 A:LEU226 4.6 11.8 1.0
C A:HIS285 4.6 8.8 1.0
N A:HIS285 4.9 10.0 1.0

Zinc binding site 4 out of 6 in 6v1p

Go back to Zinc Binding Sites List in 6v1p
Zinc binding site 4 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:7.7
occ:1.00
O13 B:QNA401 1.9 7.1 1.0
ND1 B:HIS118 2.0 8.0 1.0
NE2 B:HIS196 2.0 6.4 1.0
NE2 B:HIS116 2.1 7.3 1.0
O14 B:QNA401 2.5 8.4 1.0
B12 B:QNA401 2.7 8.2 1.0
CG B:HIS118 2.9 7.6 1.0
CE1 B:HIS118 3.0 9.3 1.0
CE1 B:HIS196 3.0 6.4 1.0
CD2 B:HIS196 3.0 6.4 1.0
CE1 B:HIS116 3.0 6.9 1.0
CD2 B:HIS116 3.1 7.3 1.0
CB B:HIS118 3.2 7.8 1.0
O11 B:QNA401 3.8 7.1 1.0
C15 B:QNA401 4.0 10.3 1.0
NE2 B:HIS118 4.1 10.0 1.0
CD2 B:HIS118 4.1 9.6 1.0
ND1 B:HIS196 4.1 6.8 1.0
CG B:HIS196 4.1 6.5 1.0
OD1 B:ASP120 4.1 7.7 1.0
ND1 B:HIS116 4.2 7.2 1.0
CG B:HIS116 4.2 7.1 1.0
ZN B:ZN403 4.3 7.4 1.0
SG B:CYS221 4.4 7.3 1.0
CB B:CYS221 4.4 6.5 1.0
CA B:HIS118 4.7 8.0 1.0
O B:HOH630 4.7 11.1 1.0
O03 B:QNA401 4.9 7.8 1.0
C10 B:QNA401 4.9 8.1 1.0
OD2 B:ASP120 4.9 7.3 1.0
CG B:ASP120 5.0 7.2 1.0
N B:HIS118 5.0 7.6 1.0

Zinc binding site 5 out of 6 in 6v1p

Go back to Zinc Binding Sites List in 6v1p
Zinc binding site 5 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:7.4
occ:1.00
NE2 B:HIS263 2.1 7.0 1.0
O11 B:QNA401 2.1 7.1 1.0
OD2 B:ASP120 2.2 7.3 1.0
O03 B:QNA401 2.2 7.8 1.0
SG B:CYS221 2.3 7.3 1.0
C10 B:QNA401 2.9 8.1 1.0
O13 B:QNA401 3.0 7.1 1.0
CD2 B:HIS263 3.0 7.1 1.0
CE1 B:HIS263 3.1 7.8 1.0
C02 B:QNA401 3.1 8.2 1.0
B12 B:QNA401 3.2 8.2 1.0
CG B:ASP120 3.3 7.2 1.0
C04 B:QNA401 3.3 8.7 1.0
CB B:CYS221 3.4 6.5 1.0
OD1 B:ASP120 3.8 7.7 1.0
NH2 B:ARG121 4.1 12.9 1.0
C15 B:QNA401 4.1 10.3 1.0
O14 B:QNA401 4.1 8.4 1.0
C09 B:QNA401 4.1 8.7 1.0
ND1 B:HIS263 4.2 7.6 1.0
CG B:HIS263 4.2 7.4 1.0
O01 B:QNA401 4.3 8.3 1.0
O B:HOH557 4.3 7.7 1.0
ZN B:ZN402 4.3 7.7 1.0
CE1 B:HIS196 4.4 6.4 1.0
C16 B:QNA401 4.5 10.5 1.0
C17 B:QNA401 4.5 9.8 1.0
CA B:CYS221 4.5 6.3 1.0
CB B:ASP120 4.5 7.3 1.0
NE2 B:HIS196 4.5 6.4 1.0
NE B:ARG121 4.6 8.0 1.0
C05 B:QNA401 4.6 9.1 1.0
CZ B:ARG121 4.8 9.6 1.0
CE1 B:HIS116 4.9 6.9 1.0

Zinc binding site 6 out of 6 in 6v1p

Go back to Zinc Binding Sites List in 6v1p
Zinc binding site 6 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:10.9
occ:1.00
OXT B:ACT405 2.0 11.5 1.0
OXT B:ACT406 2.0 11.4 1.0
ND1 B:HIS285 2.1 8.9 1.0
O B:ACT406 2.6 13.0 1.0
C B:ACT406 2.7 11.8 1.0
C B:ACT405 3.0 12.0 1.0
CE1 B:HIS285 3.0 8.8 1.0
CG B:HIS285 3.1 8.2 1.0
O B:ACT405 3.2 12.4 1.0
CB B:HIS285 3.5 8.5 1.0
CA B:HIS285 3.8 8.3 1.0
CH3 B:ACT406 4.1 14.4 1.0
NE2 B:HIS285 4.2 8.4 1.0
CD2 B:HIS285 4.2 8.3 1.0
CH3 B:ACT405 4.3 12.5 1.0
ND2 B:ASN288 4.4 11.2 1.0
CD2 B:LEU226 4.6 9.8 1.0
O B:HIS285 4.6 8.0 1.0
C B:HIS285 4.6 7.8 1.0
N B:HIS285 4.9 8.7 1.0

Reference:

S.J.Hecker, K.R.Reddy, O.Lomovskaya, D.C.Griffith, D.Rubio-Aparicio, K.Nelson, R.Tsivkovski, D.Sun, M.Sabet, Z.Tarazi, J.Parkinson, M.Totrov, S.H.Boyer, T.W.Glinka, O.A.Pemberton, Y.Chen, M.N.Dudley. Discovery of Cyclic Boronic Acid QPX7728, An Ultra-Broad-Spectrum Inhibitor of Serine and Metallo Beta-Lactamases. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32150407
DOI: 10.1021/ACS.JMEDCHEM.9B01976
Page generated: Wed Dec 16 13:00:38 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy