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Iodine in PDB 6bte: Dna Polymerase Beta I260Q Binary Complex

Enzymatic activity of Dna Polymerase Beta I260Q Binary Complex

All present enzymatic activity of Dna Polymerase Beta I260Q Binary Complex:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta I260Q Binary Complex, PDB code: 6bte was solved by B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.96 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.942, 80.568, 55.133, 90.00, 107.92, 90.00
R / Rfree (%) 18.5 / 22.9

Other elements in 6bte:

The structure of Dna Polymerase Beta I260Q Binary Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Dna Polymerase Beta I260Q Binary Complex (pdb code 6bte). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Dna Polymerase Beta I260Q Binary Complex, PDB code: 6bte:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 6bte

Go back to Iodine Binding Sites List in 6bte
Iodine binding site 1 out of 2 in the Dna Polymerase Beta I260Q Binary Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Dna Polymerase Beta I260Q Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:36.0
occ:0.35
CB A:HIS34 3.5 15.7 1.0
CB A:ALA32 3.5 16.0 1.0
CD2 A:HIS34 3.8 18.2 1.0
N A:HIS34 3.8 15.8 1.0
CA A:ALA32 3.9 17.1 1.0
CG A:HIS34 4.0 17.3 1.0
N A:LYS35 4.0 14.2 1.0
C A:ALA32 4.1 16.4 1.0
CA A:HIS34 4.1 15.0 1.0
N A:ILE33 4.3 17.0 1.0
CG A:LYS35 4.4 15.6 1.0
C A:HIS34 4.5 14.3 1.0
O6 D:DG1 4.5 18.5 1.0
O A:ALA32 4.5 15.2 1.0
CB A:LYS35 4.9 14.3 1.0
C A:ILE33 4.9 16.3 1.0

Iodine binding site 2 out of 2 in 6bte

Go back to Iodine Binding Sites List in 6bte
Iodine binding site 2 out of 2 in the Dna Polymerase Beta I260Q Binary Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Dna Polymerase Beta I260Q Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:37.0
occ:0.50
O A:HOH591 3.6 28.5 1.0
O A:HOH583 3.9 16.2 1.0
CD1 A:LEU85 3.9 14.9 1.0
N A:LEU82 4.0 17.1 1.0
CE1 A:PHE76 4.1 11.8 1.0
NH2 A:ARG89 4.1 26.5 1.0
CA A:LYS81 4.2 21.9 1.0
CD1 A:PHE76 4.3 11.8 1.0
C A:LYS81 4.4 22.5 1.0
CB A:LEU82 4.5 25.0 1.0
CB A:MET18 4.5 10.7 1.0
NH1 A:ARG89 4.5 28.4 1.0
CG A:MET18 4.6 10.9 1.0
CZ A:ARG89 4.6 26.4 1.0
OE1 A:GLU21 4.7 17.5 1.0
CB A:LEU85 4.8 16.9 1.0
CB A:LYS81 4.8 22.4 1.0
CA A:LEU82 4.8 17.2 1.0
CA A:MET18 4.9 9.8 1.0
O A:GLY80 4.9 17.3 1.0
CG A:LEU85 5.0 15.2 1.0

Reference:

C.Liptak, M.M.Mahmoud, B.E.Eckenroth, M.V.Moreno, K.East, K.S.Alnajjar, J.Huang, J.B.Towle-Weicksel, S.Doublie, J.P.Loria, J.B.Sweasy. I260Q Dna Polymerase Beta Highlights Precatalytic Conformational Rearrangements Critical For Fidelity. Nucleic Acids Res. V. 46 10740 2018.
ISSN: ESSN 1362-4962
PubMed: 30239932
DOI: 10.1093/NAR/GKY825
Page generated: Sun Dec 13 19:42:50 2020

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