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Magnesium in PDB 7u78: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S, PDB code: 7u78 was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.95 / 1.61
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 97.742, 97.742, 81.762, 90, 90, 120
R / Rfree (%) 18.6 / 21.7

Other elements in 7u78:

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S (pdb code 7u78). 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 Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S, PDB code: 7u78:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7u78

Go back to Magnesium Binding Sites List in 7u78
Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:26.4
occ:0.75
 OE1 A:GLU116 2.1 36.9 0.7
OD2 A:ASP13 2.2 39.1 0.7
OD1 A:ASP115 2.2 27.6 1.0
OD1 A:ASP13 2.3 28.2 0.2
OE1 A:GLU116 2.3 36.0 0.3
O1A A:DGT506 2.3 29.0 0.8
O A:HOH827 2.3 29.9 0.3
O A:HOH726 2.5 37.4 0.8
O3' P:DT8 2.5 29.8 0.2
OD1 A:ASP13 3.0 26.3 0.1
CG A:ASP115 3.1 28.1 1.0
CD A:GLU116 3.2 35.9 0.3
CG A:ASP13 3.3 25.6 0.7
CD A:GLU116 3.3 36.4 0.7
CG A:ASP13 3.3 26.1 0.1
CG A:ASP13 3.4 25.8 0.2
OD2 A:ASP13 3.4 28.2 0.1
C3' P:DT8 3.4 29.7 0.2
OD2 A:ASP115 3.5 28.5 1.0
OG A:SER113 3.5 32.3 1.0
PA A:DGT506 3.5 29.3 0.8
MG A:MG503 3.6 21.6 0.7
CA A:CA502 3.6 21.7 0.3
CB A:GLU116 3.7 26.6 0.3
CB A:GLU116 3.7 26.6 0.7
OE2 A:GLU116 3.9 34.3 0.3
CG A:GLU116 3.9 29.8 0.3
OD1 A:ASP13 3.9 33.8 0.7
O2A A:DGT506 4.0 34.5 0.8
CG A:GLU116 4.0 29.7 0.7
O5' A:DGT506 4.0 25.0 0.8
C5' A:DGT506 4.1 22.9 0.8
OD2 A:ASP13 4.1 27.8 0.2
O A:HOH654 4.3 47.6 1.0
C A:ASP115 4.3 27.1 1.0
OE2 A:GLU116 4.3 36.4 0.7
C4' P:DT8 4.3 32.9 0.2
CB A:ASP13 4.4 24.4 0.1
O A:ASP115 4.4 28.3 1.0
CB A:ASP13 4.4 24.2 0.2
CB A:ASP13 4.4 24.1 0.7
N A:GLU116 4.4 23.4 0.3
CB A:ASP115 4.5 23.0 1.0
N A:GLU116 4.5 23.2 0.7
NZ A:LYS224 4.5 29.7 0.5
CB A:SER113 4.7 24.8 1.0
C2' P:DT8 4.7 26.5 0.2
CA A:GLU116 4.7 24.3 0.3
CA A:GLU116 4.7 24.3 0.7
O3G A:DGT506 4.8 23.2 0.8
CA A:ASP115 4.8 22.8 1.0
O3A A:DGT506 4.8 29.0 0.8
O P:HOH115 4.9 31.6 0.4
N A:ASP115 4.9 19.2 1.0
O2B A:DGT506 4.9 21.8 0.8
O A:HOH832 5.0 31.5 0.4

