Manganese in PDB 7u75: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S, PDB code: 7u75 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) 37.88 / 1.55
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.616, 98.616, 82.057, 90, 90, 120
R / Rfree (%) 18.7 / 22.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S (pdb code 7u75). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S, PDB code: 7u75:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7u75

Go back to Manganese Binding Sites List in 7u75
Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:22.6
occ:0.40
 OE1 A:GLU116 2.0 38.6 1.0
OD1 A:ASP115 2.1 33.1 0.8
OD2 A:ASP13 2.2 35.9 0.4
O A:HOH615 2.2 32.8 0.5
OD1 A:ASP13 2.2 37.0 0.6
O1A A:DGT505 2.3 26.3 0.8
O A:HOH858 2.4 31.1 0.5
O3' P:DT8 2.5 35.9 0.3
OD1 A:ASP115 2.6 27.3 0.2
CG A:ASP115 3.0 29.6 0.8
CD A:GLU116 3.2 44.6 1.0
CG A:ASP13 3.2 29.2 0.4
OD2 A:ASP115 3.2 32.0 0.8
CG A:ASP13 3.2 29.1 0.6
CG A:ASP115 3.3 22.9 0.2
PA A:DGT505 3.5 28.1 0.8
C3' P:DT8 3.5 33.5 0.3
MN A:MN507 3.6 23.0 0.8
OD1 A:ASP13 3.7 37.0 0.4
CB A:GLU116 3.7 34.5 1.0
OG A:SER113 3.7 34.1 1.0
OD2 A:ASP115 3.8 27.7 0.2
OD2 A:ASP13 3.8 37.5 0.6
OE2 A:GLU116 3.9 47.0 1.0
O5' A:DGT505 4.0 24.6 0.8
O2A A:DGT505 4.1 31.8 0.8
CG A:GLU116 4.1 33.6 1.0
C4' P:DT8 4.2 38.4 0.3
O A:HOH888 4.3 30.9 0.6
C5' A:DGT505 4.3 24.3 0.8
CB A:ASP115 4.4 25.3 0.2
O A:HOH772 4.4 43.7 1.0
CB A:ASP13 4.4 23.4 0.6
CB A:ASP115 4.4 25.3 0.8
CB A:ASP13 4.4 23.5 0.4
C A:ASP115 4.4 29.3 1.0
N A:GLU116 4.5 21.4 1.0
NZ A:LYS224 4.5 41.6 1.0
O A:ASP115 4.5 28.2 1.0
CA A:GLU116 4.7 29.7 1.0
O2G A:DGT505 4.7 25.7 0.8
C2' P:DT8 4.8 31.0 0.3
O3A A:DGT505 4.8 26.4 0.8
CA A:ASP115 4.8 21.5 0.2
CB A:SER113 4.9 28.1 1.0
CA A:ASP115 4.9 21.3 0.8
C5' P:DT8 5.0 40.0 0.3
O2B A:DGT505 5.0 21.4 0.8

Manganese binding site 2 out of 3 in 7u75

Go back to Manganese Binding Sites List in 7u75
Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:37.4
occ:0.20
 O A:HOH993 2.1 40.9 0.6
O A:HOH628 2.2 38.7 1.0
NH1 A:ARG61 2.4 29.7 0.2
O3A A:DGT505 2.4 26.4 0.8
O2A A:DGT505 2.5 31.8 0.8
O A:HOH814 2.7 54.5 1.0
PA A:DGT505 3.1 28.1 0.8
O A:HOH894 3.1 31.6 1.0
CZ A:ARG61 3.2 28.7 0.2
O A:HOH856 3.3 26.8 0.6
O3' P:DT8 3.4 33.3 0.7
NH2 A:ARG61 3.4 25.4 0.2
O3G A:DGT505 3.4 24.1 0.8
O3B A:DGT505 3.5 22.2 0.8
PB A:DGT505 3.6 22.5 0.8
PG A:DGT505 3.9 24.2 0.8
O1A A:DGT505 4.1 26.3 0.8
O1B A:DGT505 4.1 21.4 0.8
C3' P:DT8 4.1 37.8 0.7
O5' A:DGT505 4.2 24.6 0.8
O2G A:DGT505 4.2 25.7 0.8
O A:HOH905 4.3 46.2 0.7
O A:HOH772 4.4 43.7 1.0
O A:HOH691 4.4 24.1 1.0
NE A:ARG61 4.4 28.1 0.2
NH2 A:ARG55 4.6 26.4 1.0
O2B A:DGT505 4.8 21.4 0.8
O A:HOH931 4.8 40.5 1.0
CD A:ARG61 5.0 32.2 0.8

Manganese binding site 3 out of 3 in 7u75

Go back to Manganese Binding Sites List in 7u75
Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 90S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:23.0
occ:0.75
 OD1 A:ASP13 1.8 37.0 0.4
OD2 A:ASP115 2.0 32.0 0.8
OD2 A:ASP13 2.1 37.5 0.6
O A:MET14 2.1 25.7 1.0
O2G A:DGT505 2.1 25.7 0.8
O2B A:DGT505 2.2 21.4 0.8
O1A A:DGT505 2.4 26.3 0.8
CG A:ASP13 2.7 29.1 0.6
CG A:ASP13 2.8 29.2 0.4
OD1 A:ASP13 2.8 37.0 0.6
CG A:ASP115 3.2 29.6 0.8
OD2 A:ASP13 3.2 35.9 0.4
PB A:DGT505 3.2 22.5 0.8
C A:MET14 3.3 21.5 1.0
PG A:DGT505 3.4 24.2 0.8
O3A A:DGT505 3.5 26.4 0.8
PA A:DGT505 3.5 28.1 0.8
MN A:MN501 3.6 22.6 0.4
O3B A:DGT505 3.7 22.2 0.8
OD1 A:ASP115 3.7 33.1 0.8
N A:MET14 3.8 19.9 1.0
OD2 A:ASP115 3.9 27.7 0.2
CG A:ASP115 4.0 22.9 0.2
O1G A:DGT505 4.0 22.6 0.8
O A:HOH772 4.1 43.7 1.0
CB A:ASP13 4.1 23.5 0.4
CA A:MET14 4.1 18.8 1.0
CB A:ASP13 4.1 23.4 0.6
C A:ASP13 4.1 21.6 1.0
C5' A:DGT505 4.1 24.3 0.8
NZ A:LYS231 4.2 38.9 1.0
O A:HOH615 4.3 32.8 0.5
N A:ASP15 4.3 18.2 1.0
O5' A:DGT505 4.3 24.6 0.8
CB A:ASP115 4.3 25.3 0.2
CB A:ASP115 4.4 25.3 0.8
N A:CYS16 4.4 21.5 1.0
OD1 A:ASP115 4.4 27.3 0.2
CA A:ASP15 4.4 18.6 1.0
O A:ASP13 4.5 22.6 1.0
C A:ASP15 4.6 19.5 1.0
CA A:ASP13 4.6 22.2 0.4
CA A:ASP13 4.6 22.1 0.6
O1B A:DGT505 4.6 21.4 0.8
O3G A:DGT505 4.6 24.1 0.8
CB A:MET14 4.7 20.7 1.0
O2A A:DGT505 4.7 31.8 0.8
N A:PHE17 4.7 19.5 1.0
O A:ASP115 4.8 28.2 1.0
CE A:LYS231 4.9 50.8 1.0

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: Fri Apr 7 12:31:17 2023

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