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Manganese in PDB 8e8c: Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S

Enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S, PDB code: 8e8c 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) 32.01 / 2.25
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 97.8, 97.8, 81.64, 90, 90, 120
R / Rfree (%) 19.2 / 23.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S (pdb code 8e8c). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S, PDB code: 8e8c:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8e8c

Go back to Manganese Binding Sites List in 8e8c
Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction 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-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:64.3
occ:1.00
O2B A:DGT503 2.0 38.6 0.9
OD2 A:ASP115 2.2 60.9 1.0
O2G A:DGT503 2.2 46.2 0.9
OD2 A:ASP13 2.2 51.5 1.0
O A:MET14 2.3 37.9 1.0
O1A A:DGT503 2.5 44.8 0.9
PB A:DGT503 3.1 61.1 0.9
CG A:ASP13 3.1 51.1 1.0
PG A:DGT503 3.3 55.1 0.9
CG A:ASP115 3.4 57.3 1.0
C A:MET14 3.4 37.8 1.0
OD1 A:ASP13 3.5 66.8 1.0
MN A:MN502 3.5 56.2 0.7
O3B A:DGT503 3.5 53.5 0.9
O3A A:DGT503 3.5 66.0 0.9
PA A:DGT503 3.6 60.7 0.9
O1G A:DGT503 3.7 53.0 0.9
OD1 A:ASP115 4.0 53.9 1.0
N A:MET14 4.1 43.1 1.0
NZ A:LYS231 4.1 58.9 1.0
O A:HOH608 4.1 57.5 0.7
C5' A:DGT503 4.2 53.7 0.9
CA A:MET14 4.3 40.0 1.0
N A:CYS16 4.3 45.3 1.0
CB A:ASP13 4.3 54.1 1.0
C A:ASP13 4.3 41.6 1.0
N A:ASP15 4.3 36.8 1.0
O5' A:DGT503 4.4 59.8 0.9
CA A:ASP15 4.4 40.0 1.0
CB A:ASP115 4.5 41.5 1.0
O1B A:DGT503 4.5 51.3 0.9
C A:ASP15 4.6 45.5 1.0
O3G A:DGT503 4.7 50.8 0.9
CA A:ASP13 4.7 40.4 1.0
O A:ASP115 4.8 48.1 1.0
N A:PHE17 4.8 38.2 1.0
O A:ASP13 4.8 36.6 1.0
O2A A:DGT503 4.8 57.0 0.9
CB A:MET14 4.9 44.4 1.0
CB A:PHE17 5.0 34.0 1.0

Manganese binding site 2 out of 2 in 8e8c

Go back to Manganese Binding Sites List in 8e8c
Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction 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-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:56.2
occ:0.70
O1A A:DGT503 2.2 44.8 0.9
OD1 A:ASP115 2.4 53.9 1.0
O A:HOH608 2.4 57.5 0.7
OD1 A:ASP13 2.4 66.8 1.0
O3' P:U9 2.6 50.0 0.8
OE2 A:GLU116 3.0 79.3 1.0
CG A:ASP115 3.0 57.3 1.0
OD2 A:ASP115 3.1 60.9 1.0
CG A:ASP13 3.4 51.1 1.0
CD A:GLU116 3.4 60.6 1.0
PA A:DGT503 3.4 60.7 0.9
MN A:MN501 3.5 64.3 1.0
C3' P:U9 3.6 61.9 0.8
OD2 A:ASP13 3.7 51.5 1.0
CB A:GLU116 3.8 48.2 1.0
OE1 A:GLU116 3.8 64.3 1.0
O5' A:DGT503 3.9 59.8 0.9
C5' A:DGT503 3.9 53.7 0.9
OG A:SER113 4.0 43.7 1.0
O2A A:DGT503 4.0 57.0 0.9
CG A:GLU116 4.1 53.0 1.0
C4' P:U9 4.4 57.2 0.8
C A:ASP115 4.4 46.3 1.0
O A:ASP115 4.4 48.1 1.0
CB A:ASP115 4.5 41.5 1.0
O2G A:DGT503 4.5 46.2 0.9
N A:GLU116 4.6 46.0 1.0
NZ A:LYS224 4.6 59.4 1.0
O2B A:DGT503 4.6 38.6 0.9
C5' P:U9 4.6 57.4 0.8
CB A:ASP13 4.7 54.1 1.0
O3A A:DGT503 4.7 66.0 0.9
O2' P:U9 4.7 62.3 0.8
C2' P:U9 4.8 64.8 0.8
CA A:GLU116 4.8 42.5 1.0
O5' P:U9 4.9 60.5 0.2
CA A:ASP115 4.9 43.6 1.0

Reference:

C.Chang, C.Lee Luo, S.Eleraky, A.Lin, G.Zhou, Y.Gao. Primer Terminal Ribonucleotide Alters the Active Site Dynamics of Dna Polymerase Eta and Reduce Dna Synthesis Fidelity J.Biol.Chem. 02938 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.102938
Page generated: Sun Oct 6 11:39:36 2024

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