Atomistry » Calcium » PDB 7m43-7mg7 » 7m88
Atomistry »
  Calcium »
    PDB 7m43-7mg7 »
      7m88 »

Calcium in PDB 7m88: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S

Enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S

All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 300 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 300 S, PDB code: 7m88 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) 29.96 / 1.66
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.323, 98.323, 81.937, 90, 90, 120
R / Rfree (%) 17.3 / 20.9

Other elements in 7m88:

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S also contains other interesting chemical elements:

Magnesium (Mg) 3 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 300 S (pdb code 7m88). 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 300 S, PDB code: 7m88:

Calcium binding site 1 out of 1 in 7m88

Go back to Calcium Binding Sites List in 7m88
Calcium binding site 1 out of 1 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 300 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 300 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:11.0
occ:0.40
 MG A:MG503 0.0 11.0 0.6
OD1 A:ASP13 2.2 22.8 1.0
OP1 P:DA9 2.2 17.7 0.3
O3G A:DTP504 2.2 13.9 0.7
O5 A:DPO505 2.3 14.0 0.3
O1B A:DTP504 2.3 12.2 0.7
OD2 A:ASP115 2.3 16.7 1.0
O A:MET14 2.3 14.0 1.0
O1 A:DPO505 2.3 12.7 0.3
O2A A:DTP504 2.3 16.8 0.7
CG A:ASP13 3.0 18.3 1.0
PB A:DTP504 3.3 13.1 0.7
OD2 A:ASP13 3.3 38.2 1.0
P1 A:DPO505 3.4 13.1 0.3
CG A:ASP115 3.4 16.8 1.0
PA A:DTP504 3.4 17.1 0.7
P2 A:DPO505 3.5 14.6 0.3
PG A:DTP504 3.5 14.9 0.7
C A:MET14 3.5 11.4 1.0
MG A:MG501 3.5 14.8 0.6
O3A A:DTP504 3.5 14.1 0.7
P P:DA9 3.6 11.3 0.3
O3B A:DTP504 3.7 13.6 0.7
O4 A:DPO505 3.7 13.7 0.3
O3 A:DPO505 3.8 12.1 0.3
OD1 A:ASP115 3.8 17.1 1.0
O A:HOH734 3.9 32.1 1.0
NZ A:LYS231 4.0 15.9 1.0
N A:MET14 4.0 13.4 1.0
C5' A:DTP504 4.1 13.3 0.7
O2G A:DTP504 4.1 13.8 0.7
O7 A:DPO505 4.1 14.1 0.3
C5' P:DA9 4.2 13.2 0.3
O A:HOH821 4.2 27.7 1.0
O5' P:DA9 4.2 14.6 0.3
O5' A:DTP504 4.2 14.6 0.7
CA A:MET14 4.3 13.9 1.0
C A:ASP13 4.3 12.4 1.0
CB A:ASP13 4.4 13.3 1.0
N A:ASP15 4.5 10.9 1.0
OP2 P:DA9 4.5 17.1 0.3
N A:CYS16 4.6 10.1 1.0
CE A:LYS231 4.6 27.4 1.0
O3' P:DA8 4.6 10.3 0.3
O1A A:DTP504 4.6 17.3 0.7
O6 A:DPO505 4.6 14.5 0.3
O2B A:DTP504 4.6 13.7 0.7
CA A:ASP15 4.7 13.1 1.0
O1G A:DTP504 4.7 14.4 0.7
O3' P:DA8 4.7 11.9 0.2
CB A:ASP115 4.7 13.2 1.0
O2 A:DPO505 4.7 13.8 0.3
O A:ASP13 4.7 12.4 1.0
CA A:ASP13 4.8 14.2 1.0
N A:PHE17 4.8 11.1 1.0
CB A:MET14 4.8 15.4 1.0
C A:ASP15 4.8 13.5 1.0
CB A:PHE17 4.9 9.4 1.0
MG P:MG101 5.0 18.5 0.3

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 23:26:41 2025

Last articles

Mg in 5SK5
Mg in 5SK8
Mg in 5SK4
Mg in 5SK3
Mg in 5SK2
Mg in 5SK1
Mg in 5SK0
Mg in 5SJZ
Mg in 5SJX
Mg in 5SJY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy