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

Sodium in PDB 1zqq: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar)

Protein crystallography data

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqq 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 / 3.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.065, 57.369, 47.788, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / n/a

Other elements in 1zqq:

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar) (pdb code 1zqq). 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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1zqq

Go back to Sodium Binding Sites List in 1zqq
Sodium binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:4.2
occ:1.00
O A:THR101 2.1 19.9 1.0
OP1 P:DT6 2.2 23.6 1.0
O A:ILE106 2.5 25.6 1.0
O A:VAL103 2.7 6.7 1.0
O A:HOH588 3.1 75.5 1.0
C A:THR101 3.3 16.1 1.0
C A:ILE106 3.5 20.5 1.0
P P:DT6 3.5 17.4 1.0
N A:ILE106 3.6 14.6 1.0
C A:VAL103 3.8 11.2 1.0
CA A:ILE106 3.9 21.0 1.0
OP2 P:DT6 3.9 18.8 1.0
N A:GLY105 4.1 16.4 1.0
CA A:SER104 4.1 12.5 1.0
CA A:THR101 4.1 5.9 1.0
CB A:ILE106 4.2 20.4 1.0
C A:ARG102 4.3 12.9 1.0
N A:ARG102 4.3 23.1 1.0
N A:VAL103 4.4 4.7 1.0
N A:SER104 4.5 16.2 1.0
O3' P:DA5 4.5 14.6 1.0
CA A:ARG102 4.5 22.1 1.0
O A:ARG102 4.5 13.9 1.0
O5' P:DT6 4.6 13.8 1.0
N A:GLY107 4.6 11.7 1.0
C A:SER104 4.6 12.1 1.0
C A:GLY105 4.7 9.0 1.0
CA A:VAL103 4.8 5.8 1.0
CB A:THR101 4.9 3.1 1.0
CG2 A:THR101 4.9 11.1 1.0
CA A:GLY105 5.0 10.2 1.0

Sodium binding site 2 out of 2 in 1zqq

Go back to Sodium Binding Sites List in 1zqq
Sodium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and Nacl (15 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:23.4
occ:1.00
O A:LEU62 2.3 23.8 1.0
O A:VAL65 3.0 12.9 1.0
C A:LEU62 3.2 24.1 1.0
O A:LYS60 3.2 29.1 1.0
N A:PRO63 3.9 21.7 1.0
C A:VAL65 4.0 10.1 1.0
N A:VAL65 4.0 16.0 1.0
O A:LYS61 4.0 35.4 1.0
CA A:PRO63 4.1 22.4 1.0
C A:LYS61 4.2 36.4 1.0
N A:GLY64 4.2 29.6 1.0
CA A:LEU62 4.3 23.4 1.0
N A:LEU62 4.3 30.8 1.0
C A:LYS60 4.3 29.7 1.0
CA A:VAL65 4.4 11.6 1.0
CB A:VAL65 4.5 12.2 1.0
C A:PRO63 4.5 28.3 1.0
CD A:PRO63 4.9 23.3 1.0
CA A:LYS61 5.0 43.4 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 05:44:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy