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: Fri Jul 19 01:58:09 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy