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Sodium in PDB 2bmi: Metallo-Beta-Lactamase

Enzymatic activity of Metallo-Beta-Lactamase

All present enzymatic activity of Metallo-Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Metallo-Beta-Lactamase, PDB code: 2bmi was solved by A.Carfi, E.Duee, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.256, 94.920, 111.420, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 26.2

Other elements in 2bmi:

The structure of Metallo-Beta-Lactamase also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Metallo-Beta-Lactamase (pdb code 2bmi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Metallo-Beta-Lactamase, PDB code: 2bmi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2bmi

Go back to Sodium Binding Sites List in 2bmi
Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na275

b:9.7
occ:1.00
O A:HOH493 2.2 9.0 1.0
O A:HOH494 2.4 8.6 1.0
O A:ASP86 2.4 9.9 1.0
O A:ASN38 2.4 7.0 1.0
OD2 A:ASP52 2.5 11.5 1.0
CG A:ASP52 3.3 8.4 1.0
CB A:ASP52 3.3 5.5 1.0
C A:ASN38 3.5 6.3 1.0
C A:ASP86 3.5 10.8 1.0
N A:ASN38 3.9 10.1 1.0
O A:HOH277 4.0 8.4 1.0
CB A:ASP86 4.2 7.8 1.0
CB A:SER37 4.2 12.0 1.0
CA A:ASN38 4.2 7.5 1.0
O A:GLY205 4.4 9.0 1.0
O A:THR53 4.4 7.6 1.0
CA A:ASP86 4.4 9.4 1.0
N A:CYS87 4.4 11.0 1.0
OD2 A:ASP86 4.5 6.1 1.0
N A:GLY39 4.5 7.7 1.0
OD1 A:ASP52 4.5 8.8 1.0
OH A:TYR23 4.5 8.4 1.0
C A:SER37 4.5 11.1 1.0
CA A:CYS87 4.6 10.6 1.0
OG A:SER37 4.6 17.6 1.0
CZ A:PHE161 4.6 10.2 1.0
CA A:GLY39 4.6 7.8 1.0
CA A:ASP52 4.7 5.8 1.0
CG A:ASP86 4.7 8.2 1.0
SG A:CYS87 4.7 7.7 1.0
CA A:SER37 4.9 12.5 1.0

Sodium binding site 2 out of 2 in 2bmi

Go back to Sodium Binding Sites List in 2bmi
Sodium binding site 2 out of 2 in the Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na275

b:9.3
occ:1.00
O B:HOH475 2.2 8.1 1.0
O B:ASN38 2.3 6.4 1.0
O B:ASP86 2.3 9.0 1.0
O B:HOH279 2.4 8.9 1.0
OD2 B:ASP52 2.6 8.7 1.0
CB B:ASP52 3.4 7.4 1.0
CG B:ASP52 3.4 5.0 1.0
C B:ASN38 3.4 6.5 1.0
C B:ASP86 3.5 9.1 1.0
N B:ASN38 3.9 6.9 1.0
O B:HOH280 4.0 7.5 1.0
CB B:ASP86 4.2 6.7 1.0
CB B:SER37 4.2 8.7 1.0
CA B:ASN38 4.2 7.2 1.0
OG B:SER37 4.3 14.8 1.0
O B:GLY205 4.3 8.7 1.0
O B:THR53 4.3 10.1 1.0
CA B:ASP86 4.4 7.7 1.0
N B:GLY39 4.4 8.6 1.0
CZ B:PHE161 4.5 2.8 1.0
N B:CYS87 4.5 9.8 1.0
C B:SER37 4.5 9.1 1.0
OD1 B:ASP52 4.5 5.2 1.0
OD2 B:ASP86 4.6 8.3 1.0
CA B:GLY39 4.6 10.6 1.0
CA B:CYS87 4.7 9.5 1.0
OH B:TYR23 4.7 11.3 1.0
SG B:CYS87 4.7 10.4 1.0
CG B:ASP86 4.7 9.4 1.0
CA B:ASP52 4.7 8.7 1.0
CA B:SER37 4.9 9.1 1.0

Reference:

A.Carfi, E.Duee, R.Paul-Soto, M.Galleni, J.M.Frere, O.Dideberg. X-Ray Structure of the Znii Beta-Lactamase From Bacteroides Fragilis in An Orthorhombic Crystal Form. Acta Crystallogr.,Sect.D V. 54 45 1998.
ISSN: ISSN 0907-4449
PubMed: 9761816
DOI: 10.1107/S090744499700927X
Page generated: Tue Dec 15 05:46:04 2020

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