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Manganese in PDB 7u7d: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S, PDB code: 7u7d 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) 42.13 / 1.57
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.081, 98.081, 82.346, 90, 90, 120
R / Rfree (%) 18.2 / 21.8

Other elements in 7u7d:

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S (pdb code 7u7d). 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 10.0 Mm MN2+ For 30S, PDB code: 7u7d:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7u7d

Go back to Manganese Binding Sites List in 7u7d
Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 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 10.0 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:22.7
occ:0.65
 OD1 A:ASP115 2.0 28.1 1.0
OE1 A:GLU116 2.0 31.2 0.7
OD1 A:ASP13 2.1 34.0 0.7
O A:HOH692 2.1 25.9 0.1
OD1 A:ASP13 2.2 33.9 0.3
OE1 A:GLU116 2.2 31.5 0.3
O A:HOH796 2.2 32.0 1.0
O1A A:DGT504 2.3 24.7 0.8
O3' P:DT8 2.5 27.1 0.5
CG A:ASP115 2.9 27.2 1.0
OD2 A:ASP115 3.1 32.2 1.0
CD A:GLU116 3.1 34.5 0.7
CD A:GLU116 3.1 34.2 0.3
CG A:ASP13 3.2 25.8 0.7
CG A:ASP13 3.2 25.8 0.3
C3' P:DT8 3.4 28.7 0.5
PA A:DGT504 3.5 23.2 0.8
CA A:CA502 3.6 21.6 0.8
MN A:MN503 3.6 21.9 0.2
OD2 A:ASP13 3.6 31.3 0.7
OD2 A:ASP13 3.7 31.2 0.3
OG A:SER113 3.7 29.0 1.0
OE2 A:GLU116 3.8 34.0 0.3
OE2 A:GLU116 3.9 34.3 0.7
CB A:GLU116 4.0 24.8 0.7
CB A:GLU116 4.0 24.9 0.3
O2A A:DGT504 4.0 26.1 0.8
CG A:GLU116 4.0 25.0 0.7
CG A:GLU116 4.0 25.1 0.3
O5' A:DGT504 4.0 21.1 0.8
O A:HOH744 4.2 35.8 1.0
O A:HOH902 4.2 32.5 0.5
C5' A:DGT504 4.2 22.9 0.8
CB A:ASP115 4.3 22.9 1.0
NZ A:LYS224 4.3 34.2 1.0
C4' P:DT8 4.3 31.9 0.5
O P:HOH108 4.4 33.6 0.7
C A:ASP115 4.4 23.9 1.0
CB A:ASP13 4.4 21.9 0.3
CB A:ASP13 4.5 21.8 0.7
O A:ASP115 4.6 24.6 1.0
C2' P:DT8 4.6 29.4 0.5
N A:GLU116 4.7 17.9 1.0
O1G A:DGT504 4.8 23.9 0.8
O3A A:DGT504 4.8 23.1 0.8
CA A:ASP115 4.8 20.4 1.0
CB A:SER113 4.8 22.4 1.0
CA A:GLU116 4.9 24.0 0.7
CA A:GLU116 4.9 24.0 0.3
O2B A:DGT504 4.9 19.4 0.8
O5' P:DT8 5.0 34.0 0.1

Manganese binding site 2 out of 3 in 7u7d

Go back to Manganese Binding Sites List in 7u7d
Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 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 10.0 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:21.9
occ:0.20
 CA A:CA502 0.0 21.6 0.8
OD2 A:ASP115 2.1 32.2 1.0
OD2 A:ASP13 2.1 31.3 0.7
O2B A:DGT504 2.1 19.4 0.8
O A:MET14 2.2 24.6 1.0
O1G A:DGT504 2.2 23.9 0.8
OD2 A:ASP13 2.2 31.2 0.3
O1A A:DGT504 2.4 24.7 0.8
CG A:ASP13 2.9 25.8 0.3
CG A:ASP13 2.9 25.8 0.7
OD1 A:ASP13 3.0 33.9 0.3
PB A:DGT504 3.1 20.8 0.8
CG A:ASP115 3.2 27.2 1.0
OD1 A:ASP13 3.3 34.0 0.7
C A:MET14 3.4 21.2 1.0
PG A:DGT504 3.4 22.9 0.8
O3A A:DGT504 3.5 23.1 0.8
PA A:DGT504 3.5 23.2 0.8
MN A:MN501 3.6 22.7 0.7
O3B A:DGT504 3.6 20.2 0.8
OD1 A:ASP115 3.7 28.1 1.0
N A:MET14 3.9 17.6 1.0
O A:HOH744 3.9 35.8 1.0
NZ A:LYS231 4.0 29.4 1.0
O3G A:DGT504 4.0 21.2 0.8
C5' A:DGT504 4.1 22.9 0.8
CA A:MET14 4.2 17.1 1.0
C A:ASP13 4.2 18.3 1.0
CB A:ASP13 4.3 21.8 0.7
CB A:ASP13 4.3 21.9 0.3
O5' A:DGT504 4.3 21.1 0.8
CB A:ASP115 4.3 22.9 1.0
N A:ASP15 4.3 16.8 1.0
N A:CYS16 4.4 18.2 1.0
CA A:ASP15 4.5 17.9 1.0
O A:HOH796 4.5 32.0 1.0
O1B A:DGT504 4.5 21.6 0.8
C A:ASP15 4.5 22.4 1.0
O2G A:DGT504 4.6 28.0 0.8
N A:PHE17 4.7 16.7 1.0
O A:ASP13 4.7 21.8 1.0
O2A A:DGT504 4.7 26.1 0.8
CB A:MET14 4.7 18.2 1.0
CA A:ASP13 4.7 20.8 0.3
CA A:ASP13 4.7 20.7 0.7
CB A:PHE17 4.9 15.8 1.0
O A:ASP115 4.9 24.6 1.0
CE A:LYS231 4.9 39.1 1.0

Manganese binding site 3 out of 3 in 7u7d

Go back to Manganese Binding Sites List in 7u7d
Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 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 10.0 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:25.0
occ:0.10
 O A:HOH696 2.2 32.8 1.0
O P:HOH119 2.3 48.8 1.0
O3A A:DGT504 2.3 23.1 0.8
O2A A:DGT504 2.6 26.1 0.8
NH1 A:ARG61 2.6 23.6 0.3
PA A:DGT504 3.0 23.2 0.8
O A:HOH881 3.2 31.6 1.0
O3B A:DGT504 3.4 20.2 0.8
CZ A:ARG61 3.4 28.1 0.3
O2G A:DGT504 3.5 28.0 0.8
O A:HOH819 3.5 26.4 0.5
NH2 A:ARG61 3.5 25.8 0.3
PB A:DGT504 3.5 20.8 0.8
O3' P:DT8 3.6 32.5 0.6
O1A A:DGT504 3.9 24.7 0.8
PG A:DGT504 3.9 22.9 0.8
O1G A:DGT504 4.1 23.9 0.8
O1B A:DGT504 4.1 21.6 0.8
O5' A:DGT504 4.2 21.1 0.8
O A:HOH744 4.2 35.8 1.0
C3' P:DT8 4.4 30.5 0.6
O A:HOH656 4.4 25.2 1.0
NE A:ARG61 4.6 26.7 0.3
O2B A:DGT504 4.7 19.4 0.8
NH2 A:ARG55 4.8 27.3 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: Sun Oct 6 10:42:03 2024

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