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

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

All present enzymatic activity of Vim-2-Nat, 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-Nat, Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acu 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) 24.957 / 2.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 64.422, 75.795, 79.292, 90.00, 90.00, 90.00
R / Rfree (%) 25.59 / 28.69

Other elements in 5acu:

The structure of Vim-2-Nat, 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) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2-Nat, Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening (pdb code 5acu). 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-Nat, Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5acu

Go back to Zinc Binding Sites List in 5acu
Zinc binding site 1 out of 3 in the Vim-2-Nat, 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-Nat, 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:Zn1296

b:30.9
occ:1.00
 ND1 A:HIS118 1.9 25.4 1.0
O A:OH1001 2.0 8.7 0.9
NE2 A:HIS196 2.0 24.6 1.0
NE2 A:HIS116 2.3 22.1 1.0
HO A:OH1001 2.4 10.4 0.9
HB2 A:HIS118 2.7 33.8 1.0
CG A:HIS118 2.8 24.6 1.0
CD2 A:HIS196 2.9 22.9 1.0
CE1 A:HIS118 3.0 34.6 1.0
CE1 A:HIS196 3.0 25.0 1.0
HD2 A:HIS196 3.1 27.5 1.0
CB A:HIS118 3.1 28.1 1.0
CD2 A:HIS116 3.2 21.0 1.0
HE1 A:HIS118 3.2 41.5 1.0
HE1 A:HIS196 3.2 30.0 1.0
CE1 A:HIS116 3.2 22.5 1.0
HD2 A:HIS116 3.3 25.2 1.0
HB3 A:HIS118 3.3 33.8 1.0
HE1 A:HIS116 3.4 27.1 1.0
ZN A:ZN1297 3.5 38.8 0.4
OD1 A:ASP120 4.0 30.0 1.0
CD2 A:HIS118 4.0 34.0 1.0
NE2 A:HIS118 4.0 36.2 1.0
ND1 A:HIS196 4.1 25.7 1.0
CG A:HIS196 4.1 23.1 1.0
HB2 A:CYS221 4.2 30.4 1.0
ND1 A:HIS116 4.3 20.4 1.0
CG A:HIS116 4.3 20.0 1.0
SG A:CYS221 4.3 21.8 1.0
H A:HIS118 4.4 25.6 1.0
OD2 A:ASP120 4.5 30.8 1.0
HB3 A:CYS221 4.5 30.4 1.0
CB A:CYS221 4.6 25.3 1.0
OD1 A:ASN233 4.6 48.9 1.0
CA A:HIS118 4.6 25.9 1.0
CG A:ASP120 4.7 31.7 1.0
HB3 A:SER197 4.8 19.0 1.0
HE2 A:HIS118 4.8 43.5 1.0
HD2 A:HIS118 4.8 40.8 1.0
HD1 A:HIS196 4.9 30.8 1.0
HG2 A:ARG121 4.9 35.0 1.0
N A:HIS118 5.0 21.3 1.0

Zinc binding site 2 out of 3 in 5acu

Go back to Zinc Binding Sites List in 5acu
Zinc binding site 2 out of 3 in the Vim-2-Nat, 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-Nat, 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:Zn1297

b:38.8
occ:0.38
 O A:OH1001 2.3 8.7 0.9
SG A:CYS221 2.3 21.8 1.0
HO A:OH1001 2.4 10.4 0.9
OD2 A:ASP120 2.6 30.8 1.0
NE2 A:HIS263 2.9 30.0 1.0
HB3 A:CYS221 3.4 30.4 1.0
CB A:CYS221 3.5 25.3 1.0
ZN A:ZN1296 3.5 30.9 1.0
CG A:ASP120 3.6 31.7 1.0
HH21 A:ARG121 3.7 42.9 1.0
CE1 A:HIS263 3.9 29.8 1.0
CD2 A:HIS263 3.9 30.1 1.0
HE1 A:HIS196 3.9 30.0 1.0
HB2 A:CYS221 3.9 30.4 1.0
HE1 A:HIS116 3.9 27.1 1.0
HD2 A:HIS263 3.9 36.1 1.0
HE1 A:HIS263 4.0 35.7 1.0
HE A:ARG121 4.0 36.5 1.0
OD1 A:ASP120 4.0 30.0 1.0
NE2 A:HIS196 4.0 24.6 1.0
CE1 A:HIS196 4.1 25.0 1.0
NH2 A:ARG121 4.4 35.7 1.0
CE1 A:HIS116 4.5 22.5 1.0
NE2 A:HIS116 4.5 22.1 1.0
NE A:ARG121 4.7 30.4 1.0
HA A:CYS221 4.8 29.5 1.0
CA A:CYS221 4.8 24.6 1.0
CB A:ASP120 4.9 34.9 1.0
CD2 A:HIS196 4.9 22.9 1.0
ND1 A:HIS196 5.0 25.7 1.0
HH22 A:ARG121 5.0 42.9 1.0
HB2 A:ASP120 5.0 41.8 1.0
HB3 A:ASP120 5.0 41.8 1.0

Zinc binding site 3 out of 3 in 5acu

Go back to Zinc Binding Sites List in 5acu
Zinc binding site 3 out of 3 in the Vim-2-Nat, 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-Nat, 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:36.5
occ:1.00
 NE2 A:HIS170 2.1 25.2 1.0
CL A:CL1299 2.2 64.0 1.0
CL A:CL1300 2.4 74.2 1.0
HE1 A:HIS170 2.7 31.6 1.0
CE1 A:HIS170 2.8 26.3 1.0
HB2 A:ALA135 3.3 40.4 1.0
CD2 A:HIS170 3.4 24.6 1.0
HB3 A:ALA135 3.5 40.4 1.0
HD2 A:HIS170 3.8 29.5 1.0
CB A:ALA135 3.9 33.6 1.0
ND1 A:HIS170 4.0 24.1 1.0
CG A:HIS170 4.3 23.8 1.0
HA A:ALA135 4.3 37.6 1.0
HB1 A:ALA135 4.6 40.4 1.0
HH A:TYR137 4.7 38.9 1.0
HD1 A:HIS170 4.7 28.9 1.0
CA A:ALA135 4.7 31.4 1.0
HG22 A:THR169 4.8 31.9 1.0
O A:HOH2016 4.8 21.2 1.0
OH A:TYR137 5.0 32.4 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: Thu Aug 21 00:37:38 2025

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