Atomistry » Zinc » PDB 1hlk-1hxr » 1hlk
Atomistry »
  Zinc »
    PDB 1hlk-1hxr »
      1hlk »

Zinc in PDB 1hlk: Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor

Enzymatic activity of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor

All present enzymatic activity of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor, PDB code: 1hlk was solved by D.J.Payne, J.A.Hueso-Rodriguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Chever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Diez, P.Perez, J.De La Fuente, M.Rees, A.Rivera-Sagredo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.800, 44.200, 58.500, 92.80, 95.30, 98.00
R / Rfree (%) 16.5 / 22.8

Other elements in 1hlk:

The structure of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor (pdb code 1hlk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor, PDB code: 1hlk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1hlk

Go back to Zinc Binding Sites List in 1hlk
Zinc binding site 1 out of 4 in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:23.5
occ:1.00
 NE2 A:HIS99 2.2 23.6 1.0
NE2 A:HIS162 2.2 15.3 1.0
ND1 A:HIS101 2.3 17.0 1.0
CD2 A:HIS162 3.0 15.5 1.0
CE1 A:HIS99 3.1 22.5 1.0
CG A:HIS101 3.2 17.9 1.0
CD2 A:HIS99 3.2 23.2 1.0
CE1 A:HIS162 3.3 14.4 1.0
CE1 A:HIS101 3.3 17.1 1.0
ZN A:ZN1002 3.3 62.0 1.0
CB A:HIS101 3.4 19.1 1.0
O16 A:1132002 3.9 62.5 1.0
OD1 A:ASP103 4.1 34.6 1.0
CG A:HIS162 4.2 16.3 1.0
OD2 A:ASP103 4.2 35.0 1.0
SG A:CYS181 4.3 28.9 1.0
ND1 A:HIS99 4.3 22.5 1.0
ND1 A:HIS162 4.3 15.5 1.0
CD2 A:HIS101 4.4 15.6 1.0
CG A:HIS99 4.4 21.8 1.0
NE2 A:HIS101 4.4 15.6 1.0
CB A:CYS181 4.5 22.5 1.0
CG A:ASP103 4.6 32.6 1.0
O19 A:1132002 4.7 64.7 1.0
CA A:HIS101 4.9 20.4 1.0

Zinc binding site 2 out of 4 in 1hlk

Go back to Zinc Binding Sites List in 1hlk
Zinc binding site 2 out of 4 in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:62.0
occ:1.00
 SG A:CYS181 2.1 28.9 1.0
O19 A:1132002 2.6 64.7 1.0
NE2 A:HIS223 2.7 36.2 1.0
OD2 A:ASP103 2.8 35.0 1.0
CD2 A:HIS223 3.2 33.1 1.0
CB A:CYS181 3.2 22.5 1.0
ZN A:ZN1001 3.3 23.5 1.0
O16 A:1132002 3.5 62.5 1.0
C18 A:1132002 3.6 64.9 1.0
CG A:ASP103 3.8 32.6 1.0
C6 A:1132002 3.9 64.3 1.0
C5 A:1132002 3.9 65.0 1.0
CE1 A:HIS223 4.0 34.9 1.0
NE2 A:HIS162 4.1 15.3 1.0
OD1 A:ASP103 4.1 34.6 1.0
CE1 A:HIS162 4.4 14.4 1.0
CG A:HIS223 4.5 32.5 1.0
CA A:CYS181 4.6 19.6 1.0
CE1 A:HIS99 4.6 22.5 1.0
O30 A:1132002 4.7 64.6 1.0
NE2 A:HIS99 4.7 23.6 1.0
CD2 A:HIS162 4.7 15.5 1.0
ND1 A:HIS223 4.8 34.6 1.0
C4 A:1132002 4.9 65.7 1.0
C1 A:1132002 4.9 64.3 1.0
O31 A:1132002 4.9 66.9 1.0
O A:HOH2012 4.9 17.0 1.0

