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Sodium in PDB 4m04: Human Dna Polymerase Mu Ternary Complex

Enzymatic activity of Human Dna Polymerase Mu Ternary Complex

All present enzymatic activity of Human Dna Polymerase Mu Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Mu Ternary Complex, PDB code: 4m04 was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.17 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.892, 68.467, 109.773, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.6

Other elements in 4m04:

The structure of Human Dna Polymerase Mu Ternary Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Mu Ternary Complex (pdb code 4m04). 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 Human Dna Polymerase Mu Ternary Complex, PDB code: 4m04:

Sodium binding site 1 out of 1 in 4m04

Go back to Sodium Binding Sites List in 4m04
Sodium binding site 1 out of 1 in the Human Dna Polymerase Mu Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Mu Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:12.7
occ:1.00
O A:VAL246 2.3 11.4 1.0
O A:THR241 2.3 14.7 1.0
O P:HOH105 2.4 19.8 1.0
O A:ILE243 2.4 8.9 1.0
O A:HOH986 2.6 17.7 1.0
OP1 P:DT3 2.7 10.5 1.0
C A:THR241 3.4 15.2 1.0
C A:VAL246 3.4 13.1 1.0
C A:ILE243 3.4 12.7 1.0
O P:HOH112 3.5 23.8 1.0
N A:VAL246 3.7 13.3 1.0
P P:DT3 3.7 10.8 1.0
OP2 P:DT3 3.9 9.0 1.0
CA A:VAL246 4.0 12.9 1.0
N A:ILE243 4.0 13.1 1.0
O A:HOH1055 4.1 30.6 1.0
C A:GLN242 4.1 16.1 1.0
CA A:THR241 4.1 14.3 1.0
N A:PHE244 4.2 9.8 1.0
N A:GLY245 4.2 10.9 1.0
CA A:PHE244 4.2 8.5 1.0
N A:GLN242 4.4 12.7 1.0
CA A:ILE243 4.4 10.0 1.0
CB A:VAL246 4.4 9.2 1.0
N A:GLY247 4.5 9.9 1.0
O A:GLN242 4.5 16.1 1.0
O P:HOH106 4.5 23.9 1.0
CA A:GLN242 4.6 12.7 1.0
O P:HOH113 4.6 33.4 1.0
C A:PHE244 4.6 11.4 1.0
O3' P:DG2 4.7 12.0 1.0
O A:PHE240 4.7 9.2 1.0
CA A:GLY247 4.7 11.2 1.0
C A:GLY245 4.8 11.8 1.0
CB A:THR241 4.9 11.6 1.0
O5' P:DT3 4.9 8.3 1.0

Reference:

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Sustained Active Site Rigidity During Synthesis By Human Dna Polymerase Mu. Nat.Struct.Mol.Biol. V. 21 253 2014.
ISSN: ISSN 1545-9993
PubMed: 24487959
DOI: 10.1038/NSMB.2766
Page generated: Tue Dec 15 06:53:00 2020

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