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

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

All present enzymatic activity of Vim-2-2, 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-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acx 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) 39.61 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.230, 79.220, 67.640, 90.00, 130.18, 90.00
R / Rfree (%) 14.5 / 19.3

Other elements in 5acx:

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

Fluorine (F) 2 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening (pdb code 5acx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5acx

Go back to Zinc Binding Sites List in 5acx
Zinc binding site 1 out of 6 in the Vim-2-2, 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-2-2, 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:Zn1001

b:19.9
occ:1.00
 ND1 A:HIS118 1.9 17.3 1.0
HO A:OH1299 1.9 18.1 1.0
O A:OH1299 2.0 15.1 1.0
NE2 A:HIS196 2.1 13.7 1.0
NE2 A:HIS116 2.2 12.8 1.0
CE1 A:HIS118 2.8 20.2 1.0
CG A:HIS118 2.9 16.3 1.0
HB2 A:HIS118 2.9 17.2 1.0
HE1 A:HIS118 3.0 24.3 1.0
CE1 A:HIS116 3.0 13.2 1.0
CE1 A:HIS196 3.0 14.4 1.0
CD2 A:HIS196 3.1 13.3 1.0
HE1 A:HIS116 3.1 15.9 1.0
HE1 A:HIS196 3.2 17.3 1.0
HD2 A:HIS196 3.3 15.9 1.0
CD2 A:HIS116 3.3 12.8 1.0
CB A:HIS118 3.3 14.3 1.0
HB3 A:HIS118 3.5 17.2 1.0
HD2 A:HIS116 3.5 15.4 1.0
OD3 A:OCS221 3.6 18.8 0.1
O18 A:WL31298 3.7 45.6 1.0
ZN A:ZN1002 3.7 28.8 1.0
HB2 A:OCS221 3.9 19.8 1.0
NE2 A:HIS118 3.9 20.7 1.0
CD2 A:HIS118 4.0 19.1 1.0
OD1 A:ASP120 4.0 23.0 1.0
H03 A:WL31298 4.0 55.6 1.0
C03 A:WL31298 4.1 46.4 1.0
C17 A:WL31298 4.1 46.5 1.0
C16 A:WL31298 4.1 46.1 1.0
ND1 A:HIS196 4.1 13.3 1.0
HB3 A:OCS221 4.2 19.8 1.0
ND1 A:HIS116 4.2 12.2 1.0
O15 A:WL31298 4.2 46.6 1.0
CG A:HIS196 4.2 12.4 1.0
HD21 A:ASN233 4.3 41.2 0.6
CG A:HIS116 4.3 12.1 1.0
CB A:OCS221 4.4 16.5 1.0
SG A:OCS221 4.5 20.2 1.0
H A:HIS118 4.6 17.6 1.0
OD2 A:ASP120 4.7 21.0 1.0
HE2 A:HIS118 4.7 24.8 1.0
C02 A:WL31298 4.7 46.9 1.0
C04 A:WL31298 4.8 47.3 1.0
CG A:ASP120 4.8 26.1 1.0
CA A:HIS118 4.8 15.2 1.0
HB3 A:SER197 4.8 16.7 1.0
C12 A:WL31298 4.8 47.1 1.0
HG2 A:ARG121 4.9 20.1 1.0
HD2 A:HIS118 4.9 22.9 1.0
HD1 A:HIS116 4.9 14.7 1.0
HD1 A:HIS196 4.9 16.0 1.0
ND2 A:ASN233 5.0 34.4 0.6

