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

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

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: 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 with Sp-Datp-Alpha-S: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion, PDB code: 5kfm 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) 19.90 / 1.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.350, 98.350, 81.860, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 23.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion (pdb code 5kfm). 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 with Sp-Datp-Alpha-S: Ground State at PH7.0 (K+ Mes) with 1 CA2+ Ion, PDB code: 5kfm:

Calcium binding site 1 out of 1 in 5kfm

Go back to Calcium Binding Sites List in 5kfm
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: 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 with Sp-Datp-Alpha-S: 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:14.1
occ:1.00
 OD2 A:ASP13 2.3 16.5 1.0
O1G A:STP505 2.3 13.7 1.0
OD1 A:ASP115 2.3 15.5 1.0
O1B A:STP505 2.3 13.7 1.0
O A:MET14 2.4 13.9 1.0
O2A A:STP505 2.4 15.7 1.0
CG A:ASP115 3.3 15.1 1.0
CG A:ASP13 3.4 23.5 1.0
PB A:STP505 3.4 14.9 1.0
C A:MET14 3.5 12.5 1.0
PA A:STP505 3.6 13.8 1.0
PG A:STP505 3.6 14.6 1.0
OD2 A:ASP115 3.6 19.0 1.0
O A:HOH663 3.8 16.9 1.0
O3A A:STP505 3.8 14.6 1.0
N A:MET14 3.9 14.7 1.0
OD1 A:ASP13 3.9 25.0 1.0
O3B A:STP505 3.9 14.1 1.0
NZ A:LYS231 4.0 19.0 1.0
C5' A:STP505 4.1 14.7 1.0
C A:ASP13 4.2 13.9 1.0
CA A:MET14 4.2 13.7 1.0
O2G A:STP505 4.3 15.9 1.0
O5' A:STP505 4.3 14.2 1.0
CE A:LYS231 4.5 29.5 1.0
N A:ASP15 4.5 11.4 1.0
O A:ASP13 4.6 13.2 1.0
CB A:ASP13 4.6 17.7 1.0
N A:CYS16 4.6 11.5 1.0
CA A:ASP15 4.6 12.5 1.0
CB A:ASP115 4.6 14.6 1.0
CB A:MET14 4.7 16.2 1.0
CA A:ASP13 4.7 17.2 1.0
O2B A:STP505 4.7 14.8 1.0
O3G A:STP505 4.8 14.9 1.0
C A:ASP15 4.8 13.7 1.0
N A:PHE17 4.8 14.3 1.0
O A:ASP115 4.8 16.7 1.0
CB A:PHE17 4.9 11.8 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 07:23:29 2025

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