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Zinc in PDB 5axo: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem

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

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem, PDB code: 5axo 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) 40.62 / 1.39
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.900, 41.170, 45.320, 107.95, 102.46, 106.85
R / Rfree (%) 13.7 / 16.3

Other elements in 5axo:

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

Sodium (Na) 10 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5axo

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


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 Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:5.7
occ:1.00
O A:HOH459 1.8 5.3 1.0
NE2 A:HIS72 2.0 5.0 1.0
ND1 A:HIS74 2.0 5.1 1.0
NE2 A:HIS150 2.1 4.7 1.0
CE1 A:HIS74 3.0 5.1 1.0
CD2 A:HIS150 3.0 4.9 1.0
CD2 A:HIS72 3.0 5.2 1.0
CE1 A:HIS72 3.0 5.5 1.0
CG A:HIS74 3.1 5.6 1.0
CE1 A:HIS150 3.2 5.0 1.0
O62 A:LMP317 3.3 14.5 1.0
O32 A:LMP317 3.4 9.1 1.0
CB A:HIS74 3.5 5.4 1.0
ZN A:ZN302 3.5 6.5 1.0
CD2 A:HIS77 4.0 5.5 1.0
ND1 A:HIS72 4.1 5.1 1.0
OD1 A:ASP76 4.1 7.1 1.0
NE2 A:HIS74 4.1 5.7 1.0
CG A:HIS72 4.1 5.2 1.0
C31 A:LMP317 4.1 14.2 1.0
NE2 A:HIS77 4.2 5.0 1.0
CG A:HIS150 4.2 4.9 1.0
CD2 A:HIS74 4.2 5.9 1.0
ND1 A:HIS150 4.2 5.5 1.0
N4 A:LMP317 4.3 13.6 1.0
C62 A:LMP317 4.4 20.7 1.0
C61 A:LMP317 4.4 17.0 1.0
NE2 A:GLN113 4.5 7.8 1.0
C3 A:LMP317 4.5 13.5 1.0
OD2 A:ASP76 4.8 6.6 1.0
CA A:HIS74 4.9 4.8 1.0
CG A:ASP76 4.9 6.1 1.0
OG A:SER175 5.0 2.9 0.5

Zinc binding site 2 out of 2 in 5axo

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


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 Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:6.5
occ:1.00
O A:HOH459 2.1 5.3 1.0
NE2 A:HIS215 2.1 5.9 1.0
NE2 A:HIS77 2.1 5.0 1.0
OD2 A:ASP76 2.2 6.6 1.0
O32 A:LMP317 2.3 9.1 1.0
N4 A:LMP317 2.4 13.6 1.0
C31 A:LMP317 3.0 14.2 1.0
C3 A:LMP317 3.0 13.5 1.0
CG A:ASP76 3.0 6.1 1.0
CE1 A:HIS215 3.0 5.8 1.0
CD2 A:HIS77 3.1 5.5 1.0
CE1 A:HIS77 3.1 6.2 1.0
CD2 A:HIS215 3.1 5.7 1.0
OD1 A:ASP76 3.3 7.1 1.0
ZN A:ZN301 3.5 5.7 1.0
C5 A:LMP317 3.6 16.5 1.0
O62 A:LMP317 4.0 14.5 1.0
C6 A:LMP317 4.0 17.9 1.0
O31 A:LMP317 4.2 12.8 1.0
ND1 A:HIS215 4.2 6.2 1.0
ND1 A:HIS77 4.2 5.7 1.0
CG A:HIS77 4.2 5.6 1.0
CG A:HIS215 4.3 5.7 1.0
NE2 A:HIS72 4.3 5.0 1.0
OG A:SER175 4.3 2.9 0.5
CB A:ASP76 4.4 6.0 1.0
CE1 A:HIS72 4.4 5.5 1.0
C61 A:LMP317 4.4 17.0 1.0
C2 A:LMP317 4.5 15.2 1.0
C1 A:LMP317 4.7 18.1 1.0
NE2 A:HIS150 4.8 4.7 1.0
C62 A:LMP317 4.8 20.7 1.0
CD1 A:ILE26 5.0 6.4 1.0

Reference:

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

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