Atomistry » Sodium » PDB 4dy7-4egs » 4ed3
Atomistry »
  Sodium »
    PDB 4dy7-4egs »
      4ed3 »

Sodium in PDB 4ed3: Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion, PDB code: 4ed3 was solved by T.Nakamura, Y.Zhao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.52 / 1.79
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.786, 98.786, 82.431, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 21.6

Other elements in 4ed3:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion (pdb code 4ed3). 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 Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion, PDB code: 4ed3:

Sodium binding site 1 out of 1 in 4ed3

Go back to Sodium Binding Sites List in 4ed3
Sodium binding site 1 out of 1 in the Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion


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 Eta - Dna Ternary Complex: at Crystal at pH 7.5 (Na+ Hepes) with 1 CA2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:21.1
occ:1.00
 OD2 A:ASP115 2.3 13.9 1.0
O2A P:DTP501 2.3 11.5 1.0
O3' P:DT8 2.4 17.4 1.0
OE1 A:GLU116 2.4 26.0 1.0
OD2 A:ASP13 2.4 19.9 1.0
O A:HOH725 3.1 25.4 1.0
CG A:ASP115 3.3 13.8 1.0
C3' P:DT8 3.3 21.4 1.0
CD A:GLU116 3.4 27.5 1.0
CA A:CA503 3.5 12.3 1.0
OD1 A:ASP115 3.5 14.8 1.0
PA P:DTP501 3.5 11.7 1.0
OG A:SER113 3.6 12.6 0.5
CG A:ASP13 3.6 13.7 1.0
O5' P:DTP501 4.0 9.6 1.0
CB A:GLU116 4.0 15.4 1.0
CG A:GLU116 4.0 18.0 1.0
C5' P:DTP501 4.1 9.2 1.0
O1A P:DTP501 4.1 13.6 1.0
C4' P:DT8 4.2 19.0 1.0
OD1 A:ASP13 4.3 19.2 1.0
OE2 A:GLU116 4.3 29.3 1.0
O P:HOH101 4.3 15.2 0.5
C2' P:DT8 4.5 20.2 1.0
NZ A:LYS224 4.5 28.3 1.0
C A:ASP115 4.6 15.4 1.0
O A:HOH676 4.6 25.4 1.0
CB A:ASP115 4.6 11.4 1.0
CB A:ASP13 4.6 14.3 1.0
N A:GLU116 4.7 15.4 1.0
CB A:SER113 4.7 20.3 1.0
C5' P:DT8 4.7 20.0 0.5
O A:ASP115 4.7 15.1 1.0
OG A:SER113 4.7 21.3 0.5
C5' P:DT8 4.8 21.5 0.5
O3A P:DTP501 4.9 14.8 1.0
O3G P:DTP501 4.9 11.4 1.0
CA A:GLU116 5.0 14.8 1.0
CA A:ASP115 5.0 14.6 1.0
O1B P:DTP501 5.0 8.2 1.0

Reference:

T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, W.Yang. Watching Dna Polymerase Eta Make A Phosphodiester Bond Nature V. 487 196 2012.
ISSN: ISSN 0028-0836
PubMed: 22785315
DOI: 10.1038/NATURE11181
Page generated: Mon Oct 7 15:08:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy