Atomistry » Calcium » PDB 7m43-7mg7 » 7m7z
Atomistry »
  Calcium »
    PDB 7m43-7mg7 »
      7m7z »

Calcium in PDB 7m7z: Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S

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

All present enzymatic activity of Human Dna Pol Eta 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m7z 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) 30.08 / 1.82
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.779, 98.779, 82.064, 90, 90, 120
R / Rfree (%) 18 / 22.8

Other elements in 7m7z:

The structure of Human Dna Pol Eta 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S (pdb code 7m7z). 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m7z:

Calcium binding site 1 out of 1 in 7m7z

Go back to Calcium Binding Sites List in 7m7z
Calcium binding site 1 out of 1 in the Human Dna Pol Eta 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:10.1
occ:0.50
 MG A:MG503 0.1 10.2 0.5
OP1 P:DA9 2.1 16.0 0.2
OD1 A:ASP13 2.2 14.7 0.5
O A:MET14 2.3 10.3 1.0
O3G A:DTP506 2.3 10.3 0.8
O5 A:DPO507 2.3 11.1 0.2
OD2 A:ASP115 2.3 15.1 1.0
O1B A:DTP506 2.3 10.0 0.8
O1 A:DPO507 2.3 10.9 0.2
O2A A:DTP506 2.4 16.8 0.8
OD2 A:ASP13 2.4 15.5 0.5
OD1 A:ASP13 2.8 17.9 0.5
CG A:ASP13 2.9 15.2 0.5
MG A:MG501 3.2 18.3 0.5
PB A:DTP506 3.3 11.9 0.8
CG A:ASP13 3.3 15.3 0.5
CG A:ASP115 3.4 15.6 1.0
C A:MET14 3.5 7.6 1.0
P1 A:DPO507 3.5 11.7 0.2
PA A:DTP506 3.5 14.4 0.8
PG A:DTP506 3.5 14.7 0.8
P2 A:DPO507 3.5 14.2 0.2
O3A A:DTP506 3.5 13.7 0.8
P P:DA9 3.6 19.5 0.2
OD1 A:ASP115 3.7 13.7 1.0
O3B A:DTP506 3.7 12.7 0.8
O4 A:DPO507 3.8 12.8 0.2
O2 A:DPO507 3.9 13.3 0.2
OD2 A:ASP13 4.0 21.8 0.5
N A:MET14 4.0 8.3 1.0
O A:HOH773 4.1 29.3 1.0
C5' P:DA9 4.1 12.9 0.2
C5' A:DTP506 4.1 12.6 0.8
O5' P:DA9 4.1 14.9 0.2
O7 A:DPO507 4.1 12.9 0.2
O A:HOH647 4.1 22.9 1.0
O2G A:DTP506 4.2 11.4 0.8
NZ A:LYS231 4.2 14.7 1.0
CA A:MET14 4.3 10.2 1.0
O5' A:DTP506 4.3 15.1 0.8
C A:ASP13 4.3 7.7 1.0
CB A:ASP13 4.3 14.1 0.5
CB A:ASP13 4.4 13.9 0.5
N A:ASP15 4.5 5.7 1.0
O3' P:DA8 4.5 17.6 0.2
N A:CYS16 4.6 8.4 1.0
OP2 P:DA9 4.6 15.6 0.2
CB A:ASP115 4.6 10.3 1.0
O2B A:DTP506 4.6 9.6 0.8
CA A:ASP15 4.6 10.2 1.0
O1A A:DTP506 4.6 15.3 0.8
O1G A:DTP506 4.7 12.6 0.8
O6 A:DPO507 4.7 13.2 0.2
O A:ASP13 4.7 9.1 1.0
CA A:ASP13 4.7 12.0 0.5
O3 A:DPO507 4.7 10.1 0.2
CA A:ASP13 4.8 12.1 0.5
CB A:MET14 4.8 13.4 1.0
C A:ASP15 4.8 11.2 1.0
N A:PHE17 4.8 8.6 1.0
CE A:LYS231 4.9 25.1 1.0
CB A:PHE17 4.9 7.0 1.0
O A:ASP115 4.9 12.1 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: Fri Jul 19 01:57:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy