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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: Fri Aug 16 17:19:02 2024

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