Atomistry » Magnesium » PDB 7m0z-7m87 » 7m87
Atomistry »
  Magnesium »
    PDB 7m0z-7m87 »
      7m87 »

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

Last articles

Fe in 9CU0
Fe in 9CJE
Fe in 9CJB
Fe in 9CJF
Fe in 9CTZ
Fe in 9CJD
Fe in 9CJC
Fe in 9CUF
Fe in 9DEU
Fe in 9CCB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy