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Sodium in PDB 2znb: Metallo-Beta-Lactamase (Cadmium-Bound Form)

Enzymatic activity of Metallo-Beta-Lactamase (Cadmium-Bound Form)

All present enzymatic activity of Metallo-Beta-Lactamase (Cadmium-Bound Form):
3.5.2.6;

Protein crystallography data

The structure of Metallo-Beta-Lactamase (Cadmium-Bound Form), PDB code: 2znb was solved by N.O.Concha, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.086, 78.086, 139.746, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 25.9

Other elements in 2znb:

The structure of Metallo-Beta-Lactamase (Cadmium-Bound Form) also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Metallo-Beta-Lactamase (Cadmium-Bound Form) (pdb code 2znb). 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 (Cadmium-Bound Form), PDB code: 2znb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2znb

Go back to Sodium Binding Sites List in 2znb
Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


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 (Cadmium-Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3

b:20.4
occ:1.00
O A:HOH255 2.1 18.0 1.0
O A:ASN55 2.4 13.9 1.0
O A:ASP103 2.4 16.2 1.0
OD2 A:ASP69 2.5 12.1 1.0
O A:HOH261 2.7 11.9 1.0
CG A:ASP69 3.3 10.2 1.0
CB A:ASP69 3.4 13.2 1.0
C A:ASN55 3.5 14.2 1.0
C A:ASP103 3.6 15.3 1.0
O A:HOH256 3.6 10.0 1.0
N A:ASN55 4.0 18.0 1.0
CA A:ASN55 4.3 15.1 1.0
OD2 A:ASP103 4.3 17.8 1.0
CB A:ASP103 4.3 15.0 1.0
O A:GLY222 4.4 9.5 1.0
CB A:SER54 4.4 19.9 1.0
OD1 A:ASP69 4.5 12.0 1.0
N A:CYS104 4.5 13.8 1.0
CG A:ASP103 4.5 14.8 1.0
CA A:CYS104 4.6 9.5 1.0
CA A:ASP103 4.6 14.3 1.0
N A:GLY56 4.6 13.8 1.0
O A:THR70 4.6 15.0 1.0
CZ A:PHE178 4.6 9.2 1.0
C A:SER54 4.7 20.5 1.0
SG A:CYS104 4.7 12.8 1.0
CA A:GLY56 4.8 12.9 1.0
CA A:ASP69 4.8 11.9 1.0
OG A:SER54 4.9 22.7 1.0

Sodium binding site 2 out of 2 in 2znb

Go back to Sodium Binding Sites List in 2znb
Sodium binding site 2 out of 2 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


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 (Cadmium-Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3

b:24.7
occ:1.00
O B:ASN55 2.2 15.4 1.0
O B:HOH267 2.4 15.3 1.0
OD2 B:ASP69 2.4 16.2 1.0
O B:ASP103 2.5 22.6 1.0
O B:HOH300 2.7 31.1 1.0
CG B:ASP69 3.2 15.1 1.0
CB B:ASP69 3.3 12.0 1.0
C B:ASN55 3.3 17.5 1.0
C B:ASP103 3.7 20.0 1.0
O B:HOH286 3.7 20.2 1.0
N B:ASN55 4.0 19.8 1.0
CA B:ASN55 4.3 18.6 1.0
CB B:ASP103 4.3 16.0 1.0
N B:GLY56 4.3 17.4 1.0
O B:GLY222 4.3 13.8 1.0
OD1 B:ASP69 4.4 22.6 1.0
OD2 B:ASP103 4.4 16.2 1.0
OG B:SER54 4.5 24.9 1.0
CB B:SER54 4.5 19.3 1.0
CA B:GLY56 4.5 17.4 1.0
CA B:CYS104 4.5 17.9 1.0
N B:CYS104 4.5 18.4 1.0
CZ B:PHE178 4.6 19.7 1.0
CA B:ASP103 4.6 19.2 1.0
CG B:ASP103 4.6 16.4 1.0
O B:THR70 4.6 15.6 1.0
C B:SER54 4.6 19.3 1.0
SG B:CYS104 4.7 15.1 1.0
CA B:ASP69 4.8 12.0 1.0
OH B:TYR40 4.9 24.8 1.0

Reference:

N.O.Concha, B.A.Rasmussen, K.Bush, O.Herzberg. Crystal Structures of the Cadmium- and Mercury-Substituted Metallo-Beta-Lactamase From Bacteroides Fragilis. Protein Sci. V. 6 2671 1997.
ISSN: ISSN 0961-8368
PubMed: 9416622
Page generated: Tue Dec 15 06:01:20 2020

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