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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: Mon Dec 14 13:53:17 2020

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