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Calcium in PDB 5kfa: Human Dna Polymerase Eta-Dna Ternary Complex: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion

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

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary 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 Ternary Complex: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion, PDB code: 5kfa was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.51
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.530, 98.530, 81.960, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.3

Other elements in 5kfa:

The structure of Human Dna Polymerase Eta-Dna Ternary 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 Ternary Complex: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion (pdb code 5kfa). 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 Ternary Complex: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion, PDB code: 5kfa:

Calcium binding site 1 out of 1 in 5kfa

Go back to Calcium Binding Sites List in 5kfa
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary 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 Ternary Complex: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:10.7
occ:1.00
 O A:MET14 2.3 10.4 1.0
O1G A:DTP505 2.3 12.3 1.0
O1B A:DTP505 2.3 10.1 1.0
OD1 A:ASP115 2.3 12.3 1.0
OD1 A:ASP13 2.3 15.9 1.0
O1A A:DTP505 2.4 11.1 1.0
PB A:DTP505 3.4 10.1 1.0
CG A:ASP13 3.4 23.2 1.0
CG A:ASP115 3.4 11.3 1.0
C A:MET14 3.5 8.6 1.0
K A:K506 3.5 17.6 0.3
PA A:DTP505 3.5 11.6 1.0
PG A:DTP505 3.5 10.3 1.0
O3A A:DTP505 3.7 10.7 1.0
OD2 A:ASP115 3.7 14.6 1.0
O3B A:DTP505 3.8 8.8 1.0
O A:HOH706 3.9 24.6 1.0
N A:MET14 3.9 8.7 1.0
OD2 A:ASP13 3.9 28.0 1.0
NZ A:LYS231 4.0 15.3 1.0
C5' A:DTP505 4.1 11.8 1.0
O2G A:DTP505 4.1 11.8 1.0
CA A:MET14 4.2 8.9 1.0
C A:ASP13 4.3 10.4 1.0
O5' A:DTP505 4.3 11.2 1.0
N A:ASP15 4.5 7.1 1.0
N A:CYS16 4.5 8.4 1.0
CB A:ASP13 4.5 12.3 1.0
O A:ASP13 4.6 11.2 1.0
CA A:ASP15 4.6 8.5 1.0
CB A:MET14 4.7 11.7 1.0
CB A:ASP115 4.7 8.9 1.0
O2B A:DTP505 4.7 10.5 1.0
CE A:LYS231 4.7 26.9 1.0
CA A:ASP13 4.7 12.7 1.0
O3G A:DTP505 4.8 12.1 1.0
O2A A:DTP505 4.8 14.4 1.0
N A:PHE17 4.8 8.8 1.0
C A:ASP15 4.8 9.6 1.0
CB A:PHE17 4.9 6.2 1.0
O A:ASP115 4.9 13.0 1.0

Reference:

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633
Page generated: Wed Jul 9 07:22:49 2025

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