Zinc binding site 2 out of 6 in 5acx

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Zinc binding site 2 out of 6 in the Vim-2-2, 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-2-2, 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:Zn1002

b:28.8
occ:1.00
 OD3 A:OCS221 1.8 18.8 0.1
HO A:OH1299 2.0 18.1 1.0
O15 A:WL31298 2.1 46.6 1.0
OD1 A:OCS221 2.2 24.4 0.1
SG A:OCS221 2.3 20.2 1.0
NE2 A:HIS263 2.3 30.5 1.0
O A:OH1299 2.4 15.1 1.0
OD2 A:ASP120 2.6 21.0 1.0
HB3 A:OCS221 2.9 19.8 1.0
HH21 A:ARG121 3.0 30.9 1.0
CB A:OCS221 3.1 16.5 1.0
C12 A:WL31298 3.2 47.1 1.0
CE1 A:HIS263 3.2 29.4 1.0
CD2 A:HIS263 3.3 23.9 1.0
HE1 A:HIS263 3.4 35.2 1.0
HD2 A:HIS263 3.4 28.7 1.0
HE A:ARG121 3.4 23.5 1.0
HE1 A:HIS116 3.6 15.9 1.0
CG A:ASP120 3.6 26.1 1.0
HB2 A:OCS221 3.6 19.8 1.0
OD2 A:OCS221 3.6 19.2 0.0
C10 A:WL31298 3.6 46.9 1.0
ZN A:ZN1001 3.7 19.9 1.0
NH2 A:ARG121 3.8 25.8 1.0
OD1 A:ASP120 3.9 23.0 1.0
C01 A:WL31298 4.0 46.3 1.0
C16 A:WL31298 4.0 46.1 1.0
NE A:ARG121 4.2 19.6 1.0
H04 A:WL31298 4.2 56.8 1.0
O18 A:WL31298 4.2 45.6 1.0
O A:HOH2243 4.3 21.7 1.0
NE2 A:HIS196 4.3 13.7 1.0
O14 A:WL31298 4.3 45.8 1.0
ND1 A:HIS263 4.3 21.5 1.0
CE1 A:HIS116 4.3 13.2 1.0
HA A:OCS221 4.3 14.4 1.0
HH22 A:ARG121 4.4 30.9 1.0
CG A:HIS263 4.4 18.1 1.0
C09 A:WL31298 4.4 46.6 1.0
CA A:OCS221 4.4 12.0 1.0
HE1 A:HIS196 4.4 17.3 1.0
CZ A:ARG121 4.5 23.7 1.0
CE1 A:HIS196 4.5 14.4 1.0
C17 A:WL31298 4.5 46.5 1.0
HA3 A:GLY262 4.6 16.4 1.0
H09 A:WL31298 4.6 55.9 1.0
C04 A:WL31298 4.6 47.3 1.0
NE2 A:HIS116 4.6 12.8 1.0
CB A:ASP120 4.9 29.8 1.0
HG2 A:ARG121 4.9 20.1 1.0
HB2 A:ASP120 4.9 35.8 1.0
C11 A:WL31298 5.0 47.0 1.0

Zinc binding site 3 out of 6 in 5acx

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Zinc binding site 3 out of 6 in the Vim-2-2, 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-2-2, 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:Zn1003

b:15.1
occ:0.95
 NE2 A:HIS170 2.0 13.6 1.0
CL A:CL1300 2.1 30.0 1.0
CL A:CL1301 2.2 20.7 1.0
CE1 A:HIS170 2.8 15.5 1.0
HE1 A:HIS170 2.9 18.6 1.0
CD2 A:HIS170 3.1 12.4 1.0
HD2 A:HIS170 3.4 14.9 1.0
HB2 A:ALA135 3.6 14.1 1.0
HB3 A:ALA135 3.9 14.1 1.0
ND1 A:HIS170 4.0 16.7 1.0
CG A:HIS170 4.1 13.6 1.0
HG22 A:THR169 4.2 18.4 1.0
CB A:ALA135 4.2 11.7 1.0
O A:HOH2163 4.5 31.0 1.0
HA A:ALA135 4.6 14.9 1.0
HG23 A:THR169 4.7 18.4 1.0
HD1 A:HIS170 4.7 20.1 1.0
HH A:TYR137 4.9 21.5 1.0
CG2 A:THR169 4.9 15.3 1.0
HB1 A:ALA135 5.0 14.1 1.0

