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Manganese in PDB 7u76: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 300S

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 300S

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 300S:
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 300S, PDB code: 7u76 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) 42.29 / 1.69
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 97.657, 97.657, 81.441, 90, 90, 120
R / Rfree (%) 18.3 / 21.9

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 300S (pdb code 7u76). 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 300S, PDB code: 7u76:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7u76

Go back to Manganese Binding Sites List in 7u76
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 300S


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 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:28.9
occ:0.50
 OE1 A:GLU116 1.9 44.9 0.5
OD2 A:ASP13 2.0 41.8 0.5
OP1 P:DG9 2.1 28.4 0.1
OE2 A:GLU116 2.1 43.8 0.5
OD2 A:ASP13 2.1 38.9 0.5
O A:HOH812 2.2 32.4 0.2
O P:HOH211 2.2 33.0 0.5
O1A A:DGT506 2.2 27.9 0.3
OD1 A:ASP115 2.2 32.4 1.0
O3' P:DT8 2.5 34.4 0.1
O3' P:DT8 2.5 35.0 0.1
P P:DG9 2.8 32.1 0.1
O A:HOH872 2.8 47.2 1.0
CD A:GLU116 2.8 42.5 0.5
CD A:GLU116 2.9 42.5 0.5
CG A:ASP13 3.1 32.5 0.5
CG A:ASP13 3.1 32.6 0.5
CG A:ASP115 3.2 35.9 1.0
OD2 A:ASP115 3.4 32.6 1.0
OP1 P:DG9 3.4 35.9 0.2
OE1 A:GLU116 3.4 45.7 0.5
C3' P:DT8 3.5 36.3 0.1
PA A:DGT506 3.5 28.8 0.3
MN A:MN502 3.5 25.6 0.8
OD1 A:ASP13 3.5 32.4 0.5
OE2 A:GLU116 3.6 45.0 0.5
CG A:GLU116 3.7 39.1 0.5
CB A:GLU116 3.7 36.6 0.5
CB A:GLU116 3.7 36.7 0.5
OD1 A:ASP13 3.7 35.7 0.5
C3' P:DT8 3.8 36.5 0.1
OP2 P:DG9 3.8 35.8 0.1
CG A:GLU116 3.9 39.3 0.5
OG A:SER113 3.9 37.9 1.0
O2A A:DGT506 3.9 36.1 0.3
O5' P:DG9 4.0 33.3 0.1
O5' P:DG9 4.0 33.5 0.2
C5' P:DG9 4.1 31.0 0.2
C4' P:DT8 4.1 38.2 0.1
O5' A:DGT506 4.2 33.6 0.3
C5' P:DG9 4.2 29.4 0.1
C4' P:DT8 4.2 38.2 0.1
CB A:ASP13 4.3 27.3 0.5
NZ A:LYS224 4.3 36.8 1.0
C5' P:DT8 4.3 40.2 0.1
P P:DG9 4.3 35.8 0.2
C5' A:DGT506 4.4 29.2 0.3
CB A:ASP13 4.4 27.4 0.5
O A:ASP115 4.5 26.5 1.0
C A:ASP115 4.5 30.2 1.0
CB A:ASP115 4.5 26.1 1.0
O1G A:DGT506 4.6 27.1 0.3
C5' P:DT8 4.6 38.4 0.2
O5 A:DPO505 4.6 27.2 0.3
N A:GLU116 4.6 26.8 1.0
C5' P:DT8 4.7 39.8 0.1
O3A A:DGT506 4.7 33.2 0.3
C4' P:DT8 4.7 38.6 0.2
C2' P:DT8 4.7 35.0 0.1
O P:HOH214 4.7 35.3 0.2
CA A:GLU116 4.8 28.9 0.5
CA A:GLU116 4.8 28.8 0.5
O1 A:DPO505 4.9 24.4 0.3
C2' P:DT8 4.9 36.0 0.1
O2B A:DGT506 4.9 22.1 0.3
CA A:ASP115 5.0 24.0 1.0

Manganese binding site 2 out of 3 in 7u76

Go back to Manganese Binding Sites List in 7u76
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 300S


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 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:25.6
occ:0.75
 OD1 A:ASP13 1.9 32.4 0.5
OD2 A:ASP115 2.1 32.6 1.0
O5 A:DPO505 2.1 27.2 0.3
O2B A:DGT506 2.1 22.1 0.3
O1G A:DGT506 2.1 27.1 0.3
O A:MET14 2.2 26.8 1.0
O1 A:DPO505 2.2 24.4 0.3
OD1 A:ASP13 2.2 35.7 0.5
O1A A:DGT506 2.4 27.9 0.3
OP1 P:DG9 2.5 28.4 0.1
CG A:ASP13 2.9 32.5 0.5
CG A:ASP13 2.9 32.6 0.5
OD2 A:ASP13 3.0 41.8 0.5
PB A:DGT506 3.1 27.6 0.3
O A:HOH872 3.1 47.2 1.0
CG A:ASP115 3.2 35.9 1.0
OD2 A:ASP13 3.2 38.9 0.5
P2 A:DPO505 3.3 29.5 0.3
P1 A:DPO505 3.3 28.0 0.3
PG A:DGT506 3.3 29.5 0.3
C A:MET14 3.3 23.4 1.0
O3A A:DGT506 3.4 33.2 0.3
PA A:DGT506 3.5 28.8 0.3
O3B A:DGT506 3.5 27.1 0.3
MN A:MN501 3.5 28.9 0.5
OD1 A:ASP115 3.6 32.4 1.0
O4 A:DPO505 3.6 27.0 0.3
C5' P:DG9 3.8 31.0 0.2
O2 A:DPO505 3.8 35.9 0.3
N A:MET14 3.9 21.9 1.0
P P:DG9 3.9 32.1 0.1
O7 A:DPO505 3.9 28.0 0.3
OP1 P:DG9 3.9 35.9 0.2
O3G A:DGT506 4.0 28.1 0.3
NZ A:LYS231 4.1 33.8 1.0
CA A:MET14 4.2 22.1 1.0
C5' A:DGT506 4.2 29.2 0.3
CB A:ASP13 4.2 27.4 0.5
C A:ASP13 4.2 23.0 1.0
C5' P:DG9 4.2 29.4 0.1
CB A:ASP13 4.3 27.3 0.5
O5' A:DGT506 4.3 33.6 0.3
N A:ASP15 4.3 22.3 1.0
CB A:ASP115 4.4 26.1 1.0
O5' P:DG9 4.4 33.3 0.1
N A:CYS16 4.4 25.8 1.0
OP2 P:DG9 4.4 35.8 0.2
P P:DG9 4.4 35.8 0.2
CA A:ASP15 4.5 22.9 1.0
O6 A:DPO505 4.5 32.4 0.3
O1B A:DGT506 4.5 25.5 0.3
O5' P:DG9 4.5 33.5 0.2
O P:HOH211 4.5 33.0 0.5
O2G A:DGT506 4.5 32.4 0.3
C A:ASP15 4.6 24.8 1.0
O3 A:DPO505 4.6 25.6 0.3
O A:ASP13 4.6 24.8 1.0
CA A:ASP13 4.6 27.4 0.5
CA A:ASP13 4.6 27.4 0.5
CB A:MET14 4.7 28.3 1.0
O2A A:DGT506 4.7 36.1 0.3
N A:PHE17 4.7 22.4 1.0
O A:ASP115 4.7 26.5 1.0
OP2 P:DG9 4.7 35.8 0.1
O3' P:DT8 4.9 35.0 0.1
CB A:PHE17 4.9 20.5 1.0
CE A:LYS231 4.9 52.4 1.0
O A:HOH812 5.0 32.4 0.2
C4' P:DG9 5.0 28.0 0.2

Manganese binding site 3 out of 3 in 7u76

Go back to Manganese Binding Sites List in 7u76
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 300S


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 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:36.4
occ:0.20
 O A:HOH682 1.8 34.5 0.5
OP2 P:DG9 2.1 35.8 0.2
OP1 P:DG9 2.1 35.9 0.2
P P:DG9 2.1 35.8 0.2
O2A A:DGT506 2.1 36.1 0.3
O3A A:DGT506 2.3 33.2 0.3
O A:HOH639 2.3 42.5 1.0
OP2 P:DG9 2.3 35.8 0.1
O2 A:DPO505 2.3 35.9 0.3
O P:HOH214 2.4 35.3 0.2
O3' P:DT8 2.5 35.2 0.2
NH1 A:ARG61 2.5 32.2 0.1
O A:HOH850 2.6 62.4 1.0
PA A:DGT506 2.7 28.8 0.3
C3' P:DT8 3.1 37.2 0.2
O3' P:DT8 3.1 40.9 0.5
O A:HOH872 3.3 47.2 1.0
P P:DG9 3.4 32.1 0.1
CZ A:ARG61 3.5 32.4 0.1
P1 A:DPO505 3.5 28.0 0.3
O A:HOH883 3.5 35.8 1.0
O2G A:DGT506 3.6 32.4 0.3
O6 A:DPO505 3.6 32.4 0.3
PB A:DGT506 3.6 27.6 0.3
O A:HOH831 3.7 27.6 0.3
O3B A:DGT506 3.7 27.1 0.3
O4 A:DPO505 3.7 27.0 0.3
NH2 A:ARG61 3.7 29.6 0.1
O5' P:DG9 3.7 33.5 0.2
O1A A:DGT506 3.7 27.9 0.3
C3' P:DT8 3.8 37.4 0.5
OP1 P:DG9 3.8 28.4 0.1
O5' A:DGT506 4.0 33.6 0.3
O5' P:DG9 4.0 33.3 0.1
O1G A:DGT506 4.0 27.1 0.3
O5 A:DPO505 4.0 27.2 0.3
P2 A:DPO505 4.0 29.5 0.3
PG A:DGT506 4.1 29.5 0.3
C4' P:DT8 4.1 38.6 0.2
C2' P:DT8 4.2 37.0 0.2
O1B A:DGT506 4.3 25.5 0.3
O3 A:DPO505 4.5 25.6 0.3
C5' P:DG9 4.5 31.0 0.2
O1 A:DPO505 4.6 24.4 0.3
O A:HOH933 4.6 48.4 0.5
O P:HOH211 4.6 33.0 0.5
C4' P:DT8 4.6 38.1 0.5
NE A:ARG61 4.7 30.2 0.1
O3' P:DT8 4.7 35.0 0.1
C5' P:DT8 4.7 38.4 0.2
O2B A:DGT506 4.7 22.1 0.3
O A:HOH644 4.8 29.8 1.0
NH2 A:ARG55 4.9 33.4 1.0
C3' P:DT8 5.0 36.3 0.1

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 10:41:41 2024

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