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Zinc in PDB 5aya: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril

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

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril, PDB code: 5aya 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) 50.00 / 2.02
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 68.097, 68.097, 49.110, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 28.2

Other elements in 5aya:

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

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril (pdb code 5aya). 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 L-Captopril, PDB code: 5aya:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5aya

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


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 L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:37.6
occ:1.00
NE2 A:HIS150 2.0 32.9 1.0
ND1 A:HIS74 2.1 37.6 1.0
NE2 A:HIS72 2.2 36.5 1.0
S A:X8Z307 2.3 42.3 1.0
CD2 A:HIS150 2.9 27.7 1.0
CE1 A:HIS74 2.9 36.9 1.0
CD2 A:HIS72 3.0 31.6 1.0
CE1 A:HIS72 3.1 39.0 1.0
CG A:HIS74 3.1 32.8 1.0
CE1 A:HIS150 3.1 31.0 1.0
C1 A:X8Z307 3.4 55.0 1.0
CB A:HIS74 3.5 31.5 1.0
ZN A:ZN302 4.0 44.2 1.0
NE2 A:HIS74 4.0 33.2 1.0
CD2 A:HIS74 4.1 36.6 1.0
ND1 A:HIS72 4.1 37.6 1.0
CG A:HIS150 4.1 28.9 1.0
CG A:HIS72 4.1 36.3 1.0
ND1 A:HIS150 4.2 30.4 1.0
NE2 A:HIS77 4.2 30.6 1.0
CD2 A:HIS77 4.3 35.6 1.0
NE2 A:GLN113 4.4 43.4 1.0
OD1 A:ASP76 4.5 40.1 1.0
OG A:SER175 4.6 38.6 1.0
C2 A:X8Z307 4.7 58.4 1.0
CB A:SER175 4.9 29.9 1.0
CA A:HIS74 4.9 38.7 1.0
CD A:GLN113 5.0 45.1 1.0
C3 A:X8Z307 5.0 61.0 1.0

Zinc binding site 2 out of 2 in 5aya

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


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 L-Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:44.2
occ:1.00
OD2 A:ASP76 2.0 36.3 1.0
NE2 A:HIS77 2.1 30.6 1.0
NE2 A:HIS215 2.2 45.1 1.0
S A:X8Z307 2.4 42.3 1.0
CG A:ASP76 2.8 43.2 1.0
CE1 A:HIS77 2.9 25.6 1.0
CE1 A:HIS215 3.0 41.9 1.0
OD1 A:ASP76 3.0 40.1 1.0
CD2 A:HIS77 3.1 35.6 1.0
C1 A:X8Z307 3.1 55.0 1.0
CD2 A:HIS215 3.3 41.6 1.0
C2 A:X8Z307 3.7 58.4 1.0
ND1 A:HIS77 3.9 27.5 1.0
ZN A:ZN301 4.0 37.6 1.0
CG A:HIS77 4.1 30.1 1.0
ND1 A:HIS215 4.1 42.3 1.0
CB A:ASP76 4.2 34.5 1.0
CD1 A:ILE26 4.3 42.9 1.0
CG A:HIS215 4.3 41.7 1.0
NE2 A:HIS72 4.4 36.5 1.0
CE1 A:HIS72 4.5 39.0 1.0
OG A:SER175 4.6 38.6 1.0
C4 A:X8Z307 4.7 61.1 1.0
C3 A:X8Z307 4.8 61.0 1.0

Reference:

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

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