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Sodium in PDB 4yd1: Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp

Enzymatic activity of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp, PDB code: 4yd1 was solved by A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.97 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.259, 69.042, 116.988, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19

Other elements in 4yd1:

The structure of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp (pdb code 4yd1). 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 Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp, PDB code: 4yd1:

Sodium binding site 1 out of 1 in 4yd1

Go back to Sodium Binding Sites List in 4yd1
Sodium binding site 1 out of 1 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na612

b:29.7
occ:1.00
O A:HOH838 2.3 36.0 1.0
O A:HOH982 2.4 33.1 1.0
O A:VAL246 2.4 19.3 1.0
O A:ILE243 2.4 16.4 1.0
O A:THR241 2.6 23.4 1.0
O P:HOH114 2.8 55.1 1.0
OP1 P:DT3 3.3 22.8 1.0
C A:ILE243 3.4 17.4 1.0
C A:VAL246 3.5 17.6 1.0
C A:THR241 3.6 21.9 1.0
O P:HOH112 3.7 35.9 1.0
N A:VAL246 3.8 15.2 1.0
N A:ILE243 4.1 20.8 1.0
CA A:VAL246 4.1 16.5 1.0
N A:PHE244 4.1 17.8 1.0
C A:GLN242 4.2 24.0 1.0
N A:GLY245 4.2 15.4 1.0
CA A:PHE244 4.2 16.2 1.0
P P:DT3 4.3 21.6 1.0
OP2 P:DT3 4.3 21.2 1.0
CA A:ILE243 4.4 17.6 1.0
CA A:THR241 4.4 18.8 1.0
CA A:GLN242 4.4 25.6 1.0
N A:GLN242 4.4 23.1 1.0
O A:HOH1016 4.4 38.7 1.0
CB A:VAL246 4.4 17.6 1.0
O A:GLN242 4.5 21.0 1.0
C A:PHE244 4.6 16.5 1.0
N A:GLY247 4.6 19.4 1.0
C A:GLY245 4.9 16.9 1.0
O A:PHE240 4.9 17.3 1.0
CA A:GLY247 5.0 18.4 1.0

Reference:

A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Creative Template-Dependent Synthesis By Human Polymerase Mu. Proc.Natl.Acad.Sci.Usa V. 112 E4530 2015.
ISSN: ESSN 1091-6490
PubMed: 26240373
DOI: 10.1073/PNAS.1505798112
Page generated: Mon Oct 7 19:29:05 2024

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