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Magnesium in PDB 7m87: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S

Enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S

All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 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 230 S, PDB code: 7m87 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) 29.94 / 1.85
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.262, 98.262, 81.935, 90, 90, 120
R / Rfree (%) 20.1 / 22.8

Other elements in 7m87:

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S (pdb code 7m87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S, PDB code: 7m87:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7m87

Go back to Magnesium Binding Sites List in 7m87
Magnesium binding site 1 out of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.7
occ:0.65
 OD1 A:ASP13 2.0 22.9 0.7
OE2 A:GLU116 2.2 25.4 1.0
OP1 P:DA9 2.2 13.6 0.2
O3' P:DA8 2.2 13.8 0.3
O3' P:DA8 2.3 13.9 0.2
OD1 A:ASP115 2.3 12.4 1.0
O2A A:DTP504 2.5 12.3 0.8
O A:HOH678 2.6 21.6 1.0
P P:DA9 2.7 14.2 0.2
OD1 A:ASP13 2.9 11.6 0.3
O3' P:DA8 3.0 17.7 0.5
OD2 A:ASP13 3.2 14.8 0.3
C3' P:DA8 3.2 15.9 0.5
CG A:ASP115 3.2 14.6 1.0
CG A:ASP13 3.2 13.2 0.7
CD A:GLU116 3.3 26.6 1.0
CG A:ASP13 3.3 13.7 0.3
C3' P:DA8 3.4 17.3 0.3
OD2 A:ASP115 3.4 15.9 1.0
CA A:CA502 3.5 9.9 0.5
C3' P:DA8 3.5 17.3 0.2
MG A:MG503 3.5 9.8 0.5
PA A:DTP504 3.7 15.9 0.8
OP2 P:DA9 3.8 15.4 0.2
OD2 A:ASP13 3.8 14.7 0.7
C4' P:DA8 3.9 20.4 1.0
O5' P:DA9 4.0 13.9 0.2
CB A:GLU116 4.0 18.5 1.0
CG A:GLU116 4.0 25.8 1.0
C5' P:DA8 4.0 18.7 0.5
C5' P:DA8 4.1 18.4 0.3
OE1 A:GLU116 4.2 29.8 1.0
O5' A:DTP504 4.2 13.6 0.8
O1A A:DTP504 4.2 14.2 0.8
C5' A:DTP504 4.2 13.8 0.8
C5' P:DA9 4.2 13.7 0.2
CB A:ASP13 4.4 12.3 0.7
C A:ASP115 4.5 16.0 1.0
O A:ASP115 4.5 12.7 1.0
CB A:ASP13 4.6 12.2 0.3
O A:HOH818 4.6 30.8 1.0
CB A:ASP115 4.6 10.4 1.0
C2' P:DA8 4.6 18.7 0.3
C2' P:DA8 4.6 18.8 0.5
C2' P:DA8 4.6 18.6 0.2
NZ A:LYS224 4.6 20.5 0.6
N A:GLU116 4.6 14.0 1.0
O5' P:DA8 4.8 19.6 0.3
CB A:ALA113 4.9 15.0 1.0
CA A:GLU116 4.9 12.5 1.0
O5 A:DPO505 4.9 11.3 0.2
CA A:ASP115 5.0 14.6 1.0
O3A A:DTP504 5.0 13.0 0.8
O3G A:DTP504 5.0 10.4 0.8

