Sodium in PDB 1zjm: Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus:
2.7.7.7;

The structure of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus, PDB code: 1zjm was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.33 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.100, 79.100, 54.900, 90.00, 105.90, 90.00
R / Rfree (%)	22.8 / 23.4

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus (pdb code 1zjm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus, PDB code: 1zjm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus


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 Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ P:Na903 b:42.0 occ:1.00 O P:HOH914 2.4 38.5 1.0 O4' P:DG4 2.4 35.0 1.0 O T:HOH32 2.4 43.9 1.0 O P:HOH932 2.4 50.5 1.0 O2 P:DT3 2.4 30.6 1.0 C4' P:DG4 3.1 35.8 1.0 C1' P:DG4 3.2 33.4 1.0 C2 P:DT3 3.6 31.6 1.0 N9 P:DG4 3.7 31.9 1.0 C5' P:DG4 3.8 37.7 1.0 C1' P:DT3 4.0 37.4 1.0 C4 P:DG4 4.1 31.1 1.0 N3 P:DG4 4.2 31.3 1.0 N1 P:DT3 4.3 33.7 1.0 C3' P:DG4 4.4 36.8 1.0 O T:HOH29 4.5 36.5 1.0 N2 T:DG15 4.5 27.6 1.0 C2' P:DG4 4.5 35.2 1.0 C2 T:DA14 4.5 29.8 1.0 C8 P:DG4 4.5 30.9 1.0 N3 P:DT3 4.7 31.4 1.0 O4' P:DT3 4.7 39.7 1.0 O3' P:DG4 4.8 36.2 1.0 O5' P:DG4 4.8 39.7 1.0 N3 T:DG15 4.9 30.4 1.0 C2' P:DT3 4.9 38.8 1.0 C2 T:DG15 5.0 29.3 1.0

Sodium binding site 2 out of 3 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:21.6 occ:1.00 O A:THR101 2.2 22.4 1.0 O A:ILE106 2.4 18.7 1.0 OP1 P:DG9 2.4 17.9 1.0 O P:HOH904 2.4 21.4 1.0 O A:VAL103 2.5 19.4 1.0 O P:HOH921 2.9 26.7 1.0 C A:THR101 3.2 21.9 1.0 C A:ILE106 3.3 19.1 1.0 C A:VAL103 3.4 20.8 1.0 O A:HOH903 3.5 25.8 1.0 P P:DG9 3.5 21.1 1.0 N A:ILE106 3.7 18.4 1.0 CA A:THR101 3.8 21.5 1.0 OP2 P:DG9 3.8 20.3 1.0 CA A:SER104 3.9 18.7 1.0 N A:SER104 4.0 18.9 1.0 N A:VAL103 4.0 20.5 1.0 CA A:ILE106 4.0 18.8 1.0 N A:GLY105 4.0 17.1 1.0 C A:ARG102 4.2 21.4 1.0 N A:ARG102 4.3 21.9 1.0 N A:GLY107 4.3 17.9 1.0 CB A:THR101 4.3 23.3 1.0 C A:SER104 4.3 18.1 1.0 CA A:VAL103 4.3 20.2 1.0 CB A:ILE106 4.4 20.8 1.0 CA A:GLY107 4.5 20.1 1.0 O3' P:DC8 4.5 20.6 1.0 CA A:ARG102 4.6 20.9 1.0 O5' P:DG9 4.6 21.1 1.0 C A:GLY105 4.7 18.2 1.0 O A:LEU100 4.7 23.6 1.0 O A:ARG102 4.7 21.7 1.0 CA A:GLY105 5.0 17.8 1.0

Sodium binding site 3 out of 3 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:32.4 occ:1.00 O D:HOH181 2.3 36.2 1.0 O A:VAL65 2.4 27.6 1.0 O A:LYS60 2.4 35.3 1.0 O A:LEU62 2.5 32.6 1.0 OP1 D:DC3 2.6 28.9 1.0 O A:HOH980 2.7 28.3 1.0 C A:VAL65 3.5 24.5 1.0 C A:LYS60 3.5 35.0 1.0 C A:LEU62 3.6 33.9 1.0 P D:DC3 3.7 26.9 1.0 N A:VAL65 3.8 24.1 1.0 OP2 D:DC3 3.9 26.2 1.0 CA A:VAL65 4.1 24.6 1.0 N A:GLY64 4.2 30.7 1.0 CG A:LYS60 4.2 37.2 1.0 CA A:PRO63 4.2 33.5 1.0 N A:LEU62 4.2 34.9 1.0 CA A:LYS60 4.2 32.8 1.0 N A:PRO63 4.3 33.8 1.0 C A:LYS61 4.3 36.2 1.0 CB A:VAL65 4.4 25.5 1.0 N A:LYS61 4.5 35.9 1.0 O3' D:DT2 4.5 26.5 1.0 CA A:LEU62 4.5 34.0 1.0 N A:GLY66 4.5 23.6 1.0 C A:PRO63 4.6 31.7 1.0 O A:LYS61 4.7 38.1 1.0 CA A:LYS61 4.7 36.2 1.0 CA A:GLY66 4.8 22.8 1.0 CB A:LYS60 4.9 34.2 1.0 C A:GLY64 4.9 28.1 1.0 O5' D:DC3 4.9 25.8 1.0 O A:ALA59 5.0 28.2 1.0

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Nucleotide-Induced Dna Polymerase Active Site Motions Accommodating A Mutagenic Dna Intermediate. Structure V. 13 1225 2005.
ISSN: ISSN 0969-2126
PubMed: 16084394
DOI: 10.1016/J.STR.2005.05.010