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Zinc in PDB 1kr3: Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.

Enzymatic activity of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.

All present enzymatic activity of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050., PDB code: 1kr3 was solved by D.J.Payne, J.A.Hueso-Rodrguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Cheever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Dez, P.Prez, 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) 29.07 / 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 (%) n/a / n/a

Other elements in 1kr3:

The structure of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. (pdb code 1kr3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050., PDB code: 1kr3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1kr3

Go back to Zinc Binding Sites List in 1kr3
Zinc binding site 1 out of 4 in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.3
occ:1.00
 NE2 A:HIS99 2.1 15.6 1.0
ND1 A:HIS101 2.4 19.2 1.0
NE2 A:HIS162 2.4 16.1 1.0
CD2 A:HIS162 3.1 15.9 1.0
CE1 A:HIS99 3.1 17.1 1.0
CD2 A:HIS99 3.2 18.5 1.0
CG A:HIS101 3.3 19.6 1.0
ZN A:ZN302 3.4 55.5 1.0
CE1 A:HIS162 3.4 15.3 1.0
CE1 A:HIS101 3.4 18.0 1.0
CB A:HIS101 3.4 20.3 1.0
O16 A:113602 3.9 37.1 1.0
OD1 A:ASP103 4.0 36.7 1.0
CG A:HIS162 4.2 14.8 1.0
ND1 A:HIS99 4.2 15.1 1.0
CG A:HIS99 4.3 16.1 1.0
ND1 A:HIS162 4.3 14.9 1.0
SG A:CYS181 4.4 30.0 1.0
CD2 A:HIS101 4.5 18.1 1.0
CB A:CYS181 4.5 20.9 1.0
NE2 A:HIS101 4.5 17.5 1.0
OD2 A:ASP103 4.6 37.9 1.0
CG A:ASP103 4.7 35.7 1.0
CA A:HIS101 4.9 19.3 1.0
SG A:CYS104 4.9 25.3 1.0
ND2 A:ASN193 4.9 54.9 1.0
O19 A:113602 4.9 41.8 1.0

Zinc binding site 2 out of 4 in 1kr3

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Zinc binding site 2 out of 4 in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:55.5
occ:1.00
 SG A:CYS181 2.1 30.0 1.0
O19 A:113602 2.6 41.8 1.0
NE2 A:HIS223 3.0 33.1 1.0
CB A:CYS181 3.0 20.9 1.0
OD2 A:ASP103 3.0 37.9 1.0
CD2 A:HIS223 3.3 25.9 1.0
ZN A:ZN301 3.4 26.3 1.0
O16 A:113602 3.6 37.1 1.0
C18 A:113602 3.6 42.6 1.0
CG A:ASP103 4.0 35.7 1.0
C5 A:113602 4.0 41.6 1.0
C6 A:113602 4.1 39.6 1.0
OD1 A:ASP103 4.2 36.7 1.0
CE1 A:HIS223 4.2 30.1 1.0
NE2 A:HIS162 4.3 16.1 1.0
CA A:CYS181 4.3 17.0 1.0
CE1 A:HIS162 4.4 15.3 1.0
NE2 A:HIS99 4.5 15.6 1.0
CE1 A:HIS99 4.5 17.1 1.0
O30 A:113602 4.6 44.5 1.0
CG A:HIS223 4.6 30.1 1.0
CD2 A:HIS162 4.8 15.9 1.0
N A:CYS181 4.9 15.3 1.0
ND1 A:HIS162 4.9 14.9 1.0
O31 A:113602 4.9 44.4 1.0

Zinc binding site 3 out of 4 in 1kr3

Go back to Zinc Binding Sites List in 1kr3
Zinc binding site 3 out of 4 in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.7
occ:1.00
 ND1 B:HIS101 2.0 3.1 1.0
NE2 B:HIS162 2.1 5.8 1.0
O B:HOH616 2.2 4.8 1.0
NE2 B:HIS99 2.4 30.4 1.0
CE1 B:HIS162 2.9 4.0 1.0
CG B:HIS101 3.0 8.0 1.0
CE1 B:HIS101 3.1 4.5 1.0
CD2 B:HIS162 3.2 6.1 1.0
O16 B:113601 3.2 24.1 1.0
CE1 B:HIS99 3.3 25.2 1.0
CB B:HIS101 3.3 7.9 1.0
CD2 B:HIS99 3.6 26.1 1.0
ZN B:ZN402 3.7 34.5 1.0
ND1 B:HIS162 4.1 9.7 1.0
O19 B:113601 4.1 39.1 1.0
OD1 B:ASP103 4.1 12.5 1.0
CD2 B:HIS101 4.2 12.7 1.0
NE2 B:HIS101 4.2 8.1 1.0
CG B:HIS162 4.2 7.2 1.0
SG B:CYS181 4.3 25.9 1.0
C6 B:113601 4.5 32.4 1.0
CB B:CYS181 4.5 15.9 1.0
ND1 B:HIS99 4.5 22.4 1.0
OD2 B:ASP103 4.5 14.7 1.0
CG B:HIS99 4.7 20.7 1.0
C18 B:113601 4.8 34.6 1.0
CG B:ASP103 4.8 10.7 1.0
CA B:HIS101 4.8 8.8 1.0
O B:HOH603 4.9 14.0 1.0

Zinc binding site 4 out of 4 in 1kr3

Go back to Zinc Binding Sites List in 1kr3
Zinc binding site 4 out of 4 in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:34.5
occ:1.00
 O B:HOH616 2.2 4.8 1.0
NE2 B:HIS223 2.2 23.4 1.0
SG B:CYS181 2.3 25.9 1.0
O19 B:113601 2.5 39.1 1.0
OD2 B:ASP103 2.5 14.7 1.0
CD2 B:HIS223 3.0 20.3 1.0
CE1 B:HIS223 3.3 18.3 1.0
C18 B:113601 3.4 34.6 1.0
CB B:CYS181 3.4 15.9 1.0
O16 B:113601 3.5 24.1 1.0
C5 B:113601 3.5 32.1 1.0
C6 B:113601 3.5 32.4 1.0
CG B:ASP103 3.5 10.7 1.0
O B:HOH617 3.7 14.4 1.0
ZN B:ZN401 3.7 22.7 1.0
OD1 B:ASP103 3.9 12.5 1.0
CG B:HIS223 4.2 18.1 1.0
C4 B:113601 4.3 31.1 1.0
CE1 B:HIS162 4.3 4.0 1.0
ND1 B:HIS223 4.3 23.4 1.0
C1 B:113601 4.4 33.6 1.0
NE2 B:HIS162 4.5 5.8 1.0
O30 B:113601 4.6 31.5 1.0
CA B:CYS181 4.6 7.7 1.0
O31 B:113601 4.8 32.2 1.0
CB B:ASP103 4.8 13.3 1.0
C11 B:113601 4.9 30.9 1.0
CE1 B:HIS99 5.0 25.2 1.0
ND1 B:HIS162 5.0 9.7 1.0

Reference:

D.J.Payne, J.A.Hueso-Rodrguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Cheever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Dez, P.Prez, 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 04:37:59 2024

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