Zinc binding site 4 out of 6 in 5acx

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Zinc binding site 4 out of 6 in the Vim-2-2, 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-2-2, 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:Zn1001

b:21.3
occ:1.00
 HO B:OH1299 1.9 23.2 1.0
ND1 B:HIS118 1.9 18.6 1.0
O B:OH1299 2.0 19.4 1.0
NE2 B:HIS196 2.0 14.1 1.0
NE2 B:HIS116 2.2 14.7 1.0
HB2 B:HIS118 2.9 22.1 1.0
CE1 B:HIS118 2.9 23.1 1.0
CG B:HIS118 3.0 16.6 1.0
CE1 B:HIS196 3.0 14.2 1.0
CD2 B:HIS196 3.0 12.6 1.0
CE1 B:HIS116 3.1 15.7 1.0
HE1 B:HIS118 3.1 27.8 1.0
HE1 B:HIS116 3.2 18.8 1.0
HE1 B:HIS196 3.2 17.0 1.0
HD2 B:HIS196 3.2 15.2 1.0
CD2 B:HIS116 3.2 15.1 1.0
CB B:HIS118 3.3 18.4 1.0
OD2 B:OCS221 3.4 19.9 0.1
HD2 B:HIS116 3.4 18.2 1.0
O18 B:WL31298 3.5 35.3 1.0
HB3 B:HIS118 3.5 22.1 1.0
ZN B:ZN1002 3.7 28.6 1.0
HB2 B:OCS221 3.8 17.4 1.0
NE2 B:HIS118 4.0 20.8 1.0
O15 B:WL31298 4.1 36.5 1.0
CD2 B:HIS118 4.1 17.5 1.0
ND1 B:HIS196 4.1 13.4 1.0
C16 B:WL31298 4.1 36.5 1.0
CG B:HIS196 4.1 13.0 1.0
HB3 B:OCS221 4.1 17.4 1.0
H03 B:WL31298 4.1 45.5 1.0
OD1 B:ASP120 4.2 24.3 1.0
ND1 B:HIS116 4.2 14.8 1.0
C03 B:WL31298 4.2 37.9 1.0
C17 B:WL31298 4.2 37.8 1.0
CB B:OCS221 4.3 14.5 1.0
CG B:HIS116 4.3 14.1 1.0
HD21 B:ASN233 4.4 63.9 1.0
SG B:OCS221 4.4 18.7 1.0
H B:HIS118 4.6 21.9 1.0
OD2 B:ASP120 4.6 23.1 1.0
CA B:HIS118 4.8 19.6 1.0
HB3 B:SER197 4.8 13.1 1.0
HE2 B:HIS118 4.8 24.9 1.0
CG B:ASP120 4.8 25.8 1.0
HG2 B:ARG121 4.9 19.2 1.0
C12 B:WL31298 4.9 38.8 1.0
HD1 B:HIS196 4.9 16.1 1.0
HD2 B:HIS118 4.9 21.1 1.0
HE B:ARG121 4.9 22.6 1.0
HD1 B:HIS116 4.9 17.8 1.0
C04 B:WL31298 4.9 39.2 1.0
C02 B:WL31298 5.0 39.5 1.0
HG3 B:ARG121 5.0 19.2 1.0

Zinc binding site 5 out of 6 in 5acx

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Zinc binding site 5 out of 6 in the Vim-2-2, 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 5 of Vim-2-2, 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:Zn1002

b:28.6
occ:1.00
 OD2 B:OCS221 1.7 19.9 0.1
O B:OH1299 2.0 19.4 1.0
OD3 B:OCS221 2.1 16.5 0.4
O15 B:WL31298 2.2 36.5 1.0
SG B:OCS221 2.2 18.7 1.0
NE2 B:HIS263 2.3 22.1 1.0
OD2 B:ASP120 2.5 23.1 1.0
HO B:OH1299 2.9 23.2 1.0
HB3 B:OCS221 3.0 17.4 1.0
HH21 B:ARG121 3.0 25.6 1.0
CB B:OCS221 3.2 14.5 1.0
CD2 B:HIS263 3.2 24.4 1.0
C12 B:WL31298 3.3 38.8 1.0
HD2 B:HIS263 3.3 29.3 1.0
CE1 B:HIS263 3.3 20.8 1.0
HE B:ARG121 3.4 22.6 1.0
OD1 B:OCS221 3.5 22.7 0.2
HE1 B:HIS263 3.5 25.0 1.0
CG B:ASP120 3.6 25.8 1.0
HB2 B:OCS221 3.6 17.4 1.0
HE1 B:HIS116 3.6 18.8 1.0
ZN B:ZN1001 3.7 21.3 1.0
C10 B:WL31298 3.7 38.5 1.0
NH2 B:ARG121 3.8 21.3 1.0
C16 B:WL31298 3.9 36.5 1.0
C01 B:WL31298 4.0 37.0 1.0
OD1 B:ASP120 4.0 24.3 1.0
O18 B:WL31298 4.1 35.3 1.0
H04 B:WL31298 4.2 47.1 1.0
NE B:ARG121 4.2 18.8 1.0
O B:HOH2231 4.3 22.4 1.0
NE2 B:HIS196 4.3 14.1 1.0
HA B:OCS221 4.3 15.4 1.0
O14 B:WL31298 4.4 35.4 1.0
CG B:HIS263 4.4 20.6 1.0
HE1 B:HIS196 4.4 17.0 1.0
CE1 B:HIS116 4.4 15.7 1.0
ND1 B:HIS263 4.4 19.7 1.0
CA B:OCS221 4.4 12.8 1.0
HH22 B:ARG121 4.4 25.6 1.0
CE1 B:HIS196 4.5 14.2 1.0
CZ B:ARG121 4.5 20.9 1.0
HA3 B:GLY262 4.5 18.9 1.0
C17 B:WL31298 4.5 37.8 1.0
C09 B:WL31298 4.5 36.9 1.0
C04 B:WL31298 4.5 39.2 1.0
NE2 B:HIS116 4.6 14.7 1.0
H09 B:WL31298 4.8 44.3 1.0
CB B:ASP120 4.9 27.6 1.0
HB2 B:ASP120 4.9 33.1 1.0
H B:OCS221 5.0 15.5 1.0
HG2 B:ARG121 5.0 19.2 1.0

Zinc binding site 6 out of 6 in 5acx

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Zinc binding site 6 out of 6 in the Vim-2-2, 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 6 of Vim-2-2, 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:Zn1003

b:20.1
occ:1.00
 HE2 B:HIS170 1.8 29.8 1.0
HE1 B:HIS170 1.9 37.8 1.0
NE2 B:HIS170 2.2 24.8 1.0
CL B:CL1301 2.2 25.8 1.0
CE1 B:HIS170 2.2 31.5 1.0
CL B:CL1300 2.3 30.8 1.0
CD2 B:HIS170 3.5 20.3 1.0
ND1 B:HIS170 3.5 32.4 1.0
HB2 B:ALA135 3.6 19.5 1.0
HB3 B:ALA135 3.8 19.5 1.0
HD2 B:HIS170 4.1 24.4 1.0
CG B:HIS170 4.2 22.5 1.0
CB B:ALA135 4.2 16.3 1.0
O B:HOH2152 4.5 22.2 1.0
HA B:ALA135 4.6 19.7 1.0
HG22 B:THR169 4.8 33.0 1.0
O B:HOH2066 4.8 20.5 1.0
HB1 B:ALA135 4.9 19.5 1.0
HH B:TYR137 5.0 31.0 1.0
CA B:ALA135 5.0 16.4 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: Sun Oct 27 12:50:27 2024

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