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Arsenic in PDB 3erp: Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium

Protein crystallography data

The structure of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium, PDB code: 3erp was solved by A.U.Singer, G.Minasov, E.Evdokimova, J.S.Brunzelle, M.Kudritska, A.M.Edwards, W.F.Anderson, A.Savchenko, Center For Structural Genomicsof Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 1.55
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 127.096, 127.096, 120.492, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.8

Other elements in 3erp:

The structure of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium (pdb code 3erp). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium, PDB code: 3erp:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 3erp

Go back to Arsenic Binding Sites List in 3erp
Arsenic binding site 1 out of 2 in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As337

b:30.2
occ:0.60
AS A:CAC337 0.0 30.2 0.6
O2 A:CAC337 1.8 18.6 0.6
O1 A:CAC337 1.8 17.7 0.6
C1 A:CAC337 2.0 25.8 0.6
C2 A:CAC337 2.0 24.2 0.6
NA A:NA334 3.4 35.0 1.0
CZ A:PHE221 3.5 17.6 0.3
CE1 A:PHE221 3.6 16.7 0.3
NE2 A:HIS138 3.7 14.8 1.0
CE2 A:PHE221 4.0 17.5 0.3
OH A:TYR66 4.1 20.4 1.0
O A:HOH771 4.2 30.4 0.6
CD1 A:PHE221 4.2 18.0 0.3
CE2 A:TRP33 4.3 25.0 0.7
CZ2 A:TRP33 4.3 29.4 0.7
CZ A:PHE221 4.4 15.4 0.7
C1 A:EDO342 4.4 28.4 1.0
CE1 A:PHE221 4.4 15.8 0.7
CD2 A:HIS138 4.5 15.3 1.0
CD2 A:TRP33 4.6 23.7 0.7
CH2 A:TRP33 4.6 29.6 0.7
CD2 A:PHE221 4.6 14.3 0.3
CE1 A:HIS138 4.6 16.9 1.0
NE1 A:TRP33 4.6 21.1 0.7
CG A:PHE221 4.7 15.7 0.3
CD1 A:PHE221 4.8 16.3 0.7
ND2 A:ASN169 4.8 18.4 1.0
CE2 A:PHE221 4.8 16.6 0.7
CZ3 A:TRP33 4.9 29.1 0.7
CE3 A:TRP33 4.9 29.6 0.7
CE1 A:TYR66 4.9 16.6 1.0
O1 A:EDO342 4.9 28.6 1.0
CZ A:TYR66 5.0 19.7 1.0

Arsenic binding site 2 out of 2 in 3erp

Go back to Arsenic Binding Sites List in 3erp
Arsenic binding site 2 out of 2 in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As338

b:27.5
occ:0.70
AS B:CAC338 0.0 27.5 0.7
O2 B:CAC338 1.7 16.5 0.7
O1 B:CAC338 1.8 18.5 0.7
C1 B:CAC338 1.9 25.8 0.7
C2 B:CAC338 2.0 29.8 0.7
NA B:NA334 3.5 29.0 1.0
NE2 B:HIS138 3.8 13.3 1.0
O B:HOH824 3.9 36.2 1.0
CZ2 B:TRP33 4.2 27.6 1.0
OH B:TYR66 4.2 18.3 1.0
CE1 B:PHE221 4.2 15.0 1.0
CZ B:PHE221 4.3 15.9 1.0
CE2 B:TRP33 4.3 22.7 1.0
CH2 B:TRP33 4.3 28.4 1.0
CD2 B:HIS138 4.5 13.4 1.0
ND2 B:ASN169 4.6 16.5 1.0
CD1 B:PHE221 4.6 16.1 1.0
CD2 B:TRP33 4.7 23.9 1.0
CZ3 B:TRP33 4.7 29.4 1.0
CE2 B:PHE221 4.7 19.1 1.0
CE1 B:HIS138 4.7 14.5 1.0
O B:HOH839 4.7 43.5 1.0
NE1 B:TRP33 4.8 22.7 1.0
CE3 B:TRP33 4.8 23.5 1.0

Reference:

T.Kim, R.Flick, J.Brunzelle, A.Singer, E.Evdokimova, G.Brown, J.C.Joo, G.A.Minasov, W.F.Anderson, R.Mahadevan, A.Savchenko, A.F.Yakunin. Structural and Biochemical Studies of Novel Aldo-Keto Reductases For the Biocatalytic Conversion of 3-Hydroxybutanal to 1,3-Butanediol. Appl.Environ.Microbiol. 2017.
ISSN: ESSN 1098-5336
PubMed: 28130301
DOI: 10.1128/AEM.03172-16
Page generated: Tue Oct 27 16:50:02 2020

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