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Sodium in PDB 1a7t: Metallo-Beta-Lactamase with Mes

Enzymatic activity of Metallo-Beta-Lactamase with Mes

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

Protein crystallography data

The structure of Metallo-Beta-Lactamase with Mes, PDB code: 1a7t was solved by P.M.D.Fitzgerald, J.K.Wu, J.H.Toney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.270, 66.960, 69.480, 90.00, 103.77, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1a7t:

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

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Metallo-Beta-Lactamase with Mes (pdb code 1a7t). 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 with Mes, PDB code: 1a7t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1a7t

Go back to Sodium Binding Sites List in 1a7t
Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase with Mes


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 with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na255

b:37.6
occ:1.00
O A:ASN38 2.4 6.8 1.0
O A:HOH258 2.4 5.3 1.0
O A:HOH266 2.4 10.5 1.0
O A:ASP86 2.5 6.0 1.0
OD2 A:ASP52 2.5 4.5 1.0
CG A:ASP52 3.2 5.2 1.0
CB A:ASP52 3.2 5.4 1.0
C A:ASN38 3.5 8.4 1.0
C A:ASP86 3.7 7.3 1.0
N A:ASN38 3.8 9.1 1.0
O A:HOH265 4.0 9.7 1.0
CA A:ASN38 4.3 8.2 1.0
CB A:SER37 4.3 9.2 1.0
C A:SER37 4.4 10.0 1.0
OD1 A:ASP52 4.4 5.3 1.0
CB A:ASP86 4.4 7.6 1.0
N A:GLY39 4.4 8.6 1.0
O A:THR53 4.4 7.3 1.0
O A:GLY205 4.4 8.4 1.0
N A:CYS87 4.4 6.4 1.0
OD2 A:ASP86 4.5 7.9 1.0
CA A:CYS87 4.5 5.5 1.0
CA A:GLY39 4.6 8.3 1.0
CA A:ASP86 4.6 6.7 1.0
SG A:CYS87 4.7 7.8 1.0
CA A:ASP52 4.7 5.8 1.0
CA A:SER37 4.7 10.2 1.0
OH A:TYR23 4.8 11.4 1.0
CZ A:PHE161 4.8 10.1 1.0
CG A:ASP86 4.9 8.0 1.0

Sodium binding site 2 out of 2 in 1a7t

Go back to Sodium Binding Sites List in 1a7t
Sodium binding site 2 out of 2 in the Metallo-Beta-Lactamase with Mes


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 with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na255

b:35.4
occ:1.00
OD2 B:ASP52 2.4 4.3 1.0
O B:HOH263 2.4 7.9 1.0
O B:ASN38 2.4 2.4 1.0
O B:ASP86 2.5 5.1 1.0
O B:HOH259 2.6 6.1 1.0
CG B:ASP52 3.1 4.8 1.0
CB B:ASP52 3.2 5.0 1.0
C B:ASN38 3.5 5.9 1.0
C B:ASP86 3.7 5.2 1.0
O B:HOH265 3.8 9.1 1.0
N B:ASN38 3.9 7.0 1.0
OD1 B:ASP52 4.3 5.8 1.0
CA B:ASN38 4.3 6.6 1.0
CB B:ASP86 4.5 6.2 1.0
O B:GLY205 4.5 5.5 1.0
CA B:CYS87 4.5 6.0 1.0
N B:CYS87 4.5 5.7 1.0
OD2 B:ASP86 4.5 7.1 1.0
C B:SER37 4.5 8.1 1.0
N B:GLY39 4.5 4.5 1.0
CB B:SER37 4.5 9.4 1.0
O B:THR53 4.6 7.2 1.0
CZ B:PHE161 4.6 10.7 1.0
CA B:GLY39 4.6 6.0 1.0
CA B:ASP52 4.6 5.9 1.0
CA B:ASP86 4.7 5.6 1.0
SG B:CYS87 4.7 6.1 1.0
CG B:ASP86 4.8 7.3 1.0
OH B:TYR23 4.9 8.6 1.0
CA B:SER37 4.9 8.3 1.0
C B:ASP52 5.0 6.8 1.0

Reference:

P.M.Fitzgerald, J.K.Wu, J.H.Toney. Unanticipated Inhibition of the Metallo-Beta-Lactamase From Bacteroides Fragilis By 4-Morpholineethanesulfonic Acid (Mes): A Crystallographic Study at 1.85-A Resolution. Biochemistry V. 37 6791 1998.
ISSN: ISSN 0006-2960
PubMed: 9578564
DOI: 10.1021/BI9730339
Page generated: Tue Dec 15 05:21:43 2020

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