Atomistry » Magnesium » PDB 4e7z-4egh » 4ecv
Atomistry »
  Magnesium »
    PDB 4e7z-4egh »
      4ecv »

Magnesium in PDB 4ecv: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec, PDB code: 4ecv was solved by T.Nakamura, Y.Zhao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.01 / 1.52
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.786, 98.786, 82.431, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.5

Other elements in 4ecv:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec (pdb code 4ecv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec, PDB code: 4ecv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ecv

Go back to Magnesium Binding Sites List in 4ecv
Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:12.9
occ:0.40
 OD2 A:ASP13 2.0 24.8 0.8
OP1 P:DA9 2.0 16.7 0.6
OE2 A:GLU116 2.1 35.2 1.0
O A:HOH604 2.2 27.3 1.0
O3' P:DT8 2.3 19.6 0.4
O2A P:DTP504 2.3 20.8 0.4
OD2 A:ASP115 2.4 17.4 1.0
O3' P:DT8 2.5 20.5 0.6
OD2 A:ASP13 2.7 27.2 0.2
P P:DA9 2.7 19.0 0.6
CD A:GLU116 3.1 35.7 1.0
OD1 A:ASP13 3.2 15.4 0.2
C3' P:DT8 3.2 18.6 0.4
CG A:ASP13 3.2 18.7 0.8
CG A:ASP13 3.2 20.1 0.2
CG A:ASP115 3.3 13.6 1.0
MG A:MG503 3.5 8.9 0.8
PA P:DTP504 3.5 13.7 0.4
CA A:CA502 3.5 10.3 0.1
OD1 A:ASP115 3.6 15.2 1.0
C3' P:DT8 3.7 15.4 0.6
OP2 P:DA9 3.7 22.8 0.6
OD1 A:ASP13 3.8 29.5 0.8
OE1 A:GLU116 3.9 30.7 1.0
O1A P:DTP504 3.9 14.4 0.4
OG A:SER113 3.9 19.5 1.0
O5' P:DA9 4.0 13.8 0.6
C4' P:DT8 4.0 18.2 0.6
CG A:GLU116 4.0 24.1 1.0
C4' P:DT8 4.0 19.6 0.4
CB A:GLU116 4.0 24.3 1.0
O5' P:DTP504 4.1 17.6 0.4
C5' P:DT8 4.1 20.7 0.6
C5' P:DA9 4.2 13.9 0.6
C5' P:DTP504 4.2 18.0 0.4
O A:HOH889 4.3 29.7 1.0
CB A:ASP13 4.4 11.6 0.8
NZ A:LYS224 4.5 24.2 0.5
C2' P:DT8 4.5 13.3 0.4
C5' P:DT8 4.6 21.8 0.4
O A:ASP115 4.6 13.9 1.0
C A:ASP115 4.6 13.5 1.0
CB A:ASP13 4.6 9.9 0.2
CB A:ASP115 4.7 13.6 1.0
O7 P:DPO505 4.7 16.0 0.6
N A:GLU116 4.8 11.5 1.0
O3G P:DTP504 4.8 22.5 0.4
C2' P:DT8 4.8 14.4 0.6
O3A P:DTP504 4.9 21.4 0.4
O1B P:DTP504 4.9 18.7 0.4
O2 P:DPO505 4.9 14.1 0.6