Magnesium binding site 2 out of 3 in 7m87

Go back to Magnesium Binding Sites List in 7m87
Magnesium binding site 2 out of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:9.8
occ:0.50
 CA A:CA502 0.0 9.9 0.5
OD1 A:ASP13 2.2 11.6 0.3
OP1 P:DA9 2.2 13.6 0.2
OD2 A:ASP115 2.2 15.9 1.0
OD2 A:ASP13 2.2 14.7 0.7
O A:MET14 2.3 10.8 1.0
O5 A:DPO505 2.3 11.3 0.2
O1 A:DPO505 2.3 10.9 0.2
O1B A:DTP504 2.3 10.5 0.8
O3G A:DTP504 2.3 10.4 0.8
O2A A:DTP504 2.3 12.3 0.8
CG A:ASP13 2.9 13.2 0.7
OD1 A:ASP13 3.0 22.9 0.7
CG A:ASP13 3.2 13.7 0.3
PB A:DTP504 3.3 12.7 0.8
CG A:ASP115 3.3 14.6 1.0
P1 A:DPO505 3.4 12.8 0.2
PA A:DTP504 3.4 15.9 0.8
C A:MET14 3.4 8.9 1.0
MG A:MG501 3.5 13.7 0.7
O3A A:DTP504 3.5 13.0 0.8
P2 A:DPO505 3.5 13.3 0.2
PG A:DTP504 3.5 13.9 0.8
OD2 A:ASP13 3.6 14.8 0.3
P P:DA9 3.7 14.2 0.2
O3B A:DTP504 3.7 13.4 0.8
O3 A:DPO505 3.7 12.7 0.2
O4 A:DPO505 3.7 13.5 0.2
OD1 A:ASP115 3.7 12.4 1.0
N A:MET14 3.9 12.0 1.0
NZ A:LYS231 4.0 14.3 1.0
C5' A:DTP504 4.0 13.8 0.8
O7 A:DPO505 4.1 12.6 0.2
O2G A:DTP504 4.2 12.4 0.8
O A:HOH818 4.2 30.8 1.0
C5' P:DA9 4.2 13.7 0.2
CA A:MET14 4.2 13.1 1.0
O5' A:DTP504 4.2 13.6 0.8
O A:HOH678 4.2 21.6 1.0
C A:ASP13 4.3 10.8 1.0
O5' P:DA9 4.3 13.9 0.2
CB A:ASP13 4.3 12.3 0.7
CB A:ASP13 4.4 12.2 0.3
N A:ASP15 4.5 10.1 1.0
OP2 P:DA9 4.6 15.4 0.2
N A:CYS16 4.6 11.4 1.0
O2B A:DTP504 4.6 9.5 0.8
O1A A:DTP504 4.6 14.2 0.8
CB A:ASP115 4.6 10.4 1.0
CA A:ASP15 4.6 11.5 1.0
O3' P:DA8 4.7 13.9 0.2
CE A:LYS231 4.7 24.4 1.0
CB A:MET14 4.7 11.5 1.0
O3' P:DA8 4.7 13.8 0.3
O A:ASP13 4.7 13.0 1.0
O2 A:DPO505 4.7 9.8 0.2
CA A:ASP13 4.7 13.0 0.3
O6 A:DPO505 4.7 13.3 0.2
CA A:ASP13 4.7 13.1 0.7
O1G A:DTP504 4.7 13.1 0.8
N A:PHE17 4.8 9.6 1.0
C A:ASP15 4.8 13.3 1.0
MG P:MG101 4.8 15.9 0.2
CB A:PHE17 4.9 8.0 1.0
O A:ASP115 4.9 12.7 1.0

Magnesium binding site 3 out of 3 in 7m87

Go back to Magnesium Binding Sites List in 7m87
Magnesium binding site 3 out of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:15.9
occ:0.25
 O1A A:DTP504 1.8 14.2 0.8
O3 A:DPO505 2.0 12.7 0.2
O A:HOH885 2.1 15.7 0.2
O A:HOH774 2.1 32.3 1.0
O3A A:DTP504 2.1 13.0 0.8
OP2 P:DA9 2.2 15.4 0.2
PA A:DTP504 2.4 15.9 0.8
O A:HOH703 2.8 17.7 1.0
O A:HOH818 2.9 30.8 1.0
NH1 A:ARG61 3.0 25.6 0.8
O2A A:DTP504 3.2 12.3 0.8
P P:DA9 3.2 14.2 0.2
P1 A:DPO505 3.4 12.8 0.2
PB A:DTP504 3.5 12.7 0.8
OP1 P:DA9 3.7 13.6 0.2
O5' A:DTP504 3.7 13.6 0.8
NH1 A:ARG61 3.8 22.6 0.2
O3B A:DTP504 3.8 13.4 0.8
NH2 A:ARG61 3.8 14.0 0.8
O4 A:DPO505 3.8 13.5 0.2
O5' P:DA9 3.8 13.9 0.2
O1G A:DTP504 3.8 13.1 0.8
CZ A:ARG61 3.8 22.4 0.8
O6 A:DPO505 3.8 13.3 0.2
O5 A:DPO505 3.9 11.3 0.2
O A:HOH1022 3.9 43.8 1.0
O3G A:DTP504 3.9 10.4 0.8
O A:HOH798 4.1 20.8 0.8
PG A:DTP504 4.1 13.9 0.8
P2 A:DPO505 4.1 13.3 0.2
O A:HOH678 4.1 21.6 1.0
O A:HOH948 4.2 21.9 1.0
O2B A:DTP504 4.3 9.5 0.8
O1 A:DPO505 4.3 10.9 0.2
O2 A:DPO505 4.4 9.8 0.2
O1B A:DTP504 4.5 10.5 0.8
O3' P:DA8 4.6 13.9 0.2
O3' P:DA8 4.7 13.8 0.3
CA A:CA502 4.8 9.9 0.5
MG A:MG503 4.8 9.8 0.5
CZ A:ARG61 4.8 25.2 0.2
C5' A:DTP504 4.9 13.8 0.8
C3' P:DA8 4.9 17.3 0.3
C8 P:DA9 4.9 17.5 0.2
C3' P:DA8 4.9 17.3 0.2

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: Thu Oct 3 00:23:16 2024

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