Magnesium binding site 2 out of 3 in 7u78

Go back to Magnesium Binding Sites List in 7u78
Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:21.6
occ:0.70
 CA A:CA502 0.0 21.7 0.3
OD1 A:ASP13 1.7 33.8 0.7
OD1 A:ASP13 2.0 26.3 0.1
OD2 A:ASP13 2.1 27.8 0.2
O3G A:DGT506 2.2 23.2 0.8
OD2 A:ASP115 2.2 28.5 1.0
O2B A:DGT506 2.2 21.8 0.8
O A:MET14 2.3 24.4 1.0
O1A A:DGT506 2.3 29.0 0.8
OD1 A:ASP13 2.4 28.2 0.2
CG A:ASP13 2.5 25.6 0.7
CG A:ASP13 2.5 25.8 0.2
CG A:ASP13 2.7 26.1 0.1
OD2 A:ASP13 2.7 39.1 0.7
OD2 A:ASP13 2.9 28.2 0.1
CG A:ASP115 3.2 28.1 1.0
PB A:DGT506 3.2 22.0 0.8
C A:MET14 3.4 19.3 1.0
PG A:DGT506 3.4 22.2 0.8
PA A:DGT506 3.5 29.3 0.8
O3A A:DGT506 3.5 29.0 0.8
MG A:MG501 3.6 26.4 0.8
OD1 A:ASP115 3.6 27.6 1.0
O3B A:DGT506 3.7 20.0 0.8
N A:MET14 3.8 17.9 1.0
O A:HOH654 3.9 47.6 1.0
CB A:ASP13 3.9 24.1 0.7
CB A:ASP13 4.0 24.2 0.2
O2G A:DGT506 4.1 21.6 0.8
CB A:ASP13 4.1 24.4 0.1
NZ A:LYS231 4.1 26.8 1.0
CA A:MET14 4.1 18.1 1.0
C5' A:DGT506 4.1 22.9 0.8
C A:ASP13 4.2 18.8 1.0
O5' A:DGT506 4.3 25.0 0.8
O A:HOH726 4.4 37.4 0.8
N A:ASP15 4.4 16.2 1.0
CB A:ASP115 4.5 23.0 1.0
N A:CYS16 4.5 18.5 1.0
CA A:ASP13 4.5 21.9 0.7
CA A:ASP13 4.5 22.0 0.2
CA A:ASP15 4.5 15.8 1.0
CA A:ASP13 4.6 22.0 0.1
C A:ASP15 4.6 22.3 1.0
O1B A:DGT506 4.6 21.5 0.8
O A:ASP115 4.7 28.3 1.0
O2A A:DGT506 4.7 34.5 0.8
CB A:MET14 4.7 22.7 1.0
O A:ASP13 4.7 23.2 1.0
O1G A:DGT506 4.7 23.9 0.8
N A:PHE17 4.7 17.6 1.0
CE A:LYS231 4.9 39.5 1.0
CB A:PHE17 4.9 16.6 1.0

Magnesium binding site 3 out of 3 in 7u78

Go back to Magnesium Binding Sites List in 7u78
Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 80S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:26.9
occ:0.15
 O A:HOH875 1.8 26.0 0.2
O A:HOH601 2.0 31.1 0.6
O A:HOH834 2.1 41.2 0.6
O A:HOH875 2.3 21.0 0.2
O3A A:DGT506 2.4 29.0 0.8
O2A A:DGT506 2.5 34.5 0.8
NH1 A:ARG61 2.5 26.4 0.2
PA A:DGT506 3.0 29.3 0.8
O A:HOH654 3.1 47.6 1.0
O3' P:DT8 3.3 31.1 0.8
O1G A:DGT506 3.3 23.9 0.8
O A:HOH825 3.4 33.7 1.0
CZ A:ARG61 3.5 27.4 0.2
O3B A:DGT506 3.6 20.0 0.8
NH2 A:ARG61 3.6 25.0 0.2
O A:HOH722 3.6 25.7 0.6
PB A:DGT506 3.7 22.0 0.8
PG A:DGT506 3.9 22.2 0.8
O1A A:DGT506 4.1 29.0 0.8
O3G A:DGT506 4.1 23.2 0.8
C3' P:DT8 4.1 29.4 0.8
O5' A:DGT506 4.2 25.0 0.8
O1B A:DGT506 4.3 21.5 0.8
O A:HOH695 4.6 23.5 1.0
O A:HOH726 4.6 37.4 0.8
NE A:ARG61 4.7 24.6 0.2
NH2 A:ARG55 4.8 26.6 1.0
O2B A:DGT506 4.9 21.8 0.8
O A:HOH845 4.9 40.8 1.0
C4' P:DT8 5.0 27.3 0.8

Reference:

C.Chang, C.Lee Luo, Y.Gao. In Crystallo Observation of Three Metal Ion Promoted Dna Polymerase Misincorporation. Nat Commun V. 13 2346 2022.
ISSN: ESSN 2041-1723
PubMed: 35487947
DOI: 10.1038/S41467-022-30005-3
Page generated: Thu Oct 3 09:48:21 2024

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