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Calcium in PDB 7m8b: Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S

Enzymatic activity of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S

All present enzymatic activity of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S, PDB code: 7m8b 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) 31.46 / 1.85
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.707, 98.707, 81.679, 90, 90, 120
R / Rfree (%) 16.2 / 21

Other elements in 7m8b:

The structure of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 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 Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S (pdb code 7m8b). 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 Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S, PDB code: 7m8b:

Calcium binding site 1 out of 1 in 7m8b

Go back to Calcium Binding Sites List in 7m8b
Calcium binding site 1 out of 1 in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 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 Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:20.5
occ:0.15
 MG A:MG503 0.0 20.5 0.7
O5 A:DPO508 2.1 20.7 0.5
OD1 A:ASP13 2.1 21.8 0.7
OD2 A:ASP115 2.2 15.8 0.5
O1B A:DTP507 2.2 16.8 0.3
O1 A:DPO508 2.2 16.7 0.5
O3G A:DTP507 2.3 20.3 0.3
O A:MET14 2.3 17.6 1.0
OD2 A:ASP13 2.3 21.4 0.3
OP1 P:DA9 2.5 25.1 0.6
O2A A:DTP507 2.5 24.9 0.3
OD2 A:ASP115 2.6 28.5 0.5
CG A:ASP13 3.0 22.3 0.3
OD1 A:ASP13 3.1 23.9 0.3
PB A:DTP507 3.2 20.5 0.3
CG A:ASP13 3.3 23.5 0.7
CG A:ASP115 3.3 21.3 0.5
P1 A:DPO508 3.3 20.2 0.5
P2 A:DPO508 3.3 23.2 0.5
PG A:DTP507 3.4 24.1 0.3
C A:MET14 3.5 13.8 1.0
O4 A:DPO508 3.6 22.4 0.5
O3B A:DTP507 3.6 20.6 0.3
PA A:DTP507 3.6 22.0 0.3
CG A:ASP115 3.6 23.4 0.5
O3A A:DTP507 3.6 21.0 0.3
MG A:MG501 3.7 20.8 0.3
OD1 A:ASP115 3.8 23.1 0.5
OD2 A:ASP13 3.8 36.2 0.7
O2 A:DPO508 3.9 24.1 0.5
P P:DA9 3.9 19.8 0.6
O A:HOH633 3.9 22.9 1.0
O2G A:DTP507 3.9 17.2 0.3
O6 A:DPO508 4.0 19.2 0.5
N A:MET14 4.0 13.0 1.0
O A:HOH774 4.0 22.3 0.4
C5' A:DTP507 4.0 19.2 0.3
CB A:ASP115 4.2 17.2 0.5
C5' P:DA9 4.2 19.0 0.6
O A:HOH812 4.2 38.3 1.0
C A:ASP13 4.3 13.6 0.3
C A:ASP13 4.3 13.5 0.7
CA A:MET14 4.3 13.3 1.0
O5' A:DTP507 4.3 21.2 0.3
CB A:ASP13 4.3 17.5 0.3
N A:CYS16 4.4 15.1 1.0
O5' P:DA9 4.4 21.4 0.6
CB A:ASP13 4.4 16.6 0.7
N A:ASP15 4.5 13.3 1.0
CB A:ASP115 4.5 15.6 0.5
CA A:ASP15 4.5 13.5 1.0
O2B A:DTP507 4.5 16.7 0.3
O3 A:DPO508 4.6 17.8 0.5
OD1 A:ASP115 4.6 17.3 0.5
O7 A:DPO508 4.6 23.1 0.5
C A:ASP15 4.7 18.2 1.0
O1G A:DTP507 4.7 22.9 0.3
N A:PHE17 4.7 11.0 1.0
O3' P:A8 4.7 27.6 0.6
NZ A:LYS231 4.7 38.9 1.0
CA A:ASP13 4.7 14.6 0.7
O A:ASP13 4.8 13.8 0.7
O A:ASP13 4.8 13.8 0.3
CA A:ASP13 4.8 14.6 0.3
O3' P:A8 4.8 26.2 0.5
CB A:MET14 4.8 17.4 1.0
O1A A:DTP507 4.8 23.7 0.3
O A:ASP115 4.9 18.3 1.0
CB A:PHE17 4.9 9.8 1.0
OP2 P:DA9 5.0 23.9 0.6

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 01:58:29 2024

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