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Calcium in PDB 4ed8: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation, PDB code: 4ed8 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 / 1.52
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 (%) 17.1 / 20

Other elements in 4ed8:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation (pdb code 4ed8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation, PDB code: 4ed8:

Calcium binding site 1 out of 1 in 4ed8

Go back to Calcium Binding Sites List in 4ed8
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:9.6
occ:0.50
 MG A:MG504 0.0 11.9 0.5
OD1 A:ASP13 2.2 12.2 0.5
OD1 A:ASP115 2.2 14.7 1.0
O3G P:DTP501 2.3 14.3 1.0
O1B P:DTP501 2.3 12.1 1.0
O A:MET14 2.3 13.0 1.0
O2A P:DTP501 2.4 15.1 1.0
OD1 A:ASP13 2.4 19.1 0.5
CG A:ASP13 3.0 15.2 0.5
OD2 A:ASP13 3.0 20.9 0.5
CG A:ASP13 3.3 16.0 0.5
CG A:ASP115 3.3 14.2 1.0
PB P:DTP501 3.3 12.0 1.0
C A:MET14 3.5 11.3 1.0
MG A:MG502 3.5 13.5 0.5
PA P:DTP501 3.5 17.9 1.0
PG P:DTP501 3.5 12.7 1.0
O3A P:DTP501 3.6 13.5 1.0
OD2 A:ASP115 3.6 17.2 1.0
OD2 A:ASP13 3.8 19.7 0.5
O3B P:DTP501 3.8 13.2 1.0
N A:MET14 3.9 9.8 1.0
NZ A:LYS231 4.0 18.6 1.0
O A:HOH601 4.1 29.6 1.0
C5' P:DTP501 4.1 13.3 1.0
O A:HOH726 4.1 32.2 1.0
O2G P:DTP501 4.2 13.2 1.0
CA A:MET14 4.2 10.4 1.0
C A:ASP13 4.2 11.3 1.0
O5' P:DTP501 4.3 13.6 1.0
CB A:ASP13 4.4 12.5 0.5
N A:ASP15 4.5 9.5 1.0
CB A:ASP13 4.5 14.5 0.5
N A:CYS16 4.5 9.9 1.0
CB A:ASP115 4.6 12.5 1.0
O A:ASP13 4.6 14.0 1.0
CA A:ASP15 4.6 11.3 1.0
CA A:ASP13 4.7 13.0 0.5
O2B P:DTP501 4.7 12.2 1.0
CB A:MET14 4.7 15.8 1.0
O1G P:DTP501 4.7 14.2 1.0
CA A:ASP13 4.7 12.9 0.5
C A:ASP15 4.7 9.4 1.0
O1A P:DTP501 4.8 17.7 1.0
N A:PHE17 4.8 9.5 1.0
CE A:LYS231 4.9 33.5 1.0
O A:ASP115 4.9 13.7 1.0
CB A:PHE17 4.9 11.3 1.0
O3' P:DA9 4.9 29.5 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: Tue Jul 8 19:45:35 2025

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