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Calcium in PDB 5kfi: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S, PDB code: 5kfi 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 / 1.65
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.530, 98.530, 81.840, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.1

Other elements in 5kfi:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S (pdb code 5kfi). 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: Reaction with 10 Mm MN2+ For 120S, PDB code: 5kfi:

Calcium binding site 1 out of 1 in 5kfi

Go back to Calcium Binding Sites List in 5kfi
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S


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: Reaction with 10 Mm MN2+ For 120S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:12.7
occ:0.25
 MN A:MN503 0.1 12.7 0.8
O5 A:DPO508 2.0 11.8 0.4
O1A A:DTP507 2.2 14.4 0.6
O1B A:DTP507 2.2 10.6 0.6
OD1 A:ASP13 2.2 12.3 1.0
OD2 A:ASP115 2.3 10.8 1.0
O1G A:DTP507 2.3 11.9 0.6
O1 A:DPO508 2.3 10.9 0.4
O A:MET14 2.4 11.7 1.0
OP1 P:DA9 2.5 14.3 0.4
CG A:ASP13 3.1 13.6 1.0
PB A:DTP507 3.2 12.0 0.6
P2 A:DPO508 3.3 11.7 0.4
OD2 A:ASP13 3.3 14.8 1.0
P1 A:DPO508 3.3 11.8 0.4
PA A:DTP507 3.3 10.2 0.6
CG A:ASP115 3.4 12.1 1.0
O3A A:DTP507 3.4 10.8 0.6
PG A:DTP507 3.4 11.3 0.6
C A:MET14 3.5 9.6 1.0
MN A:MN501 3.5 12.2 1.0
O2 A:DPO508 3.7 11.3 0.4
O3B A:DTP507 3.7 11.0 0.6
O4 A:DPO508 3.7 11.1 0.4
OD1 A:ASP115 3.8 12.9 1.0
P P:DA9 3.9 11.3 0.4
O7 A:DPO508 3.9 11.4 0.4
O2G A:DTP507 4.0 10.0 0.6
O A:HOH796 4.0 13.2 0.6
C5' A:DTP507 4.0 12.4 0.6
N A:MET14 4.0 8.7 1.0
NZ A:LYS231 4.0 12.6 0.5
O A:HOH796 4.1 11.2 0.4
O5' A:DTP507 4.2 9.9 0.6
CA A:MET14 4.3 10.7 1.0
C5' P:DA9 4.3 11.7 0.4
O A:HOH780 4.3 14.0 1.0
C A:ASP13 4.3 9.2 1.0
O5' P:DA9 4.4 11.5 0.4
CB A:ASP13 4.4 11.3 1.0
N A:ASP15 4.5 8.4 1.0
O6 A:DPO508 4.5 11.4 0.4
N A:CYS16 4.5 9.0 1.0
O2B A:DTP507 4.5 10.8 0.6
O2A A:DTP507 4.6 13.4 0.6
CA A:ASP15 4.6 7.7 1.0
CB A:ASP115 4.6 10.0 1.0
OP2 P:DA9 4.7 14.9 0.4
O3 A:DPO508 4.7 10.8 0.4
CE A:LYS231 4.7 14.8 0.5
O A:ASP13 4.7 9.6 1.0
O3G A:DTP507 4.7 11.3 0.6
C A:ASP15 4.8 10.3 1.0
N A:PHE17 4.8 11.5 1.0
CA A:ASP13 4.9 9.3 1.0
O3' P:DT8 4.9 12.4 0.4
CB A:MET14 4.9 13.9 1.0
MN P:MN101 4.9 16.5 0.4
CB A:PHE17 5.0 9.2 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 07:23:13 2025

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