Atomistry » Magnesium » PDB 4j9k-4jj2 » 4j9m
Atomistry »
  Magnesium »
    PDB 4j9k-4jj2 »
      4j9m »

Magnesium in PDB 4j9m: Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G)

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G)

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G):
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G), PDB code: 4j9m was solved by Y.Zhao, M.Gregory, C.Biertumpfel, Y.Hua, F.Hanaoka, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.25
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.430, 98.430, 82.010, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 22.3

Other elements in 4j9m:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G) (pdb code 4j9m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G), PDB code: 4j9m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4j9m

Go back to Magnesium Binding Sites List in 4j9m
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:10.9
occ:1.00
 O A:MET14 2.1 8.7 1.0
O1B A:XG4504 2.1 7.9 1.0
OD2 A:ASP115 2.1 9.4 1.0
O1G A:XG4504 2.1 9.0 1.0
OD1 A:ASP13 2.2 11.7 1.0
O1A A:XG4504 2.2 10.1 1.0
CG A:ASP115 3.1 10.7 1.0
CG A:ASP13 3.2 11.9 1.0
C A:MET14 3.2 11.4 1.0
PB A:XG4504 3.3 9.9 1.0
PG A:XG4504 3.3 11.5 1.0
MG A:MG502 3.5 14.8 1.0
O3B A:XG4504 3.5 12.8 1.0
OD1 A:ASP115 3.5 12.1 1.0
PA A:XG4504 3.6 15.3 1.0
OD2 A:ASP13 3.6 13.5 1.0
N3A A:XG4504 3.8 12.1 1.0
NZ A:LYS231 3.8 8.5 1.0
N A:MET14 3.8 14.6 1.0
O2G A:XG4504 3.9 9.9 1.0
O A:HOH607 3.9 14.9 1.0
CA A:MET14 4.0 9.9 1.0
C5' A:XG4504 4.0 8.7 1.0
O5' A:XG4504 4.2 11.6 1.0
C A:ASP13 4.3 12.9 1.0
N A:ASP15 4.3 8.0 1.0
N A:CYS16 4.4 11.4 1.0
CB A:ASP115 4.4 7.1 1.0
CB A:MET14 4.5 12.1 1.0
CB A:ASP13 4.5 16.1 1.0
CA A:ASP15 4.5 13.7 1.0
N A:PHE17 4.5 7.7 1.0
O3G A:XG4504 4.6 13.3 1.0
O2B A:XG4504 4.6 10.4 1.0
O A:HOH710 4.6 9.4 0.8
C A:ASP15 4.6 11.7 1.0
CB A:PHE17 4.6 10.1 1.0
O A:ASP13 4.7 12.4 1.0
CE A:LYS231 4.7 15.8 1.0
O2A A:XG4504 4.7 17.3 1.0
CA A:ASP13 4.8 10.6 1.0
O A:ASP115 5.0 14.3 1.0

Magnesium binding site 2 out of 2 in 4j9m

Go back to Magnesium Binding Sites List in 4j9m
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After An A at the Primer 3' End (Aa/G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:14.8
occ:1.00
 OD1 A:ASP115 2.0 12.1 1.0
OD2 A:ASP13 2.1 13.5 1.0
OE2 A:GLU116 2.2 16.3 1.0
O1A A:XG4504 2.3 10.1 1.0
O A:HOH710 2.3 9.4 0.8
O A:HOH609 2.3 13.2 0.8
O3' P:DA9 2.8 15.2 0.1
CG A:ASP115 3.0 10.7 1.0
CG A:ASP13 3.1 11.9 1.0
CD A:GLU116 3.2 15.2 1.0
C3' P:DA9 3.2 18.1 0.1
OD2 A:ASP115 3.3 9.4 1.0
OD1 A:ASP13 3.3 11.7 1.0
PA A:XG4504 3.4 15.3 1.0
MG A:MG501 3.5 10.9 1.0
O5' A:XG4504 3.5 11.6 1.0
O2A A:XG4504 3.7 17.3 1.0
C5' A:XG4504 3.9 8.7 1.0
OG A:SER113 3.9 15.4 1.0
O A:HOH607 3.9 14.9 1.0
OE1 A:GLU116 3.9 16.6 1.0
CG A:GLU116 4.2 13.9 1.0
CB A:GLU116 4.2 9.4 1.0
C4' P:DA9 4.2 19.2 0.1
CB A:ASP115 4.4 7.1 1.0
O1G A:XG4504 4.4 9.0 1.0
CB A:ASP13 4.5 16.1 1.0
C2' P:DA9 4.5 19.1 0.1
NZ A:LYS224 4.5 17.0 1.0
O A:HOH718 4.6 21.9 0.8
C5' P:DA9 4.6 21.1 0.1
C A:ASP115 4.6 12.0 1.0
O1B A:XG4504 4.7 7.9 1.0
O A:ASP115 4.8 14.3 1.0
N A:GLU116 4.8 12.1 1.0
N3A A:XG4504 4.8 12.1 1.0
O A:HOH711 4.9 17.8 1.0
CA A:ASP115 4.9 11.2 1.0
O5' P:DA9 5.0 22.4 0.1

Reference:

Y.Zhao, M.T.Gregory, C.Biertumpfel, Y.J.Hua, F.Hanaoka, W.Yang. Mechanism of Somatic Hypermutation at the Wa Motif By Human Dna Polymerase Eta. Proc.Natl.Acad.Sci.Usa V. 110 8146 2013.
ISSN: ISSN 0027-8424
PubMed: 23630267
DOI: 10.1073/PNAS.1303126110
Page generated: Mon Dec 14 18:56:07 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