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Sodium 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:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1kr3

Go back to Sodium Binding Sites List in 1kr3
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na501

b:3.1
occ:1.00
O A:HOH616 2.9 13.4 1.0
O A:ASP103 3.1 23.9 1.0
OH A:TYR40 3.1 15.8 1.0
O A:THR70 3.1 25.2 1.0
O A:ASN55 3.1 19.7 1.0
C A:THR70 3.6 21.4 1.0
CB A:ASP69 3.6 16.9 1.0
C A:ASN55 3.7 21.8 1.0
CB A:SER54 3.9 29.6 1.0
CZ A:TYR40 3.9 11.4 1.0
N A:THR70 4.0 19.2 1.0
CE1 A:TYR40 4.0 12.1 1.0
C A:ASP103 4.0 26.5 1.0
OD2 A:ASP69 4.1 16.1 1.0
N A:PRO71 4.1 22.3 1.0
C A:SER54 4.1 25.5 1.0
O A:SER54 4.2 22.9 1.0
CA A:PRO71 4.2 25.5 1.0
N A:ASN55 4.2 25.6 1.0
C A:ASP69 4.3 20.4 1.0
CG A:ASP69 4.3 15.2 1.0
N A:GLY56 4.3 21.0 1.0
CA A:THR70 4.3 21.0 1.0
CA A:ASN55 4.4 23.6 1.0
OG A:SER42 4.5 36.7 1.0
CA A:GLY56 4.5 20.7 1.0
CA A:ASP69 4.6 17.0 1.0
CA A:SER54 4.7 28.2 1.0
CA A:ASP103 4.7 29.1 1.0
O A:ASP69 4.8 18.5 1.0
CB A:ASP103 4.8 29.4 1.0
OG A:SER54 4.9 32.2 1.0
N A:CYS104 5.0 24.4 1.0
C A:PRO71 5.0 26.6 1.0

Sodium binding site 2 out of 2 in 1kr3

Go back to Sodium Binding Sites List in 1kr3
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
B:Na502

b:3.1
occ:1.00
O B:ASP103 2.3 19.1 1.0
O B:ASN55 2.7 18.4 1.0
O B:THR70 3.3 19.9 1.0
C B:ASN55 3.5 19.4 1.0
C B:ASP103 3.5 15.7 1.0
O B:HOH617 3.6 14.4 1.0
CB B:SER54 3.6 23.4 1.0
CB B:ASP69 3.8 6.1 1.0
OD2 B:ASP69 3.8 11.1 1.0
N B:ASN55 3.8 24.7 1.0
C B:SER54 4.0 25.9 1.0
CA B:ASN55 4.2 19.2 1.0
CG B:ASP69 4.2 4.5 1.0
OH B:TYR40 4.2 7.8 1.0
N B:GLY56 4.3 19.9 1.0
CA B:ASP103 4.3 16.6 1.0
CB B:ASP103 4.3 13.3 1.0
OG B:SER54 4.3 26.6 1.0
O B:SER54 4.4 25.9 1.0
C B:THR70 4.4 13.8 1.0
CA B:SER54 4.4 25.8 1.0
N B:CYS104 4.5 18.8 1.0
CA B:GLY56 4.5 19.9 1.0
N B:THR70 4.6 17.1 1.0
CA B:CYS104 4.7 16.9 1.0
C B:ASP69 4.8 13.5 1.0
OD2 B:ASP103 4.9 14.7 1.0
CZ B:TYR40 4.9 6.9 1.0
CA B:ASP69 4.9 10.8 1.0
CE1 B:TYR40 4.9 3.3 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: Tue Dec 15 05:28:39 2020

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