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Calcium in PDB 8e8b: Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion

Enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion, PDB code: 8e8b 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) 32.04 / 2.20
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 97.87, 97.87, 82.13, 90, 90, 120
R / Rfree (%) 19.5 / 24.3

Other elements in 8e8b:

The structure of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion also contains other interesting chemical elements:

Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion (pdb code 8e8b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion, PDB code: 8e8b:

Calcium binding site 1 out of 1 in 8e8b

Go back to Calcium Binding Sites List in 8e8b
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:54.7
occ:1.00
 O2B A:DGT501 2.0 37.1 0.9
OD2 A:ASP115 2.3 55.2 1.0
OD1 A:ASP13 2.3 56.1 1.0
O A:MET14 2.3 32.9 1.0
O2G A:DGT501 2.3 43.1 0.9
O1A A:DGT501 2.4 57.9 0.9
PB A:DGT501 3.1 65.3 0.9
CG A:ASP115 3.3 50.6 1.0
CG A:ASP13 3.3 48.4 1.0
C A:MET14 3.4 31.9 1.0
PG A:DGT501 3.5 52.0 0.9
O3B A:DGT501 3.5 51.0 0.9
O3A A:DGT501 3.6 58.7 0.9
PA A:DGT501 3.6 54.2 0.9
OD1 A:ASP115 3.8 48.2 1.0
OD2 A:ASP13 3.8 74.7 1.0
O1G A:DGT501 4.0 49.3 0.9
K A:K502 4.0 43.9 0.3
C5' A:DGT501 4.1 47.0 0.9
N A:MET14 4.1 40.3 1.0
N A:CYS16 4.2 37.4 1.0
CA A:MET14 4.3 35.0 1.0
O5' A:DGT501 4.3 52.4 0.9
N A:ASP15 4.4 28.6 1.0
C A:ASP13 4.4 36.5 1.0
NZ A:LYS231 4.4 46.3 1.0
O1B A:DGT501 4.4 42.4 0.9
CA A:ASP15 4.5 36.1 1.0
C A:ASP15 4.5 43.9 1.0
CB A:ASP13 4.6 47.1 1.0
N A:PHE17 4.6 34.6 1.0
CB A:ASP115 4.6 42.5 1.0
O A:ASP115 4.6 48.3 1.0
O A:HOH625 4.7 68.0 1.0
O2A A:DGT501 4.7 51.8 0.9
O3G A:DGT501 4.8 50.6 0.9
CB A:PHE17 4.8 33.1 1.0
CA A:ASP13 4.8 37.4 1.0
CB A:MET14 4.8 36.9 1.0
O A:ASP13 4.9 33.0 1.0
CA A:CYS16 4.9 38.0 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: Fri Jul 19 08:07:47 2024

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