Calcium in PDB 5ewg: Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion

Enzymatic activity of Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion, PDB code: 5ewg was solved by Y.Su, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.33 / 1.75
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 99.024, 99.024, 81.571, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion (pdb code 5ewg). 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 Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion, PDB code: 5ewg:

Calcium binding site 1 out of 1 in 5ewg

Go back to Calcium Binding Sites List in 5ewg
Calcium binding site 1 out of 1 in the Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Human Dna Polymerase Eta Inserting Ratp Opposite An 8-Oxodeoxyguanosine Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:23.6
occ:1.00
 O3G A:ATP501 2.2 24.7 1.0
OD1 A:ASP13 2.2 29.7 1.0
O2B A:ATP501 2.3 23.3 1.0
O2A A:ATP501 2.3 28.1 1.0
OD2 A:ASP115 2.3 26.6 1.0
O A:MET14 2.3 23.5 1.0
CG A:ASP13 3.4 33.9 1.0
CG A:ASP115 3.4 26.9 1.0
PB A:ATP501 3.4 25.2 1.0
C A:MET14 3.5 19.6 1.0
PG A:ATP501 3.5 25.5 1.0
PA A:ATP501 3.5 27.8 1.0
O3A A:ATP501 3.8 30.6 1.0
OD1 A:ASP115 3.8 29.0 1.0
O3B A:ATP501 3.8 26.5 1.0
O A:HOH626 3.9 30.9 0.5
OD2 A:ASP13 3.9 42.6 1.0
N A:MET14 4.0 21.2 1.0
C5' A:ATP501 4.2 27.2 1.0
NZ A:LYS231 4.2 24.2 1.0
O2G A:ATP501 4.2 23.3 1.0
CA A:MET14 4.3 21.7 1.0
C A:ASP13 4.3 18.9 1.0
O5' A:ATP501 4.3 29.6 1.0
N A:ASP15 4.5 19.8 1.0
CB A:ASP13 4.6 24.3 1.0
CB A:ASP115 4.6 24.6 1.0
N A:CYS16 4.7 23.7 1.0
CA A:ASP15 4.7 22.8 1.0
O1G A:ATP501 4.7 25.3 1.0
CB A:MET14 4.7 24.8 1.0
O1A A:ATP501 4.8 27.7 1.0
O1B A:ATP501 4.8 24.1 1.0
CA A:ASP13 4.8 23.0 1.0
O A:HOH626 4.8 26.8 0.5
O A:ASP13 4.8 22.0 1.0
CE A:LYS231 4.8 38.8 1.0
C A:ASP15 4.8 22.5 1.0
O A:ASP115 4.9 24.5 1.0
N A:PHE17 4.9 19.9 1.0
CB A:PHE17 5.0 19.3 1.0
O3' P:DT8 5.0 36.3 1.0

Reference:

Y.Su, M.Egli, F.P.Guengerich. Mechanism of Ribonucleotide Incorporation By Human Dna Polymerase Eta. J.Biol.Chem. V. 291 3747 2016.
ISSN: ESSN 1083-351X
PubMed: 26740629
DOI: 10.1074/JBC.M115.706226
Page generated: Sat Dec 12 05:24:12 2020

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