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Zinc in PDB 5axr: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate, PDB code: 5axr was solved by J.Wachino, Y.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.12 / 2.10
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 67.112, 67.112, 46.717, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 21.4

Other elements in 5axr:

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate (pdb code 5axr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate, PDB code: 5axr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5axr

Go back to Zinc Binding Sites List in 5axr
Zinc binding site 1 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.9
occ:1.00
S1 A:COM309 2.0 27.4 1.0
ND1 A:HIS74 2.0 19.8 1.0
NE2 A:HIS72 2.1 13.8 1.0
NE2 A:HIS150 2.1 15.7 1.0
CE1 A:HIS74 2.9 21.5 1.0
CD2 A:HIS72 3.0 16.2 1.0
CD2 A:HIS150 3.0 15.6 1.0
CE1 A:HIS72 3.0 15.5 1.0
CE1 A:HIS150 3.1 17.1 1.0
C1 A:COM309 3.1 34.1 1.0
CG A:HIS74 3.1 17.7 1.0
CB A:HIS74 3.5 17.9 1.0
ZN A:ZN302 3.7 17.6 1.0
NE2 A:HIS74 4.1 21.5 1.0
CD2 A:HIS77 4.1 18.1 1.0
NE2 A:HIS77 4.1 18.6 1.0
ND1 A:HIS72 4.1 15.0 1.0
CG A:HIS72 4.1 15.9 1.0
CD2 A:HIS74 4.2 18.6 1.0
CG A:HIS150 4.2 17.9 1.0
ND1 A:HIS150 4.2 18.3 1.0
OD1 A:ASP76 4.3 14.5 1.0
C2 A:COM309 4.5 39.8 1.0
OG A:SER175 4.6 17.9 1.0
OE1 A:GLN113 4.7 45.1 1.0
CB A:SER175 4.8 16.0 1.0
O A:HOH450 4.9 20.2 1.0
CA A:HIS74 4.9 18.4 1.0

Zinc binding site 2 out of 2 in 5axr

Go back to Zinc Binding Sites List in 5axr
Zinc binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:17.6
occ:1.00
OD2 A:ASP76 2.0 15.1 1.0
NE2 A:HIS77 2.1 18.6 1.0
NE2 A:HIS215 2.1 14.6 1.0
S1 A:COM309 2.3 27.4 1.0
CG A:ASP76 2.8 15.3 1.0
CE1 A:HIS77 2.9 16.0 1.0
OD1 A:ASP76 3.0 14.5 1.0
CD2 A:HIS77 3.0 18.1 1.0
CD2 A:HIS215 3.0 13.7 1.0
CE1 A:HIS215 3.1 14.3 1.0
C1 A:COM309 3.1 34.1 1.0
C2 A:COM309 3.3 39.8 1.0
ZN A:ZN301 3.7 17.9 1.0
O3S A:COM309 3.9 37.2 1.0
ND1 A:HIS77 4.0 16.4 1.0
CG A:HIS77 4.1 16.3 1.0
CB A:ASP76 4.2 15.7 1.0
ND1 A:HIS215 4.2 16.3 1.0
CG A:HIS215 4.2 14.4 1.0
S2 A:COM309 4.3 39.6 1.0
CD1 A:ILE26 4.4 15.5 1.0
NE2 A:HIS72 4.4 13.8 1.0
CE1 A:HIS72 4.5 15.5 1.0
OG A:SER175 4.6 17.9 1.0
O A:HOH466 4.8 25.8 1.0

Reference:

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2-Mercaptoethanesulfonate To Be Published.
Page generated: Wed Dec 16 06:04:06 2020

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