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Calcium in PDB 7m84: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S

Enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S

All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m84 was solved by M.T.Gregory, Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.91 / 1.47
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.104, 98.104, 82.126, 90, 90, 120
R / Rfree (%) 17.2 / 19.9

Other elements in 7m84:

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S (pdb code 7m84). 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 Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m84:

Calcium binding site 1 out of 1 in 7m84

Go back to Calcium Binding Sites List in 7m84
Calcium binding site 1 out of 1 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:7.9
occ:0.60
 MG A:MG502 0.0 8.3 0.4
OD1 A:ASP13 2.2 12.3 0.7
OD2 A:ASP115 2.3 12.4 1.0
O3G A:DTP506 2.3 11.7 1.0
O A:MET14 2.3 10.7 1.0
O1B A:DTP506 2.4 9.3 1.0
O2A A:DTP506 2.4 11.3 1.0
OD2 A:ASP13 2.4 11.3 0.3
OD1 A:ASP13 2.7 16.0 0.3
CG A:ASP13 2.9 13.2 0.3
CG A:ASP13 3.3 14.4 0.7
CG A:ASP115 3.3 11.5 1.0
PB A:DTP506 3.4 9.0 1.0
C A:MET14 3.5 8.6 1.0
PA A:DTP506 3.5 11.1 1.0
PG A:DTP506 3.5 9.9 1.0
MG A:MG507 3.6 13.6 0.6
O3A A:DTP506 3.6 9.8 1.0
OD1 A:ASP115 3.8 12.8 1.0
O3B A:DTP506 3.8 9.3 1.0
OD2 A:ASP13 3.9 21.2 0.7
NZ A:LYS231 4.0 14.7 1.0
N A:MET14 4.0 9.4 1.0
O A:HOH616 4.0 27.3 1.0
C5' A:DTP506 4.0 9.6 1.0
O2G A:DTP506 4.2 11.8 1.0
CA A:MET14 4.2 8.8 1.0
C A:ASP13 4.3 10.5 1.0
O5' A:DTP506 4.3 10.8 1.0
CB A:ASP13 4.3 12.3 0.3
O A:HOH862 4.4 34.9 1.0
N A:ASP15 4.5 8.3 1.0
CB A:ASP13 4.5 11.6 0.7
N A:CYS16 4.6 8.6 1.0
CB A:ASP115 4.6 10.2 1.0
CE A:LYS231 4.7 21.2 1.0
CA A:ASP15 4.7 8.6 1.0
O A:ASP13 4.7 11.9 1.0
O3' P:DA8 4.7 13.9 0.3
CB A:MET14 4.7 11.3 1.0
CA A:ASP13 4.7 11.8 0.7
O2B A:DTP506 4.7 10.2 1.0
O1A A:DTP506 4.7 12.8 1.0
CA A:ASP13 4.7 11.9 0.3
O1G A:DTP506 4.8 12.1 1.0
N A:PHE17 4.8 8.4 1.0
C A:ASP15 4.8 9.2 1.0
CB A:PHE17 4.9 7.5 1.0
O A:ASP115 4.9 11.9 1.0

Reference:

M.T.Gregory, Y.Gao, Q.Cui, W.Yang. Multiple Deprotonation Paths of the Nucleophile 3'-Oh in the Dna Synthesis Reaction Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490
Page generated: Wed Jul 9 23:26:11 2025

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