Magnesium 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:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 140 S, PDB code: 7m8b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7m8b

Go back to Magnesium Binding Sites List in 7m8b
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg501

b:20.8
occ:0.30
 OD2 A:ASP115 2.0 28.5 0.5
OD1 A:ASP13 2.1 23.9 0.3
O3' P:A8 2.1 26.2 0.5
OE2 A:GLU116 2.3 35.8 0.5
OE2 A:GLU116 2.3 35.8 0.5
OD1 A:ASP115 2.4 23.1 0.5
O3' P:A8 2.5 27.6 0.6
OD1 A:ASP115 2.6 17.3 0.5
CG A:ASP115 2.6 23.4 0.5
OP1 P:DA9 2.6 25.1 0.6
O A:HOH812 2.6 38.3 1.0
O2A A:DTP507 2.7 24.9 0.3
CD A:GLU116 3.1 30.0 0.5
CD A:GLU116 3.1 30.0 0.5
P P:DA9 3.2 19.8 0.6
OD2 A:ASP13 3.2 36.2 0.7
CG A:ASP115 3.2 21.3 0.5
OD1 A:ASP13 3.2 21.8 0.7
CG A:GLU116 3.3 29.4 0.5
CG A:GLU116 3.3 29.4 0.5
CG A:ASP13 3.3 22.3 0.3
OD2 A:ASP115 3.4 15.8 0.5
C3' P:A8 3.4 28.8 0.5
CG A:ASP13 3.5 23.5 0.7
C3' P:A8 3.6 28.8 0.6
MG A:MG503 3.7 20.5 0.7
CA A:CA502 3.7 20.5 0.1
CB A:GLU116 3.7 27.6 1.0
C4' P:A8 3.8 28.7 0.6
C4' P:A8 3.8 28.6 0.5
OD2 A:ASP13 3.8 21.4 0.3
PA A:DTP507 4.0 22.0 0.3
CB A:ASP115 4.1 17.2 0.5
C5' P:A8 4.1 29.8 0.6
C5' P:A8 4.2 29.7 0.5
OP2 P:DA9 4.3 23.9 0.6
O5' P:DA9 4.3 21.4 0.6
O2' P:A8 4.3 29.8 0.5
OE1 A:GLU116 4.3 33.4 0.5
C5' P:DA9 4.3 19.0 0.6
OE1 A:GLU116 4.3 33.4 0.5
O2' P:A8 4.3 30.2 0.6
O5' A:DTP507 4.4 21.2 0.3
C5' A:DTP507 4.4 19.2 0.3
O1A A:DTP507 4.4 23.7 0.3
C A:ASP115 4.4 22.2 1.0
CB A:ASP13 4.5 17.5 0.3
C2' P:A8 4.5 27.8 0.5
O A:HOH774 4.5 22.3 0.4
N A:GLU116 4.5 18.0 1.0
O A:ASP115 4.5 18.3 1.0
NZ A:LYS224 4.6 25.4 0.5
CB A:ASP115 4.6 15.6 0.5
C2' P:A8 4.6 27.7 0.6
CA A:GLU116 4.7 15.2 1.0
CB A:ASP13 4.7 16.6 0.7
CA A:ASP115 4.8 17.2 0.5
O5 A:DPO508 4.9 20.7 0.5
CB A:ALA113 4.9 21.4 1.0
CA A:ASP115 4.9 17.1 0.5
O3G A:DTP507 4.9 20.3 0.3
O5' P:A8 5.0 28.9 0.5

Magnesium binding site 2 out of 3 in 7m8b

Go back to Magnesium Binding Sites List in 7m8b
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg503

b:20.5
occ:0.70
 CA A:CA502 0.0 20.5 0.1
O5 A:DPO508 2.1 20.7 0.5
OD1 A:ASP13 2.1 21.8 0.7
OD2 A:ASP115 2.1 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 4.0 17.2 0.3
O6 A:DPO508 4.0 19.2 0.5
N A:MET14 4.0 13.0 1.0
C5' A:DTP507 4.0 19.2 0.3
O A:HOH774 4.0 22.3 0.4
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

Magnesium binding site 3 out of 3 in 7m8b

Go back to Magnesium Binding Sites List in 7m8b
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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
P:Mg101

b:22.9
occ:0.30
 O2 A:DPO508 2.0 24.1 0.5
O A:HOH823 2.0 20.5 0.4
O1A A:DTP507 2.1 23.7 0.3
O3A A:DTP507 2.2 21.0 0.3
O A:HOH743 2.3 28.4 1.0
O P:HOH216 2.3 41.2 1.0
OP2 P:DA9 2.4 23.9 0.6
O A:HOH774 2.5 22.3 0.4
PA A:DTP507 2.6 22.0 0.3
NH1 A:ARG61 2.7 28.9 0.5
P P:DA9 3.3 19.8 0.6
P1 A:DPO508 3.4 20.2 0.5
PB A:DTP507 3.5 20.5 0.3
O2A A:DTP507 3.5 24.9 0.3
NH2 A:ARG61 3.5 16.2 0.5
OP1 P:DA9 3.5 25.1 0.6
CZ A:ARG61 3.5 27.8 0.5
O3B A:DTP507 3.6 20.6 0.3
O A:HOH920 3.7 33.7 1.0
O4 A:DPO508 3.8 22.4 0.5
O5' P:DA9 3.9 21.4 0.6
O7 A:DPO508 3.9 23.1 0.5
O1G A:DTP507 3.9 22.9 0.3
O5' A:DTP507 3.9 21.2 0.3
O3G A:DTP507 4.0 20.3 0.3
PG A:DTP507 4.1 24.1 0.3
P2 A:DPO508 4.2 23.2 0.5
O5 A:DPO508 4.2 20.7 0.5
O2B A:DTP507 4.2 16.7 0.3
NH1 A:ARG61 4.2 36.6 0.5
O3 A:DPO508 4.3 17.8 0.5
O A:HOH805 4.3 35.0 1.0
O1 A:DPO508 4.4 16.7 0.5
O A:HOH812 4.4 38.3 1.0
O1B A:DTP507 4.6 16.8 0.3
O A:HOH640 4.7 24.0 1.0
O3' P:A8 4.7 27.6 0.6
NE A:ARG61 4.8 31.7 0.5

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 00:24:15 2024

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