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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

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