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Manganese in PDB 7u74: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S

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 30S

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 30S:
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 30S, PDB code: 7u74 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) 32.30 / 1.52
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.675, 98.675, 82.213, 90, 90, 120
R / Rfree (%) 19 / 22.5

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 30S (pdb code 7u74). 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 30S, PDB code: 7u74:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7u74

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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 30S


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 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:24.0
occ:0.50
 OE1 A:GLU116 2.1 37.2 1.0
O1A A:DGT505 2.2 23.8 0.7
OD1 A:ASP115 2.2 30.6 0.8
OD1 A:ASP13 2.2 35.2 0.6
OD2 A:ASP13 2.2 32.6 0.4
O A:HOH660 2.2 37.1 1.0
O A:HOH845 2.3 33.4 0.6
O3' P:DT8 2.5 35.5 0.4
OD1 A:ASP115 2.9 23.0 0.2
CG A:ASP115 3.0 25.4 0.8
CD A:GLU116 3.2 40.9 1.0
CG A:ASP115 3.2 22.8 0.2
OD2 A:ASP115 3.2 27.6 0.8
CG A:ASP13 3.3 25.4 0.4
CG A:ASP13 3.3 25.3 0.6
PA A:DGT505 3.4 25.9 0.7
C3' P:DT8 3.5 31.2 0.4
OD2 A:ASP115 3.5 22.5 0.2
MN A:MN502 3.6 22.5 0.8
OD1 A:ASP13 3.8 26.1 0.4
CB A:GLU116 3.8 31.2 1.0
OG A:SER113 3.8 30.1 1.0
O5' A:DGT505 3.9 22.7 0.7
OE2 A:GLU116 3.9 42.1 1.0
OD2 A:ASP13 4.0 32.6 0.6
O2A A:DGT505 4.0 28.6 0.7
CG A:GLU116 4.1 28.4 1.0
CB A:ASP115 4.1 22.9 0.2
C5' A:DGT505 4.1 22.0 0.7
O A:HOH750 4.2 40.6 1.0
O P:HOH203 4.3 33.3 0.7
C4' P:DT8 4.3 35.3 0.4
C A:ASP115 4.3 25.6 1.0
CB A:ASP115 4.4 23.1 0.8
O A:ASP115 4.4 26.8 1.0
NZ A:LYS224 4.4 38.0 1.0
CB A:ASP13 4.4 23.0 0.6
CB A:ASP13 4.4 23.0 0.4
N A:GLU116 4.5 20.0 1.0
O P:HOH221 4.6 36.1 0.7
O1G A:DGT505 4.7 24.2 0.7
O3A A:DGT505 4.7 23.7 0.7
C2' P:DT8 4.7 31.6 0.4
CA A:ASP115 4.7 21.0 0.2
CA A:GLU116 4.8 26.7 1.0
CA A:ASP115 4.8 20.9 0.8
O5' P:DT8 4.9 42.1 0.4
O2B A:DGT505 4.9 18.3 0.7
C5' P:DT8 4.9 35.4 0.4
CB A:SER113 4.9 25.6 1.0

Manganese binding site 2 out of 3 in 7u74

Go back to Manganese Binding Sites List in 7u74
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 30S


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 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:22.5
occ:0.80
 OD1 A:ASP13 1.8 26.1 0.4
OD2 A:ASP115 2.0 27.6 0.8
O A:MET14 2.1 26.9 1.0
O1G A:DGT505 2.2 24.2 0.7
O2B A:DGT505 2.2 18.3 0.7
OD2 A:ASP13 2.2 32.6 0.6
O1A A:DGT505 2.4 23.8 0.7
OD1 A:ASP13 2.7 35.2 0.6
CG A:ASP13 2.7 25.3 0.6
CG A:ASP13 2.7 25.4 0.4
OD2 A:ASP13 3.0 32.6 0.4
CG A:ASP115 3.1 25.4 0.8
PB A:DGT505 3.2 20.5 0.7
C A:MET14 3.3 19.6 1.0
PG A:DGT505 3.4 22.3 0.7
PA A:DGT505 3.5 25.9 0.7
O3A A:DGT505 3.5 23.7 0.7
MN A:MN501 3.6 24.0 0.5
O3B A:DGT505 3.7 20.8 0.7
O A:HOH663 3.7 20.4 0.5
OD1 A:ASP115 3.7 30.6 0.8
N A:MET14 3.8 17.2 1.0
OD2 A:ASP115 3.8 22.5 0.2
O A:HOH750 4.0 40.6 1.0
O3G A:DGT505 4.0 19.8 0.7
CA A:MET14 4.1 18.4 1.0
CG A:ASP115 4.1 22.8 0.2
C5' A:DGT505 4.1 22.0 0.7
CB A:ASP13 4.1 23.0 0.4
CB A:ASP13 4.1 23.0 0.6
C A:ASP13 4.1 17.7 1.0
CB A:ASP115 4.2 22.9 0.2
O5' A:DGT505 4.2 22.7 0.7
N A:ASP15 4.3 16.4 1.0
CB A:ASP115 4.3 23.1 0.8
N A:CYS16 4.4 20.6 1.0
CA A:ASP15 4.4 17.3 1.0
O A:HOH660 4.5 37.1 1.0
C A:ASP15 4.5 20.0 1.0
O A:ASP13 4.6 20.7 1.0
CA A:ASP13 4.6 21.7 0.4
CA A:ASP13 4.6 21.6 0.6
CB A:MET14 4.6 19.7 1.0
O A:ASP115 4.7 26.8 1.0
O2G A:DGT505 4.7 24.9 0.7
O1B A:DGT505 4.7 19.2 0.7
N A:PHE17 4.7 18.2 1.0
O2A A:DGT505 4.7 28.6 0.7
OD1 A:ASP115 4.9 23.0 0.2
NZ A:LYS231 4.9 26.4 0.5

Manganese binding site 3 out of 3 in 7u74

Go back to Manganese Binding Sites List in 7u74
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 30S


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 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:29.6
occ:0.10
 O A:HOH636 2.1 35.2 1.0
O3A A:DGT505 2.3 23.7 0.7
O P:HOH219 2.3 37.0 0.5
O2A A:DGT505 2.6 28.6 0.7
NH1 A:ARG61 2.9 26.6 0.2
O A:HOH912 3.1 31.0 1.0
O2G A:DGT505 3.1 24.9 0.7
PA A:DGT505 3.1 25.9 0.7
O3B A:DGT505 3.2 20.8 0.7
PB A:DGT505 3.4 20.5 0.7
O A:HOH817 3.6 31.4 0.8
CZ A:ARG61 3.6 26.3 0.2
PG A:DGT505 3.7 22.3 0.7
O3' P:DT8 3.7 31.6 0.6
NH2 A:ARG61 3.7 25.9 0.2
O1G A:DGT505 4.0 24.2 0.7
O1B A:DGT505 4.0 19.2 0.7
O1A A:DGT505 4.1 23.8 0.7
O A:HOH750 4.2 40.6 1.0
O A:HOH645 4.3 22.6 1.0
O5' A:DGT505 4.3 22.7 0.7
C3' P:DT8 4.4 33.1 0.6
NH2 A:ARG55 4.4 24.6 1.0
O2B A:DGT505 4.6 18.3 0.7
NE A:ARG61 4.7 27.1 0.2
O A:HOH926 4.8 36.4 1.0
NZ A:LYS231 4.8 37.6 0.6

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: Sun Oct 6 10:41:20 2024

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