Atomistry » Calcium » PDB 5kaf-5klb » 5kfx
Atomistry »
  Calcium »
    PDB 5kaf-5klb »
      5kfx »

Calcium in PDB 5kfx: Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S

Enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S, PDB code: 5kfx 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) 19.98 / 1.52
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.480, 98.480, 82.200, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5kfx:

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S (pdb code 5kfx). 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 R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S, PDB code: 5kfx:

Calcium binding site 1 out of 1 in 5kfx

Go back to Calcium Binding Sites List in 5kfx
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S


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 R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:7.9
occ:0.20
 MG A:MG503 0.0 7.7 0.8
OD1 A:ASP13 2.1 11.5 0.4
O5 A:DPO508 2.1 10.8 0.3
O1 A:DPO508 2.1 8.8 0.3
OD1 A:ASP13 2.2 13.4 0.6
OD2 A:ASP115 2.2 10.4 1.0
O1A A:DTP507 2.2 12.5 0.7
O1B A:DTP507 2.3 9.5 0.7
O1G A:DTP507 2.3 11.0 0.7
O A:MET14 2.3 9.3 1.0
OP1 P:DA9 2.3 12.5 0.3
CG A:ASP13 2.9 12.2 0.6
OD2 A:ASP13 3.1 12.8 0.6
P1 A:DPO508 3.2 9.4 0.3
PB A:DTP507 3.2 9.6 0.7
CG A:ASP115 3.2 10.5 1.0
CG A:ASP13 3.3 12.7 0.4
PA A:DTP507 3.3 7.8 0.7
P2 A:DPO508 3.4 10.6 0.3
PG A:DTP507 3.4 10.7 0.7
C A:MET14 3.4 9.3 1.0
O2 A:DPO508 3.5 9.8 0.3
O3A A:DTP507 3.5 9.8 0.7
MG A:MG501 3.6 8.8 0.7
K A:K509 3.6 11.6 0.1
OD1 A:ASP115 3.6 11.5 1.0
O3B A:DTP507 3.7 9.3 0.7
O4 A:DPO508 3.7 9.4 0.3
P P:DA9 3.8 15.3 0.3
NZ A:LYS231 3.8 11.1 0.8
O A:HOH611 3.9 21.3 1.0
N A:MET14 3.9 8.5 1.0
OD2 A:ASP13 3.9 13.6 0.4
C5' A:DTP507 4.0 11.0 0.7
O2G A:DTP507 4.1 10.2 0.7
O7 A:DPO508 4.1 10.3 0.3
O5' A:DTP507 4.1 10.5 0.7
CA A:MET14 4.2 10.3 1.0
C5' P:DA9 4.3 9.2 0.3
NZ A:LYS231 4.3 16.2 0.2
C A:ASP13 4.3 8.0 1.0
O5' P:DA9 4.3 10.9 0.3
CB A:ASP13 4.3 9.7 0.6
O A:HOH712 4.4 17.5 1.0
CB A:ASP13 4.4 9.7 0.4
N A:ASP15 4.4 7.0 1.0
N A:CYS16 4.5 8.3 1.0
O2A A:DTP507 4.5 11.5 0.7
O3 A:DPO508 4.5 10.1 0.3
CB A:ASP115 4.6 9.1 1.0
O6 A:DPO508 4.6 12.1 0.3
CA A:ASP15 4.6 7.2 1.0
OP2 P:DA9 4.6 13.3 0.3
O2B A:DTP507 4.6 10.2 0.7
O A:ASP13 4.6 9.9 1.0
CB A:MET14 4.7 10.0 1.0
O3G A:DTP507 4.7 11.9 0.7
C A:ASP15 4.7 8.6 1.0
CE A:LYS231 4.7 18.8 0.8
MG P:MG101 4.7 16.8 0.3
CA A:ASP13 4.8 10.6 0.4
CA A:ASP13 4.8 10.6 0.6
N A:PHE17 4.8 8.6 1.0
O3' P:DT8 4.8 13.2 0.3
CB A:PHE17 4.9 8.2 1.0
O A:ASP115 4.9 10.6 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: Mon Jul 15 06:52:25 2024

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy