Magnesium in PDB 7m7s: Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp

Enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp

All present enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp, PDB code: 7m7s 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) 31.49 / 1.85
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.676, 98.676, 81.832, 90, 90, 120
R / Rfree (%) 18 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp (pdb code 7m7s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp, PDB code: 7m7s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7m7s

Go back to Magnesium Binding Sites List in 7m7s
Magnesium binding site 1 out of 2 in the Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp


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 Dt-Ended Primer and 0.1 Mm Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.4
occ:0.30
OD2 A:ASP13 2.0 17.8 0.3
O A:HOH767 2.1 10.9 0.7
O1B A:DZ4501 2.1 19.0 0.3
O A:MET14 2.1 21.3 1.0
OD1 A:ASP115 2.3 19.4 0.5
O1G A:DZ4501 2.6 26.6 0.3
O1A A:DZ4501 2.7 21.1 0.3
CG A:ASP13 2.9 13.9 0.3
PB A:DZ4501 3.0 16.3 0.3
O3B A:DZ4501 3.1 14.5 0.3
PG A:DZ4501 3.2 36.1 0.3
OD1 A:ASP13 3.2 18.3 0.3
C A:MET14 3.3 14.5 1.0
CG A:ASP115 3.4 20.1 0.5
O2G A:DZ4501 3.4 34.4 0.3
MG A:MG503 3.5 18.2 0.3
N3A A:DZ4501 3.5 20.5 0.3
PA A:DZ4501 3.6 26.1 0.3
O A:HOH615 3.7 18.3 0.9
OD2 A:ASP115 3.8 10.2 0.5
OD2 A:ASP115 3.9 22.0 0.5
N A:CYS16 3.9 17.9 1.0
O A:HOH610 4.0 29.8 1.0
N A:MET14 4.0 12.8 1.0
CA A:ASP15 4.1 15.1 1.0
N A:ASP15 4.2 11.1 1.0
CG A:ASP115 4.2 19.0 0.5
CB A:ASP13 4.2 13.9 0.3
CA A:MET14 4.2 10.1 1.0
CB A:ASP13 4.2 13.6 0.7
C A:ASP15 4.3 20.4 1.0
C A:ASP13 4.3 11.8 1.0
O2B A:DZ4501 4.4 21.2 0.3
CB A:ASP115 4.4 10.5 0.5
CG A:ASP13 4.5 21.9 0.7
CB A:ASP115 4.5 10.6 0.5
N A:PHE17 4.6 15.4 1.0
O3G A:DZ4501 4.7 21.4 0.3
O A:ASP115 4.7 15.9 1.0
O5' A:DZ4501 4.7 28.4 0.3
CA A:CYS16 4.7 16.8 1.0
OD2 A:ASP13 4.7 21.7 0.7
CA A:ASP13 4.7 14.1 0.7
CA A:ASP13 4.8 14.1 0.3
O2A A:DZ4501 4.8 29.9 0.3
O A:ASP13 4.8 12.2 1.0
CB A:MET14 4.8 13.7 1.0
C4' A:DZ4501 4.8 18.9 0.3
OD1 A:ASP115 5.0 8.3 0.5

Magnesium binding site 2 out of 2 in 7m7s

Go back to Magnesium Binding Sites List in 7m7s
Magnesium binding site 2 out of 2 in the Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp


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 Dt-Ended Primer and 0.1 Mm Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:18.2
occ:0.30
OD1 A:ASP13 2.0 18.3 0.3
O A:HOH610 2.1 29.8 1.0
OD2 A:ASP115 2.2 22.0 0.5
O1A A:DZ4501 2.2 21.1 0.3
O3' P:DT9 2.2 21.4 0.3
OD1 A:ASP115 2.8 8.3 0.5
CG A:ASP115 2.8 20.1 0.5
OD1 A:ASP115 2.8 19.4 0.5
C3' P:DT9 2.9 21.9 0.3
CG A:ASP115 3.0 19.0 0.5
OD2 A:ASP13 3.1 21.7 0.7
CG A:ASP13 3.1 13.9 0.3
OD2 A:ASP115 3.2 10.2 0.5
MG A:MG502 3.5 16.4 0.3
PA A:DZ4501 3.5 26.1 0.3
OD2 A:ASP13 3.6 17.8 0.3
OE2 A:GLU116 3.6 28.7 1.0
CG A:ASP13 3.7 21.9 0.7
C2' P:DT9 3.9 25.4 0.3
CB A:GLU116 3.9 17.3 1.0
O2A A:DZ4501 3.9 29.9 0.3
O A:ASP115 3.9 15.9 1.0
CB A:ASP115 4.0 10.5 0.5
C4' P:DT9 4.1 25.8 0.3
OD1 A:ASP13 4.2 20.5 0.7
C A:ASP115 4.2 16.8 1.0
CB A:ASP115 4.3 10.6 0.5
O A:HOH767 4.3 10.9 0.7
C4' P:DT9 4.3 25.6 0.7
CB A:ASP13 4.4 13.9 0.3
O5' A:DZ4501 4.4 28.4 0.3
CD A:GLU116 4.4 33.3 1.0
O1G A:DZ4501 4.4 26.6 0.3
O3' P:DT9 4.5 25.8 0.7
CB A:ASP13 4.5 13.6 0.7
C5' P:DT9 4.6 30.7 0.7
O1B A:DZ4501 4.6 19.0 0.3
N3A A:DZ4501 4.7 20.5 0.3
CA A:ASP115 4.7 11.6 0.5
CG A:GLU116 4.7 24.5 1.0
N A:GLU116 4.7 14.7 1.0
CA A:GLU116 4.7 16.3 1.0
CA A:ASP115 4.8 11.6 0.5
C5' P:DT9 4.9 31.8 0.3
C1' P:DT9 5.0 24.1 0.3
CA A:ASP13 5.0 14.1 0.7
CA A:ASP13 5.0 14.1 0.3
C3' P:DT9 5.0 26.1 0.7

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: Mon Jul 12 14:24:43 2021

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