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Zinc in PDB 5acv: Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening

Enzymatic activity of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening

All present enzymatic activity of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening:
3.5.2.6;

Protein crystallography data

The structure of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acv was solved by T.Christopeit, T.J.O.Carlsen, R.Helland, H.K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.63 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.709, 79.484, 66.845, 90.00, 129.92, 90.00
R / Rfree (%) 16.2 / 20.9

Other elements in 5acv:

The structure of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening (pdb code 5acv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5acv

Go back to Zinc Binding Sites List in 5acv
Zinc binding site 1 out of 4 in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1298

b:13.6
occ:1.00
 ND1 A:HIS118 2.0 14.9 1.0
NE2 A:HIS196 2.0 11.7 1.0
O A:OH1001 2.1 9.1 1.0
HO A:OH1001 2.2 10.9 1.0
NE2 A:HIS116 2.3 12.5 1.0
O A:HOH2138 2.7 13.8 1.0
HB2 A:HIS118 2.9 17.2 1.0
CD2 A:HIS196 2.9 11.0 1.0
CE1 A:HIS118 3.0 15.5 1.0
CG A:HIS118 3.0 14.4 1.0
HD2 A:HIS196 3.1 13.2 1.0
CE1 A:HIS196 3.1 12.7 1.0
CE1 A:HIS116 3.1 12.4 1.0
HE1 A:HIS118 3.2 18.6 1.0
HE1 A:HIS116 3.2 14.8 1.0
CD2 A:HIS116 3.3 12.7 1.0
CB A:HIS118 3.3 14.3 1.0
HE1 A:HIS196 3.4 15.2 1.0
HD2 A:HIS116 3.5 15.3 1.0
HB3 A:HIS118 3.5 17.2 1.0
OD3 A:OCS221 3.7 14.5 1.0
O A:HOH2139 3.8 22.6 1.0
HB2 A:OCS221 4.1 13.3 1.0
NE2 A:HIS118 4.1 15.4 1.0
CG A:HIS196 4.1 11.6 1.0
CD2 A:HIS118 4.1 14.6 1.0
ND1 A:HIS196 4.2 12.6 1.0
HD21 A:ASN233 4.2 46.0 1.0
ND1 A:HIS116 4.3 12.1 1.0
OD1 A:ASP120 4.3 20.5 1.0
CG A:HIS116 4.4 12.3 1.0
O A:HOH2230 4.5 26.0 1.0
OD1 A:OCS221 4.5 14.2 1.0
SG A:OCS221 4.5 15.2 1.0
H A:HIS118 4.6 14.8 1.0
CB A:OCS221 4.6 11.1 1.0
HB3 A:OCS221 4.6 13.3 1.0
CA A:HIS118 4.8 13.9 1.0
HB3 A:SER197 4.8 13.9 1.0
O A:HOH2219 4.8 18.5 1.0
ND2 A:ASN233 4.9 38.3 1.0
HG2 A:ARG121 4.9 14.1 1.0
HE2 A:HIS118 4.9 18.5 1.0
OD2 A:ASP120 4.9 20.6 1.0
O A:HOH2146 5.0 39.0 1.0
HD1 A:HIS196 5.0 15.1 1.0
HD2 A:HIS118 5.0 17.5 1.0

Zinc binding site 2 out of 4 in 5acv

Go back to Zinc Binding Sites List in 5acv
Zinc binding site 2 out of 4 in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1299

b:15.2
occ:1.00
 NE2 A:HIS170 2.1 13.9 1.0
CL A:CL1301 2.1 40.4 1.0
CL A:CL1300 2.3 17.5 1.0
CE1 A:HIS170 2.9 14.4 1.0
HE1 A:HIS170 3.1 17.3 1.0
CD2 A:HIS170 3.1 12.7 1.0
HD2 A:HIS170 3.4 15.2 1.0
HB2 A:ALA135 3.6 17.4 1.0
HB3 A:ALA135 3.8 17.4 1.0
ND1 A:HIS170 4.1 13.5 1.0
CB A:ALA135 4.2 14.5 1.0
CG A:HIS170 4.2 12.8 1.0
HG22 A:THR169 4.4 20.2 1.0
O A:HOH2048 4.5 29.7 1.0
HA A:ALA135 4.5 16.1 1.0
HG23 A:THR169 4.8 20.2 1.0
HD1 A:HIS170 4.9 16.2 1.0
HB1 A:ALA135 4.9 17.4 1.0
CA A:ALA135 5.0 13.4 1.0
OH A:TYR137 5.0 16.7 1.0

Zinc binding site 3 out of 4 in 5acv

Go back to Zinc Binding Sites List in 5acv
Zinc binding site 3 out of 4 in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1298

b:15.9
occ:1.00
 ND1 B:HIS118 1.9 18.5 1.0
O B:OH1001 2.0 26.4 1.0
HO B:OH1001 2.1 31.7 1.0
NE2 B:HIS196 2.1 11.8 1.0
NE2 B:HIS116 2.3 13.1 1.0
O B:HOH2129 2.4 14.7 1.0
HB2 B:HIS118 2.9 20.7 1.0
CE1 B:HIS118 2.9 19.8 1.0
CG B:HIS118 2.9 18.2 1.0
CD2 B:HIS196 3.0 11.0 1.0
HE1 B:HIS118 3.1 23.7 1.0
HD2 B:HIS196 3.1 13.2 1.0
CE1 B:HIS116 3.1 13.1 1.0
CE1 B:HIS196 3.2 11.7 1.0
HE1 B:HIS116 3.2 15.7 1.0
CB B:HIS118 3.3 17.2 1.0
CD2 B:HIS116 3.3 12.9 1.0
HE1 B:HIS196 3.4 14.1 1.0
HB3 B:HIS118 3.5 20.7 1.0
HD2 B:HIS116 3.5 15.5 1.0
OD3 B:OCS221 3.9 17.0 1.0
NE2 B:HIS118 4.0 20.0 1.0
CD2 B:HIS118 4.0 19.0 1.0
CG B:HIS196 4.2 10.8 1.0
HB2 B:OCS221 4.2 16.5 1.0
ND1 B:HIS196 4.2 10.9 1.0
O B:HOH2219 4.3 23.3 1.0
ND1 B:HIS116 4.3 12.5 1.0
O B:HOH2128 4.3 31.6 1.0
OD1 B:ASP120 4.4 18.4 1.0
CG B:HIS116 4.4 12.6 1.0
H B:HIS118 4.5 17.4 1.0
OD1 B:OCS221 4.5 13.3 1.0
SG B:OCS221 4.6 14.9 1.0
HB3 B:SER197 4.6 16.0 1.0
CB B:OCS221 4.7 13.7 1.0
CA B:HIS118 4.8 16.4 1.0
HB3 B:OCS221 4.8 16.5 1.0
HE2 B:HIS118 4.8 24.0 1.0
HD2 B:HIS118 4.9 22.9 1.0
HG2 B:ARG121 4.9 15.3 1.0
OD2 B:ASP120 5.0 21.6 1.0
OD1 B:ASN233 5.0 44.5 1.0

Zinc binding site 4 out of 4 in 5acv

Go back to Zinc Binding Sites List in 5acv
Zinc binding site 4 out of 4 in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1299

b:18.9
occ:1.00
 NE2 B:HIS170 2.0 17.1 1.0
CL B:CL1301 2.2 32.6 0.7
CL B:CL1300 2.2 18.7 0.9
CE1 B:HIS170 2.8 17.7 1.0
HE1 B:HIS170 2.8 21.3 1.0
O B:HOH2292 3.2 22.4 1.0
CD2 B:HIS170 3.2 15.6 1.0
HD2 B:HIS170 3.6 18.7 1.0
HB2 B:ALA135 3.7 15.6 1.0
HB3 B:ALA135 3.8 15.6 1.0
ND1 B:HIS170 4.0 17.1 1.0
O B:HOH2048 4.2 26.7 1.0
CB B:ALA135 4.2 13.0 1.0
CG B:HIS170 4.2 15.2 1.0
HG22 B:THR169 4.4 22.2 1.0
HA B:ALA135 4.4 14.2 1.0
HD1 B:HIS170 4.7 20.5 1.0
HG23 B:THR169 4.8 22.2 1.0
O B:HOH2150 4.8 47.7 1.0
CA B:ALA135 4.9 11.8 1.0
O B:HOH2173 5.0 26.9 1.0

Reference:

T.Christopeit, T.J.O.Carlsen, R.Helland, H.K.S.Leiros. Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening J.Med.Chem. V. 58 8671 2015.
ISSN: ISSN 0022-2623
PubMed: 26477515
DOI: 10.1021/ACS.JMEDCHEM.5B01289
Page generated: Sun Oct 27 12:49:22 2024

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