Zinc binding site 3 out of 4 in 1hlk

Go back to Zinc Binding Sites List in 1hlk
Zinc binding site 3 out of 4 in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:19.3
occ:1.00
 ND1 B:HIS101 2.1 11.1 1.0
NE2 B:HIS162 2.1 9.9 1.0
O B:HOH2018 2.2 13.9 1.0
NE2 B:HIS99 2.4 21.4 1.0
CG B:HIS101 3.0 12.9 1.0
CE1 B:HIS101 3.1 12.8 1.0
CE1 B:HIS162 3.1 8.4 1.0
CD2 B:HIS162 3.1 10.2 1.0
CE1 B:HIS99 3.2 19.7 1.0
CB B:HIS101 3.3 14.3 1.0
CD2 B:HIS99 3.4 17.8 1.0
O16 B:1132003 3.5 31.2 1.0
ZN B:ZN1004 3.7 33.9 1.0
OD1 B:ASP103 4.0 16.5 1.0
O19 B:1132003 4.1 35.9 1.0
CD2 B:HIS101 4.1 14.2 1.0
NE2 B:HIS101 4.2 12.3 1.0
ND1 B:HIS162 4.2 11.7 1.0
SG B:CYS181 4.2 22.8 1.0
CG B:HIS162 4.2 10.5 1.0
ND1 B:HIS99 4.4 16.1 1.0
CB B:CYS181 4.4 16.9 1.0
OD2 B:ASP103 4.5 17.4 1.0
CG B:HIS99 4.5 15.9 1.0
CG B:ASP103 4.7 15.9 1.0
C6 B:1132003 4.7 35.2 1.0
CA B:HIS101 4.8 14.9 1.0
C18 B:1132003 4.9 35.3 1.0
O B:HOH2005 4.9 9.7 1.0

Zinc binding site 4 out of 4 in 1hlk

Go back to Zinc Binding Sites List in 1hlk
Zinc binding site 4 out of 4 in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1004

b:33.9
occ:1.00
 SG B:CYS181 2.1 22.8 1.0
NE2 B:HIS223 2.2 25.9 1.0
O B:HOH2018 2.3 13.9 1.0
O19 B:1132003 2.4 35.9 1.0
OD2 B:ASP103 2.6 17.4 1.0
CD2 B:HIS223 3.0 24.7 1.0
CE1 B:HIS223 3.3 24.2 1.0
CB B:CYS181 3.3 16.9 1.0
C18 B:1132003 3.4 35.3 1.0
O16 B:1132003 3.5 31.2 1.0
CG B:ASP103 3.6 15.9 1.0
C5 B:1132003 3.7 35.6 1.0
C6 B:1132003 3.7 35.2 1.0
ZN B:ZN1003 3.7 19.3 1.0
O B:HOH2019 3.9 24.6 1.0
OD1 B:ASP103 3.9 16.5 1.0
CG B:HIS223 4.2 23.8 1.0
ND1 B:HIS223 4.3 26.3 1.0
NE2 B:HIS162 4.3 9.9 1.0
CE1 B:HIS162 4.4 8.4 1.0
CA B:CYS181 4.5 14.0 1.0
C4 B:1132003 4.5 35.7 1.0
O30 B:1132003 4.5 34.1 1.0
C1 B:1132003 4.6 35.8 1.0
CE1 B:HIS99 4.8 19.7 1.0
CB B:ASP103 4.9 15.9 1.0
O31 B:1132003 4.9 34.9 1.0
NE2 B:HIS99 5.0 21.4 1.0

Reference:

D.J.Payne, J.A.Hueso-Rodriguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Chever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Diez, P.Perez, J.De La Fuente, M.Rees, A.Rivera-Sagredo. Identification of A Series of Tricyclic Natural Products As Potent Broad Spectrum Inhibitors of Metallo-Beta-Lactamases Antimicrob.Agents Chemother. V. 46 1880 2002.
ISSN: ISSN 0066-4804
PubMed: 12019104
DOI: 10.1128/AAC.46.6.1880-1886.2002
Page generated: Sun Oct 13 02:22:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy