Magnesium 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:

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 300 S (pdb code 7m88). 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 300 S, PDB code: 7m88:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7m88

Go back to Magnesium Binding Sites List in 7m88
Magnesium binding site 1 out of 3 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 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 300 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:14.8
occ:0.60
 OD2 A:ASP13 2.1 38.2 1.0
O3' P:DA8 2.3 11.9 0.2
OD1 A:ASP115 2.3 17.1 1.0
OE2 A:GLU116 2.3 27.2 1.0
OP1 P:DA9 2.3 17.7 0.3
O3' P:DA8 2.3 10.3 0.3
O2A A:DTP504 2.6 16.8 0.7
O A:HOH821 2.7 27.7 1.0
P P:DA9 2.9 11.3 0.3
O3' P:DA8 3.0 20.0 0.5
CG A:ASP13 3.1 18.3 1.0
CG A:ASP115 3.2 16.8 1.0
C3' P:DA8 3.3 17.2 0.5
CD A:GLU116 3.3 33.3 1.0
OD2 A:ASP115 3.4 16.7 1.0
C3' P:DA8 3.4 17.3 0.2
MG A:MG503 3.5 11.0 0.6
CA A:CA502 3.5 11.0 0.4
C3' P:DA8 3.6 17.3 0.3
OD1 A:ASP13 3.6 22.8 1.0
PA A:DTP504 3.9 17.1 0.7
CB A:GLU116 3.9 26.1 1.0
C4' P:DA8 3.9 20.8 1.0
CG A:GLU116 3.9 28.1 1.0
OP2 P:DA9 4.0 17.1 0.3
O5' P:DA9 4.0 14.6 0.3
C5' P:DA8 4.1 23.0 0.5
C5' P:DA9 4.1 13.2 0.3
OE1 A:GLU116 4.2 34.1 1.0
C5' P:DA8 4.2 23.0 0.3
O5' A:DTP504 4.3 14.6 0.7
C5' A:DTP504 4.3 13.3 0.7
O1A A:DTP504 4.3 17.3 0.7
CB A:ASP13 4.4 13.3 1.0
C A:ASP115 4.4 16.4 1.0
O A:ASP115 4.4 15.2 1.0
N A:GLU116 4.5 12.7 1.0
CB A:ASP115 4.5 13.2 1.0
O A:HOH734 4.6 32.1 1.0
C2' P:DA8 4.7 19.9 0.5
C2' P:DA8 4.7 19.8 0.3
C2' P:DA8 4.7 19.8 0.2
CA A:GLU116 4.8 15.8 1.0
CB A:ALA113 4.8 16.1 1.0
O5' P:DA8 4.9 23.1 0.3
CA A:ASP115 4.9 16.5 1.0
CA A:ASP13 5.0 14.2 1.0
O5 A:DPO505 5.0 14.0 0.3

Magnesium binding site 2 out of 3 in 7m88

Go back to Magnesium Binding Sites List in 7m88
Magnesium binding site 2 out of 3 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 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 300 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:11.0
occ:0.60
 CA A:CA502 0.0 11.0 0.4
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
OD2 A:ASP115 2.3 16.7 1.0
O1B A:DTP504 2.3 12.2 0.7
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 4.1 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

Magnesium binding site 3 out of 3 in 7m88

Go back to Magnesium Binding Sites List in 7m88
Magnesium binding site 3 out of 3 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 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 300 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:18.5
occ:0.30
 O A:HOH894 1.9 14.0 0.3
O1A A:DTP504 1.9 17.3 0.7
O3 A:DPO505 2.1 12.1 0.3
O A:HOH815 2.1 30.4 1.0
OP2 P:DA9 2.2 17.1 0.3
O3A A:DTP504 2.2 14.1 0.7
O A:HOH653 2.5 22.3 1.0
PA A:DTP504 2.6 17.1 0.7
NH1 A:ARG61 2.7 21.1 0.5
O A:HOH734 2.7 32.1 1.0
P P:DA9 3.3 11.3 0.3
O2A A:DTP504 3.5 16.8 0.7
NH2 A:ARG61 3.5 10.1 0.5
CZ A:ARG61 3.5 20.1 0.5
PB A:DTP504 3.6 13.1 0.7
P1 A:DPO505 3.6 13.1 0.3
O6 A:DPO505 3.8 14.5 0.3
OP1 P:DA9 3.8 17.7 0.3
O1G A:DTP504 3.8 14.4 0.7
O5' A:DTP504 3.8 14.6 0.7
O3B A:DTP504 3.8 13.6 0.7
O5' P:DA9 3.8 14.6 0.3
NH2 A:ARG61 3.9 35.8 0.5
O4 A:DPO505 3.9 13.7 0.3
O A:HOH1007 3.9 39.3 1.0
O5 A:DPO505 4.0 14.0 0.3
O P:HOH204 4.0 25.2 1.0
O A:HOH937 4.0 27.4 1.0
O3G A:DTP504 4.1 13.9 0.7
PG A:DTP504 4.2 14.9 0.7
P2 A:DPO505 4.2 14.6 0.3
O2B A:DTP504 4.3 13.7 0.7
NE A:ARG61 4.3 33.3 0.5
O A:HOH821 4.4 27.7 1.0
O2 A:DPO505 4.4 13.8 0.3
CZ A:ARG61 4.5 33.6 0.5
O1 A:DPO505 4.5 12.7 0.3
O1B A:DTP504 4.6 12.2 0.7
O3' P:DA8 4.6 10.3 0.3
NE A:ARG61 4.8 19.7 0.5
C8 P:DA9 5.0 16.2 0.3
CA A:CA502 5.0 11.0 0.4
MG A:MG503 5.0 11.0 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: Thu Oct 3 00:23:47 2024

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