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Sodium in PDB 4lzg: Binary Complex of Human Dna Polymerase Mu with Dna

Enzymatic activity of Binary Complex of Human Dna Polymerase Mu with Dna

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

Protein crystallography data

The structure of Binary Complex of Human Dna Polymerase Mu with Dna, PDB code: 4lzg 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) 34.93 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.003, 68.514, 110.307, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.5

Other elements in 4lzg:

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

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex of Human Dna Polymerase Mu with Dna (pdb code 4lzg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Complex of Human Dna Polymerase Mu with Dna, PDB code: 4lzg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4lzg

Go back to Sodium Binding Sites List in 4lzg
Sodium binding site 1 out of 2 in the Binary Complex of Human Dna Polymerase Mu with Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Human Dna Polymerase Mu with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:10.6
occ:1.00
O P:HOH103 2.3 16.2 1.0
O A:VAL246 2.3 9.4 1.0
O A:HOH900 2.3 25.4 1.0
O A:THR241 2.4 12.2 1.0
O A:HOH901 2.5 20.0 1.0
O A:ILE243 2.5 10.6 1.0
OP1 P:DT3 2.8 8.9 1.0
C A:VAL246 3.4 9.8 1.0
C A:THR241 3.4 9.8 1.0
C A:ILE243 3.5 11.9 1.0
O P:HOH120 3.6 27.9 1.0
N A:VAL246 3.8 7.4 1.0
P P:DT3 3.8 8.3 1.0
OP2 P:DT3 3.9 8.0 1.0
CA A:VAL246 4.0 7.5 1.0
N A:ILE243 4.1 9.0 1.0
C A:GLN242 4.1 12.0 1.0
O P:HOH121 4.2 31.1 1.0
CA A:THR241 4.2 11.1 1.0
N A:PHE244 4.3 9.0 1.0
O A:HOH934 4.3 29.2 1.0
N A:GLY245 4.3 7.2 1.0
CA A:PHE244 4.3 9.2 1.0
CB A:VAL246 4.4 6.6 1.0
CA A:ILE243 4.4 10.5 1.0
N A:GLN242 4.4 12.0 1.0
O A:HOH961 4.4 31.6 1.0
N A:GLY247 4.4 7.6 1.0
O P:HOH113 4.5 25.2 1.0
O A:GLN242 4.5 18.5 1.0
CA A:GLN242 4.6 13.3 1.0
C A:PHE244 4.7 10.1 1.0
CA A:GLY247 4.7 7.0 1.0
O A:HOH981 4.7 40.8 1.0
O3' P:DG2 4.8 7.6 1.0
O A:PHE240 4.8 8.8 1.0
CB A:THR241 4.8 9.9 1.0
C A:GLY245 4.9 6.9 1.0

Sodium binding site 2 out of 2 in 4lzg

Go back to Sodium Binding Sites List in 4lzg
Sodium binding site 2 out of 2 in the Binary Complex of Human Dna Polymerase Mu with Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex of Human Dna Polymerase Mu with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:17.4
occ:1.00
O A:PHE205 2.3 23.9 1.0
O A:HOH778 2.3 28.6 1.0
O D:HOH106 2.4 24.5 1.0
O D:HOH104 2.4 23.4 1.0
O A:HOH852 2.6 38.2 1.0
O A:HOH1016 3.4 36.6 1.0
C A:PHE205 3.5 15.2 1.0
O A:LEU202 4.2 15.3 1.0
N A:GLY206 4.3 9.8 1.0
CA A:GLY206 4.3 12.6 1.0
CA A:PHE205 4.5 10.2 1.0
O A:HOH876 4.5 25.9 1.0
CB A:PHE205 4.6 10.4 1.0
N A:PHE205 4.7 11.5 1.0
OP1 D:DC3 4.8 10.3 1.0
OP2 D:DC3 4.8 14.5 1.0
O A:HOH992 5.0 43.9 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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