Sodium in PDB 9icy: Dna Polymerase Beta (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only)

Protein crystallography data

The structure of Dna Polymerase Beta (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only), PDB code: 9icy 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 (°) 180.827, 57.645, 48.167, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only) (pdb code 9icy). 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) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only), PDB code: 9icy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9icy

Go back to Sodium Binding Sites List in 9icy
Sodium binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only)


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) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:1.0
occ:1.00
O A:THR101 2.3 20.0 1.0
O A:HOH601 2.3 77.9 1.0
OP1 P:DT6 2.3 19.4 1.0
O A:ILE106 2.6 1.0 1.0
O A:VAL103 2.6 6.5 1.0
C A:THR101 3.3 18.3 1.0
C A:VAL103 3.5 8.4 1.0
P P:DT6 3.5 15.9 1.0
C A:ILE106 3.7 1.0 1.0
N A:ILE106 3.8 4.3 1.0
C A:ARG102 3.9 25.1 1.0
OP2 P:DT6 3.9 9.1 1.0
N A:VAL103 4.0 18.0 1.0
O A:ARG102 4.1 24.7 1.0
N A:GLY105 4.1 8.6 1.0
N A:ARG102 4.2 18.8 1.0
N A:SER104 4.2 10.6 1.0
CA A:SER104 4.2 14.9 1.0
CA A:ARG102 4.2 26.1 1.0
CA A:ILE106 4.2 6.5 1.0
CA A:THR101 4.3 13.4 1.0
CA A:VAL103 4.4 15.6 1.0
CB A:ILE106 4.4 15.2 1.0
O5' P:DT6 4.6 12.8 1.0
O3' P:DA5 4.6 20.6 1.0
C A:SER104 4.6 11.9 1.0
N A:GLY107 4.7 1.0 1.0
CG2 A:THR101 4.8 7.7 1.0
C A:GLY105 4.8 6.7 1.0

Sodium binding site 2 out of 2 in 9icy

Go back to Sodium Binding Sites List in 9icy
Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only)


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) Complexed with Seven Base Pairs of Dna (Non Gapped Dna Only) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:60.5
occ:1.00
OP1 P:DT3 4.1 40.5 1.0
OP2 P:DT3 4.3 28.9 1.0
O P:HOH615 4.3 65.7 1.0
P P:DT3 4.7 37.6 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. Crystal Structures of Human Dna Polymerase Beta Complexed with Dna: Implications For Catalytic Mechanism, Processivity, and Fidelity Biochemistry V. 35 12742 1996.
ISSN: ISSN 0006-2960
PubMed: 8841118
DOI: 10.1021/BI952955D
Page generated: Wed Dec 16 01:11:09 2020

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