Atomistry » Sodium » PDB 1z2u-1zud » 1zqr
Atomistry »
  Sodium »
    PDB 1z2u-1zud »
      1zqr »

Sodium in PDB 1zqr: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2

Protein crystallography data

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2, PDB code: 1zqr 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 / 3.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.686, 57.501, 47.920, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / n/a

Other elements in 1zqr:

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 (pdb code 1zqr). 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 Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2, PDB code: 1zqr:

Sodium binding site 1 out of 1 in 1zqr

Go back to Sodium Binding Sites List in 1zqr
Sodium binding site 1 out of 1 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2


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, Soaked in the Presence of NICL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:60.8
occ:1.00
O A:THR101 1.5 9.2 1.0
O P:HOH588 2.4 0.0 1.0
O A:ILE106 2.4 8.8 1.0
C A:THR101 2.6 15.2 1.0
OP1 P:DT6 3.0 23.3 1.0
N A:ARG102 3.5 22.1 1.0
O A:VAL103 3.5 1.0 1.0
C A:ILE106 3.5 15.0 1.0
CA A:THR101 3.6 20.5 1.0
CA A:ARG102 3.8 39.4 1.0
N A:VAL103 3.8 46.1 1.0
C A:ARG102 3.8 52.9 1.0
C A:VAL103 3.9 5.5 1.0
P P:DT6 3.9 17.9 1.0
OP2 P:DT6 3.9 32.1 1.0
CG2 A:THR101 4.0 33.9 1.0
CA A:ILE106 4.2 10.8 1.0
CB A:THR101 4.3 28.9 1.0
N A:ILE106 4.3 11.6 1.0
CB A:ILE106 4.4 2.1 1.0
O A:ARG102 4.4 67.8 1.0
N A:SER104 4.4 1.0 1.0
CA A:VAL103 4.5 25.4 1.0
O A:LEU100 4.6 15.9 1.0
CA A:SER104 4.6 3.5 1.0
N A:GLY107 4.6 19.2 1.0
CG2 A:ILE106 4.7 1.0 1.0
N A:THR101 4.8 19.0 1.0
O5' P:DT6 4.9 6.8 1.0
N A:GLY105 4.9 3.9 1.0
OG1 A:THR101 5.0 23.7 1.0

Reference:

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I
Page generated: Tue Dec 15 05:44:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy