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Sodium in PDB 5u9h: Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S

Enzymatic activity of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S

All present enzymatic activity of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S, PDB code: 5u9h was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.18 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.980, 80.048, 55.074, 90.00, 108.05, 90.00
R / Rfree (%) 19.5 / 23.3

Other elements in 5u9h:

The structure of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S (pdb code 5u9h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S, PDB code: 5u9h:

Sodium binding site 1 out of 1 in 5u9h

Go back to Sodium Binding Sites List in 5u9h
Sodium binding site 1 out of 1 in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:24.9
occ:1.00
 O P:HOH105 2.4 26.1 1.0
O A:ILE106 2.4 21.0 1.0
O A:THR101 2.4 24.1 1.0
O A:HOH714 2.5 32.6 1.0
OP1 P:DG9 2.5 26.4 1.0
O A:VAL103 2.5 21.5 1.0
C A:VAL103 3.4 22.6 1.0
C A:THR101 3.4 22.5 1.0
P P:DG9 3.5 24.4 1.0
C A:ILE106 3.5 23.1 1.0
OP2 P:DG9 3.6 23.4 1.0
N A:ILE106 3.8 20.2 1.0
O A:HOH692 3.9 39.8 1.0
CA A:SER104 4.0 25.1 1.0
N A:GLY105 4.0 21.3 1.0
CA A:THR101 4.0 21.3 1.0
N A:SER104 4.1 20.4 1.0
CA A:ILE106 4.2 21.0 1.0
N A:VAL103 4.2 20.4 1.0
C A:SER104 4.3 25.6 1.0
C A:ARG102 4.4 22.7 1.0
O3' P:DC8 4.4 25.1 1.0
CA A:VAL103 4.4 22.7 1.0
N A:ARG102 4.5 20.7 1.0
N A:GLY107 4.5 20.9 1.0
CB A:THR101 4.6 26.2 1.0
CB A:ILE106 4.6 17.2 1.0
CA A:ARG102 4.7 21.5 1.0
C A:GLY105 4.7 24.2 1.0
O5' P:DG9 4.7 24.7 1.0
CA A:GLY107 4.7 21.6 1.0
O A:ARG102 4.8 22.6 1.0
CA A:GLY105 4.9 25.5 1.0
O A:LEU100 4.9 20.7 1.0

Reference:

L.Perera, B.D.Freudenthal, W.A.Beard, L.G.Pedersen, S.H.Wilson. Revealing the Role of the Product Metal in Dna Polymerase Beta Catalysis. Nucleic Acids Res. V. 45 2736 2017.
ISSN: ESSN 1362-4962
PubMed: 28108654
DOI: 10.1093/NAR/GKW1363
Page generated: Tue Dec 15 11:41:11 2020

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