Magnesium binding site 2 out of 3 in 4ecv

Go back to Magnesium Binding Sites List in 4ecv
Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:8.9
occ:0.85
 CA A:CA502 0.0 10.3 0.1
O2A P:DTP504 2.1 20.8 0.4
O1B P:DTP504 2.1 18.7 0.4
O2 P:DPO505 2.2 14.1 0.6
O3G P:DTP504 2.2 22.5 0.4
O7 P:DPO505 2.2 16.0 0.6
OD1 A:ASP13 2.2 15.4 0.2
OD1 A:ASP13 2.2 29.5 0.8
O A:MET14 2.3 13.8 1.0
OD1 A:ASP115 2.3 15.2 1.0
OP1 P:DA9 2.4 16.7 0.6
CG A:ASP13 2.9 18.7 0.8
OD2 A:ASP13 3.0 24.8 0.8
PB P:DTP504 3.2 20.6 0.4
PA P:DTP504 3.3 13.7 0.4
P1 P:DPO505 3.3 13.6 0.6
CG A:ASP115 3.3 13.6 1.0
CG A:ASP13 3.4 20.1 0.2
C A:MET14 3.4 11.0 1.0
MG A:MG501 3.5 12.9 0.4
O3A P:DTP504 3.5 21.4 0.4
P2 P:DPO505 3.5 25.1 0.6
PG P:DTP504 3.5 14.5 0.4
O1 P:DPO505 3.6 14.6 0.6
OD2 A:ASP115 3.6 17.4 1.0
O4 P:DPO505 3.7 13.8 0.6
O3B P:DTP504 3.8 21.0 0.4
P P:DA9 3.8 19.0 0.6
C5' P:DTP504 3.9 18.0 0.4
N A:MET14 4.0 10.2 1.0
NZ A:LYS231 4.0 13.0 0.8
O A:HOH889 4.0 29.7 1.0
OD2 A:ASP13 4.1 27.2 0.2
O5' P:DTP504 4.1 17.6 0.4
O5 P:DPO505 4.2 14.8 0.6
O2G P:DTP504 4.2 21.3 0.4
CA A:MET14 4.2 9.8 1.0
C5' P:DA9 4.2 13.9 0.6
O A:HOH604 4.2 27.3 1.0
C A:ASP13 4.3 10.8 1.0
O5' P:DA9 4.3 13.8 0.6
CB A:ASP13 4.3 11.6 0.8
NZ A:LYS231 4.4 10.0 0.2
N A:ASP15 4.5 8.9 1.0
O1A P:DTP504 4.5 14.4 0.4
CB A:ASP13 4.5 9.9 0.2
N A:CYS16 4.5 11.6 1.0
CA A:ASP15 4.6 10.2 1.0
O2B P:DTP504 4.6 14.2 0.4
O3 P:DPO505 4.6 14.0 0.6
CB A:ASP115 4.6 13.6 1.0
OP2 P:DA9 4.7 22.8 0.6
O1G P:DTP504 4.7 19.9 0.4
O6 P:DPO505 4.7 15.6 0.6
CB A:MET14 4.7 13.1 1.0
C A:ASP15 4.7 9.3 1.0
O A:ASP13 4.7 13.5 1.0
N A:PHE17 4.7 10.0 1.0
CA A:ASP13 4.8 11.9 0.2
CA A:ASP13 4.8 12.7 0.8
O3' P:DT8 4.8 20.5 0.6
MG P:MG506 4.8 24.0 0.6
CB A:PHE17 4.9 10.3 1.0
O A:ASP115 4.9 13.9 1.0
O3' P:DT8 4.9 19.6 0.4
CE A:LYS231 5.0 30.0 0.8

Magnesium binding site 3 out of 3 in 4ecv

Go back to Magnesium Binding Sites List in 4ecv
Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 230 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg506

b:24.0
occ:0.60
 O1A P:DTP504 1.7 14.4 0.4
O3A P:DTP504 2.0 21.4 0.4
O1 P:DPO505 2.0 14.6 0.6
O A:HOH602 2.1 17.1 0.6
O A:HOH841 2.2 33.0 1.0
OP2 P:DA9 2.2 22.8 0.6
PA P:DTP504 2.3 13.7 0.4
O A:HOH889 2.6 29.7 1.0
O A:HOH653 2.6 23.5 1.0
P P:DA9 3.3 19.0 0.6
O2A P:DTP504 3.4 20.8 0.4
P1 P:DPO505 3.5 13.6 0.6
O5' P:DTP504 3.5 17.6 0.4
PB P:DTP504 3.5 20.6 0.4
NH1 A:ARG61 3.6 36.3 0.4
OP1 P:DA9 3.6 16.7 0.6
NH2 A:ARG61 3.8 24.7 0.4
O A:HOH603 3.8 18.0 0.6
O6 P:DPO505 3.8 15.6 0.6
O3B P:DTP504 3.8 21.0 0.4
O5' P:DA9 3.9 13.8 0.6
O4 P:DPO505 3.9 13.8 0.6
O7 P:DPO505 3.9 16.0 0.6
O1G P:DTP504 3.9 19.9 0.4
O3G P:DTP504 4.0 22.5 0.4
CZ A:ARG61 4.0 30.5 0.4
O A:HOH706 4.1 25.4 1.0
P2 P:DPO505 4.2 25.1 0.6
PG P:DTP504 4.2 14.5 0.4
O2B P:DTP504 4.2 14.2 0.4
O A:HOH604 4.3 27.3 1.0
O3 P:DPO505 4.3 14.0 0.6
O A:HOH867 4.4 38.0 1.0
O A:HOH601 4.4 25.8 0.4
O2 P:DPO505 4.5 14.1 0.6
O1B P:DTP504 4.5 18.7 0.4
O P:HOH212 4.5 28.9 1.0
O3' P:DT8 4.6 20.5 0.6
C2' P:DT8 4.7 13.3 0.4
C3' P:DT8 4.8 18.6 0.4
C5' P:DTP504 4.8 18.0 0.4
MG A:MG503 4.8 8.9 0.8
CA A:CA502 4.8 10.3 0.1
C8 P:DTP504 4.9 15.7 0.4
O A:HOH939 4.9 35.1 1.0

Reference:

T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, W.Yang. Watching Dna Polymerase Eta Make A Phosphodiester Bond Nature V. 487 196 2012.
ISSN: ISSN 0028-0836
PubMed: 22785315
DOI: 10.1038/NATURE11181
Page generated: Fri Aug 16 14:26:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy