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Magnesium in PDB 7m86: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S

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

All present enzymatic activity of Human Dna Pol Eta S113A with Da-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 Da-Ended Primer and Datp: in Crystallo Reaction For 140 S, PDB code: 7m86 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 / 1.55
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.156, 98.156, 82.511, 90, 90, 120
R / Rfree (%) 17.3 / 20.5

Other elements in 7m86:

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 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 140 S (pdb code 7m86). 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 140 S, PDB code: 7m86:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7m86

Go back to Magnesium Binding Sites List in 7m86
Magnesium binding site 1 out of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 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 140 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.4
occ:0.65
 OD1 A:ASP13 2.0 20.2 0.6
OE2 A:GLU116 2.2 22.1 1.0
OP1 P:DA9 2.2 11.7 0.2
O3' P:DA8 2.2 9.6 0.3
O3' P:DA8 2.3 10.5 0.2
OD1 A:ASP115 2.3 12.8 1.0
O2A A:DTP504 2.5 12.6 0.8
O A:HOH675 2.6 26.0 1.0
P P:DA9 2.7 11.3 0.2
OD1 A:ASP13 2.9 13.5 0.5
O3' P:DA8 3.0 20.2 0.5
OD2 A:ASP13 3.2 19.3 0.5
C3' P:DA8 3.2 13.4 0.5
CG A:ASP115 3.2 12.4 1.0
CG A:ASP13 3.2 12.1 0.6
CD A:GLU116 3.3 31.5 1.0
CG A:ASP13 3.3 13.8 0.5
C3' P:DA8 3.4 16.7 0.3
OD2 A:ASP115 3.4 13.7 1.0
CA A:CA502 3.5 8.2 0.5
C3' P:DA8 3.5 16.8 0.2
MG A:MG503 3.5 8.3 0.5
OP2 P:DA9 3.8 17.0 0.2
PA A:DTP504 3.8 11.4 0.8
OD2 A:ASP13 3.8 12.1 0.6
C4' P:DA8 3.9 18.2 1.0
O5' P:DA9 4.0 11.6 0.2
CB A:GLU116 4.0 20.2 1.0
CG A:GLU116 4.0 21.9 1.0
C5' P:DA8 4.0 20.6 0.5
C5' P:DA8 4.1 19.6 0.3
OE1 A:GLU116 4.2 31.9 1.0
O5' A:DTP504 4.2 10.4 0.8
C5' P:DA9 4.2 10.8 0.2
C5' A:DTP504 4.2 10.7 0.8
O1A A:DTP504 4.3 12.8 0.8
O A:HOH724 4.3 35.3 1.0
CB A:ASP13 4.4 12.5 0.6
C A:ASP115 4.5 10.8 1.0
O A:ASP115 4.5 12.0 1.0
CB A:ASP13 4.6 12.5 0.5
CB A:ASP115 4.6 10.5 1.0
C2' P:DA8 4.6 18.8 0.3
C2' P:DA8 4.6 18.9 0.5
C2' P:DA8 4.6 18.2 0.2
NZ A:LYS224 4.6 17.6 0.6
N A:GLU116 4.6 10.6 1.0
O5' P:DA8 4.8 18.5 0.3
CB A:ALA113 4.9 12.1 1.0
CA A:GLU116 4.9 13.1 1.0
O5 A:DPO505 4.9 11.0 0.2
O3G A:DTP504 5.0 11.0 0.8
CA A:ASP115 5.0 10.6 1.0

Magnesium binding site 2 out of 3 in 7m86

Go back to Magnesium Binding Sites List in 7m86
Magnesium binding site 2 out of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 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 140 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:8.3
occ:0.50
 CA A:CA502 0.0 8.2 0.5
OD1 A:ASP13 2.2 13.5 0.5
OP1 P:DA9 2.2 11.7 0.2
OD2 A:ASP115 2.2 13.7 1.0
OD2 A:ASP13 2.2 12.1 0.6
O A:MET14 2.3 10.7 1.0
O5 A:DPO505 2.3 11.0 0.2
O3G A:DTP504 2.3 11.0 0.8
O1B A:DTP504 2.3 9.9 0.8
O1 A:DPO505 2.4 10.1 0.2
O2A A:DTP504 2.4 12.6 0.8
CG A:ASP13 2.9 12.1 0.6
OD1 A:ASP13 3.0 20.2 0.6
CG A:ASP13 3.2 13.8 0.5
CG A:ASP115 3.3 12.4 1.0
PB A:DTP504 3.3 9.6 0.8
P1 A:DPO505 3.4 10.0 0.2
C A:MET14 3.4 8.6 1.0
PA A:DTP504 3.5 11.4 0.8
MG A:MG501 3.5 13.4 0.7
P2 A:DPO505 3.5 10.5 0.2
PG A:DTP504 3.5 10.8 0.8
O3A A:DTP504 3.6 10.2 0.8
OD2 A:ASP13 3.6 19.3 0.5
P P:DA9 3.7 11.3 0.2
OD1 A:ASP115 3.7 12.8 1.0
O3B A:DTP504 3.8 10.5 0.8
O4 A:DPO505 3.8 10.4 0.2
O3 A:DPO505 3.8 10.8 0.2
O A:HOH724 3.9 35.3 1.0
N A:MET14 3.9 8.9 1.0
NZ A:LYS231 4.0 13.6 1.0
C5' A:DTP504 4.1 10.7 0.8
O2G A:DTP504 4.1 9.8 0.8
O7 A:DPO505 4.1 9.9 0.2
C5' P:DA9 4.2 10.8 0.2
CA A:MET14 4.2 8.8 1.0
O A:HOH675 4.2 26.0 1.0
O5' A:DTP504 4.3 10.4 0.8
C A:ASP13 4.3 8.7 1.0
O5' P:DA9 4.3 11.6 0.2
CB A:ASP13 4.3 12.5 0.6
CB A:ASP13 4.4 12.5 0.5
N A:ASP15 4.5 7.9 1.0
OP2 P:DA9 4.6 17.0 0.2
N A:CYS16 4.6 8.2 1.0
CB A:ASP115 4.6 10.5 1.0
CA A:ASP15 4.6 8.3 1.0
O3' P:DA8 4.7 10.5 0.2
O6 A:DPO505 4.7 11.5 0.2
O1A A:DTP504 4.7 12.8 0.8
O2B A:DTP504 4.7 10.6 0.8
CE A:LYS231 4.7 20.7 1.0
CB A:MET14 4.7 10.0 1.0
O3' P:DA8 4.7 9.6 0.3
O2 A:DPO505 4.7 10.7 0.2
O A:ASP13 4.7 11.1 1.0
CA A:ASP13 4.7 10.8 0.5
O1G A:DTP504 4.7 11.2 0.8
CA A:ASP13 4.7 10.8 0.6
N A:PHE17 4.8 7.8 1.0
C A:ASP15 4.8 9.8 1.0
MG P:MG101 4.8 15.6 0.2
CB A:PHE17 4.9 7.0 1.0
O A:ASP115 4.9 12.0 1.0

Magnesium binding site 3 out of 3 in 7m86

Go back to Magnesium Binding Sites List in 7m86
Magnesium binding site 3 out of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 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 140 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:15.6
occ:0.20
 O1A A:DTP504 1.7 12.8 0.8
O3 A:DPO505 2.0 10.8 0.2
O A:HOH866 2.1 9.3 0.2
O A:HOH772 2.1 36.9 1.0
O3A A:DTP504 2.1 10.2 0.8
OP2 P:DA9 2.2 17.0 0.2
PA A:DTP504 2.3 11.4 0.8
O A:HOH655 2.8 17.7 1.0
NH1 A:ARG61 3.0 26.7 0.8
O2A A:DTP504 3.2 12.6 0.8
P P:DA9 3.2 11.3 0.2
O A:HOH724 3.3 35.3 1.0
P1 A:DPO505 3.4 10.0 0.2
PB A:DTP504 3.5 9.6 0.8
OP1 P:DA9 3.7 11.7 0.2
O5' A:DTP504 3.7 10.4 0.8
O6 A:DPO505 3.7 11.5 0.2
O3B A:DTP504 3.7 10.5 0.8
O4 A:DPO505 3.7 10.4 0.2
O1G A:DTP504 3.8 11.2 0.8
NH1 A:ARG61 3.8 25.0 0.2
NH2 A:ARG61 3.8 12.1 0.8
O A:HOH1017 3.8 39.5 1.0
O5' P:DA9 3.8 11.6 0.2
CZ A:ARG61 3.8 24.4 0.8
O5 A:DPO505 3.8 11.0 0.2
O3G A:DTP504 3.9 11.0 0.8
PG A:DTP504 4.0 10.8 0.8
O A:HOH809 4.1 21.0 0.8
P2 A:DPO505 4.1 10.5 0.2
O A:HOH675 4.1 26.0 1.0
O A:HOH944 4.2 22.7 1.0
O2B A:DTP504 4.3 10.6 0.8
O1 A:DPO505 4.4 10.1 0.2
O2 A:DPO505 4.4 10.7 0.2
O1B A:DTP504 4.5 9.9 0.8
O3' P:DA8 4.6 10.5 0.2
O3' P:DA8 4.7 9.6 0.3
CA A:CA502 4.8 8.2 0.5
MG A:MG503 4.8 8.3 0.5
CZ A:ARG61 4.8 27.2 0.2
C5' A:DTP504 4.9 10.7 0.8
C3' P:DA8 4.9 16.7 0.3
C8 P:DA9 4.9 11.2 0.2
C3' P:DA8 4.9 16.8 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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