Zinc in PDB 7ove: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210)

Protein crystallography data

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210), PDB code: 7ove was solved by G.Tassone, M.Benvenuti, F.Verdirosa, F.Sannio, S.Mangani, J.D.Docquier, C.Pozzi, F.Marcoccia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.40 / 1.92
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.116, 78.133, 79.3, 90, 90, 90
R / Rfree (%) 19 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210) (pdb code 7ove). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210), PDB code: 7ove:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7ove

Go back to Zinc Binding Sites List in 7ove
Zinc binding site 1 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210)


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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.4
occ:1.00
ND1 A:HIS116 2.0 17.5 1.0
NE2 A:HIS179 2.0 15.7 1.0
NAI A:UNL306 2.0 54.0 1.0
NE2 A:HIS114 2.1 14.2 1.0
CE1 A:HIS114 2.9 13.7 1.0
NAH A:UNL306 2.9 51.7 1.0
CE1 A:HIS116 3.0 21.2 1.0
CG A:HIS116 3.0 18.3 1.0
CE1 A:HIS179 3.0 15.2 1.0
CD2 A:HIS179 3.0 14.3 1.0
CAJ A:UNL306 3.1 54.1 1.0
CD2 A:HIS114 3.2 15.7 1.0
CB A:HIS116 3.3 18.3 1.0
SAW A:UNL306 3.7 47.5 1.0
OD1 A:ASP118 4.0 27.9 1.0
ND1 A:HIS114 4.1 15.4 1.0
CAG A:UNL306 4.1 56.3 1.0
NE2 A:HIS116 4.1 18.8 1.0
CD2 A:HIS116 4.1 19.8 1.0
ND1 A:HIS179 4.1 14.8 1.0
NAK A:UNL306 4.2 57.0 1.0
CG A:HIS179 4.2 14.4 1.0
CG A:HIS114 4.2 15.1 1.0
ZN A:ZN302 4.5 35.3 1.0
CB A:CYS198 4.7 22.6 1.0
CA A:HIS116 4.7 20.1 1.0
ND2 A:ASN210 4.8 52.5 0.7
SG A:CYS198 4.8 26.6 1.0
CG A:ASP118 4.9 27.2 1.0
O A:HOH500 4.9 27.0 1.0

Zinc binding site 2 out of 3 in 7ove

Go back to Zinc Binding Sites List in 7ove
Zinc binding site 2 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210)


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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:35.3
occ:1.00
SG A:CYS198 2.2 26.6 1.0
NE2 A:HIS240 2.2 25.7 1.0
OD2 A:ASP118 2.2 27.4 1.0
SAW A:UNL306 2.3 47.5 1.0
CD2 A:HIS240 3.1 28.2 1.0
CAJ A:UNL306 3.1 54.1 1.0
CE1 A:HIS240 3.2 27.5 1.0
CG A:ASP118 3.3 27.2 1.0
CB A:CYS198 3.3 22.6 1.0
NH2 A:ARG119 3.5 33.5 1.0
NAK A:UNL306 3.7 57.0 1.0
OD1 A:ASP118 3.7 27.9 1.0
CAL A:UNL306 3.8 54.7 1.0
NE A:ARG119 3.8 24.8 1.0
NAI A:UNL306 4.0 54.0 1.0
CZ A:ARG119 4.1 29.6 1.0
CG A:HIS240 4.3 24.6 1.0
ND1 A:HIS240 4.3 26.1 1.0
O A:HOH453 4.4 31.4 1.0
CA A:CYS198 4.5 20.4 1.0
CE1 A:HIS114 4.5 13.7 1.0
ZN A:ZN301 4.5 19.4 1.0
CB A:ASP118 4.6 25.1 1.0
CAM A:UNL306 4.7 53.0 1.0
CAG A:UNL306 4.7 56.3 1.0
NAH A:UNL306 4.9 51.7 1.0
NE2 A:HIS179 4.9 15.7 1.0

Zinc binding site 3 out of 3 in 7ove

Go back to Zinc Binding Sites List in 7ove
Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210)


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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:21.4
occ:1.00
O A:ACT304 1.8 23.5 1.0
NE2 A:HIS153 2.0 19.5 1.0
OXT A:ACT305 2.1 21.2 1.0
O A:ACT305 2.6 21.6 1.0
C A:ACT305 2.7 23.3 1.0
C A:ACT304 2.9 23.6 1.0
CE1 A:HIS153 3.0 23.0 1.0
CD2 A:HIS153 3.0 18.8 1.0
OXT A:ACT304 3.2 21.7 1.0
ND1 A:HIS153 4.1 19.7 1.0
CG A:HIS153 4.2 19.4 1.0
CH3 A:ACT305 4.2 22.8 1.0
CB A:ALA132 4.2 21.0 1.0
CH3 A:ACT304 4.2 21.6 1.0
CA A:ALA132 4.7 21.9 1.0
O A:HOH420 4.8 31.7 1.0

Reference:

A.Legru, F.Verdirosa, J.F.Hernandez, G.Tassone, F.Sannio, M.Benvenuti, P.A.Conde, G.Bossis, C.A.Thomas, M.W.Crowder, M.Dillenberger, K.Becker, C.Pozzi, S.Mangani, J.D.Docquier, L.Gavara. 1,2,4-Triazole-3-Thione Compounds with A 4-Ethyl Alkyl/Aryl Sulfide Substituent Are Broad-Spectrum Metallo-Beta-Lactamase Inhibitors with Re-Sensitization Activity. Eur.J.Med.Chem. V. 226 13873 2021.
ISSN: ISSN 0223-5234
PubMed: 34626878
DOI: 10.1016/J.EJMECH.2021.113873
Page generated: Fri Nov 5 16:56:01 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy