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Zinc in PDB 5w8w: Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement

Enzymatic activity of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement

All present enzymatic activity of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement:
3.5.2.6;

Protein crystallography data

The structure of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement, PDB code: 5w8w was solved by J.M.Gonzalez, I.G.Shabalin, J.E.Raczynska, M.Jaskolski, W.Minor, A.Wlodawer, M.M.Gonzalez, A.J.Vila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.40 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.603, 60.419, 69.513, 90.00, 93.28, 90.00
R / Rfree (%) 15.3 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement (pdb code 5w8w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement, PDB code: 5w8w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5w8w

Go back to Zinc Binding Sites List in 5w8w
Zinc binding site 1 out of 2 in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:33.1
occ:1.00
NE2 A:HIS179 2.0 30.8 1.0
NE2 A:HIS116 2.1 26.6 1.0
ND1 A:HIS118 2.1 30.0 1.0
O A:HOH452 2.2 29.5 1.0
CD2 A:HIS179 3.0 29.7 1.0
CE1 A:HIS179 3.0 31.6 1.0
CD2 A:HIS116 3.1 25.9 1.0
CE1 A:HIS118 3.1 29.3 1.0
CE1 A:HIS116 3.1 25.9 1.0
CG A:HIS118 3.1 28.7 1.0
CB A:HIS118 3.4 28.3 1.0
ZN A:ZN302 3.6 55.8 1.0
OD1 A:ASP120 4.0 36.9 1.0
CB A:CYS198 4.1 32.4 1.0
ND1 A:HIS179 4.1 30.3 1.0
CG A:HIS179 4.2 29.1 1.0
ND1 A:HIS116 4.2 25.1 1.0
CG A:HIS116 4.2 24.6 1.0
NE2 A:HIS118 4.2 28.7 1.0
CD2 A:HIS118 4.2 28.2 1.0
SG A:CYS198 4.3 37.6 1.0
CG2 A:THR180 4.5 23.5 1.0
OD2 A:ASP120 4.7 43.3 1.0
CG A:ASP120 4.8 39.8 1.0
CA A:HIS118 4.9 29.3 1.0

Zinc binding site 2 out of 2 in 5w8w

Go back to Zinc Binding Sites List in 5w8w
Zinc binding site 2 out of 2 in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 7 - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:55.8
occ:1.00
NE2 A:HIS240 2.1 42.5 1.0
OD2 A:ASP120 2.2 43.3 1.0
O A:HOH452 2.2 29.5 1.0
SG A:CYS198 2.3 37.6 1.0
CE1 A:HIS240 3.1 42.3 1.0
CD2 A:HIS240 3.1 40.3 1.0
CG A:ASP120 3.1 39.8 1.0
CB A:CYS198 3.3 32.4 1.0
OD1 A:ASP120 3.4 36.9 1.0
ZN A:ZN301 3.6 33.1 1.0
NH2 A:ARG121 4.1 33.3 1.0
NE A:ARG121 4.1 33.3 1.0
ND1 A:HIS240 4.2 42.0 1.0
CG A:HIS240 4.3 39.5 1.0
CE1 A:HIS116 4.4 25.9 1.0
NE2 A:HIS179 4.4 30.8 1.0
NE2 A:HIS116 4.4 26.6 1.0
CB A:ASP120 4.5 38.6 1.0
CZ A:ARG121 4.5 33.3 1.0
CA A:CYS198 4.6 31.0 1.0
UNK A:UNX303 4.6 51.0 1.0
CE1 A:HIS179 4.7 31.6 1.0

Reference:

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001
Page generated: Wed Dec 16 11:15:31 2020

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