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Zinc in PDB 5f7r: Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer

Protein crystallography data

The structure of Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer, PDB code: 5f7r was solved by S.H.Light, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.200, 95.064, 117.144, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20

Other elements in 5f7r:

The structure of Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer (pdb code 5f7r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer, PDB code: 5f7r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5f7r

Go back to Zinc Binding Sites List in 5f7r
Zinc binding site 1 out of 2 in the Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:19.2
occ:1.00
ND1 E:HIS244 2.1 19.1 1.0
SG E:CYS256 2.3 20.3 1.0
SG E:CYS261 2.3 18.5 1.0
SG E:CYS254 2.3 19.5 1.0
CE1 E:HIS244 3.0 19.6 1.0
CB E:CYS254 3.1 19.4 1.0
CG E:HIS244 3.1 18.6 1.0
CB E:CYS261 3.2 17.6 1.0
CB E:CYS256 3.2 21.2 1.0
CB E:HIS244 3.5 18.2 1.0
CA E:HIS244 3.9 17.1 1.0
NE2 E:HIS244 4.1 19.9 1.0
N E:CYS256 4.2 21.8 1.0
CD2 E:HIS244 4.2 19.9 1.0
CA E:CYS256 4.3 22.1 1.0
NE2 E:GLN258 4.4 17.8 0.5
O E:GLY243 4.5 17.1 1.0
CA E:CYS254 4.5 20.3 1.0
CB E:GLN258 4.6 20.4 0.5
CA E:CYS261 4.6 16.5 1.0
CD E:GLN258 4.7 19.7 0.5
N E:HIS244 4.8 16.4 1.0
O E:GLN258 4.8 21.4 0.5
CG E:GLN258 4.9 20.7 0.5
C E:CYS256 5.0 23.5 1.0
C E:CYS254 5.0 21.2 1.0
C E:HIS244 5.0 16.7 1.0

Zinc binding site 2 out of 2 in 5f7r

Go back to Zinc Binding Sites List in 5f7r
Zinc binding site 2 out of 2 in the Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rok Repressor LMO0178 From Listeria Monocytogenes Bound to Inducer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:16.8
occ:1.00
ND1 A:HIS244 2.1 16.0 1.0
SG A:CYS254 2.3 18.8 1.0
SG A:CYS261 2.3 16.6 1.0
SG A:CYS256 2.3 17.7 1.0
CE1 A:HIS244 3.0 16.0 1.0
CB A:CYS254 3.0 19.2 1.0
CG A:HIS244 3.1 15.4 1.0
CB A:CYS261 3.2 16.2 1.0
CB A:CYS256 3.3 18.5 1.0
CB A:HIS244 3.5 15.1 1.0
CA A:HIS244 3.9 14.8 1.0
N A:CYS256 4.1 19.4 1.0
NE2 A:HIS244 4.1 16.0 1.0
CD2 A:HIS244 4.2 15.9 1.0
CA A:CYS256 4.3 19.1 1.0
CA A:CYS254 4.5 19.8 1.0
O A:GLY243 4.5 15.2 1.0
CB A:GLN258 4.6 20.1 1.0
CA A:CYS261 4.7 15.8 1.0
NE2 A:GLN258 4.7 20.3 1.0
N A:HIS244 4.8 14.5 1.0
CD A:GLN258 4.9 20.8 1.0
C A:CYS254 4.9 19.9 1.0
C A:CYS256 4.9 20.0 1.0
C A:HIS244 5.0 15.1 1.0

Reference:

S.H.Light, L.A.Cahoon, A.S.Halavaty, N.E.Freitag, W.F.Anderson. Structure to Function of An Alpha-Glucan Metabolic Pathway That Promotes Listeria Monocytogenes Pathogenesis. Nat Microbiol V. 2 16202 2016.
ISSN: ESSN 2058-5276
PubMed: 27819654
DOI: 10.1038/NMICROBIOL.2016.202
Page generated: Wed Dec 16 06:13:13 2020

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