Sodium in PDB 9icn: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2

Protein crystallography data

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2, PDB code: 9icn was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.896, 57.689, 48.427, 90.00, 90.00, 90.00
R / Rfree (%) 15 / n/a

Other elements in 9icn:

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 (pdb code 9icn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2, PDB code: 9icn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9icn

Go back to Sodium Binding Sites List in 9icn
Sodium binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2


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 (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:21.1
occ:1.00
O A:THR101 2.3 27.6 1.0
O A:ILE106 2.4 1.8 1.0
OP1 P:DG6 2.4 25.2 1.0
O A:VAL103 2.6 16.4 1.0
O A:HOH601 3.2 74.9 1.0
C A:THR101 3.4 18.1 1.0
P P:DG6 3.4 22.1 1.0
C A:VAL103 3.4 15.8 1.0
C A:ILE106 3.5 1.0 1.0
OP2 P:DG6 3.5 24.1 1.0
N A:ILE106 3.8 10.8 1.0
N A:GLY105 3.9 10.8 1.0
CA A:SER104 4.0 14.2 1.0
N A:VAL103 4.1 24.6 1.0
N A:SER104 4.1 9.5 1.0
CA A:THR101 4.1 9.3 1.0
C A:ARG102 4.1 26.9 1.0
CA A:ILE106 4.1 3.2 1.0
C A:SER104 4.3 19.9 1.0
CA A:VAL103 4.4 20.7 1.0
N A:ARG102 4.4 13.7 1.0
O A:ARG102 4.4 28.6 1.0
CB A:ILE106 4.5 4.2 1.0
CG2 A:THR101 4.5 15.5 1.0
O3' P:DT5 4.5 21.1 1.0
CA A:ARG102 4.5 20.6 1.0
N A:GLY107 4.5 4.6 1.0
O5' P:DG6 4.6 20.8 1.0
C A:GLY105 4.7 15.8 1.0
CB A:THR101 4.8 13.6 1.0
CA A:GLY107 4.8 3.6 1.0
CA A:GLY105 4.9 10.4 1.0
O A:LEU100 4.9 12.6 1.0

Sodium binding site 2 out of 2 in 9icn

Go back to Sodium Binding Sites List in 9icn
Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:37.6
occ:1.00
OP2 P:DG3 3.4 59.3 1.0
OP1 P:DG3 4.1 52.2 1.0
P P:DG3 4.3 56.0 1.0
O P:HOH615 4.9 98.2 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566
Page generated: Tue Dec 15 18:42:08 2020

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