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Magnesium in PDB 4ecu: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 200 Sec

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 200 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 200 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 200 Sec, PDB code: 4ecu 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) 30.10 / 1.95
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 / 21.7

Other elements in 4ecu:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 200 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 200 Sec (pdb code 4ecu). 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 200 Sec, PDB code: 4ecu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ecu

Go back to Magnesium Binding Sites List in 4ecu
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 200 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 200 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:15.2
occ:0.50
 OD2 A:ASP13 2.1 16.0 0.5
OP1 P:DA9 2.2 16.7 0.5
O2A P:DTP504 2.2 16.4 0.5
OD2 A:ASP115 2.2 14.3 1.0
O A:HOH604 2.2 20.4 1.0
OE2 A:GLU116 2.2 27.2 1.0
O3' P:DT8 2.3 16.9 0.5
O3' P:DT8 2.5 17.6 0.5
P P:DA9 2.8 19.3 0.5
OD1 A:ASP13 2.9 11.4 0.5
OD2 A:ASP13 3.0 23.1 0.5
CG A:ASP115 3.1 16.8 1.0
CG A:ASP13 3.2 12.9 0.5
CD A:GLU116 3.2 23.4 1.0
CG A:ASP13 3.3 15.0 0.5
C3' P:DT8 3.3 20.9 0.5
MG A:MG503 3.3 9.2 0.8
CA A:CA502 3.3 9.4 0.1
OD1 A:ASP115 3.4 15.0 1.0
PA P:DTP504 3.4 18.0 0.5
OD1 A:ASP13 3.7 13.6 0.5
C3' P:DT8 3.7 21.1 0.5
OP2 P:DA9 3.9 18.2 0.5
O1A P:DTP504 3.9 17.9 0.5
OE1 A:GLU116 3.9 21.8 1.0
O5' P:DA9 3.9 15.8 0.5
OG A:SER113 4.0 13.2 1.0
O5' P:DTP504 4.0 15.5 0.5
CG A:GLU116 4.0 23.1 1.0
C4' P:DT8 4.0 19.9 0.5
C5' P:DTP504 4.1 15.0 0.5
C5' P:DA9 4.1 14.5 0.5
CB A:GLU116 4.1 18.7 1.0
C4' P:DT8 4.2 20.0 0.5
O P:HOH201 4.2 18.6 0.5
O A:HOH843 4.2 24.8 1.0
C5' P:DT8 4.3 21.1 0.5
CB A:ASP13 4.4 10.5 0.5
C A:ASP115 4.5 15.3 1.0
O A:ASP115 4.5 12.0 1.0
CB A:ASP115 4.5 11.2 1.0
C2' P:DT8 4.5 18.1 0.5
O7 P:DPO505 4.6 14.6 0.5
O3G P:DTP504 4.6 14.7 0.5
CB A:ASP13 4.7 10.1 0.5
NZ A:LYS224 4.7 18.0 0.8
O3A P:DTP504 4.7 15.9 0.5
O1B P:DTP504 4.7 13.6 0.5
N A:GLU116 4.7 11.7 1.0
C2' P:DT8 4.8 18.0 0.5
C5' P:DT8 4.8 21.3 0.5
O2 P:DPO505 4.8 13.6 0.5
O1 P:DPO505 4.9 15.7 0.5
CA A:ASP115 4.9 12.0 1.0
MG P:MG506 5.0 22.3 0.5

Magnesium binding site 2 out of 3 in 4ecu

Go back to Magnesium Binding Sites List in 4ecu
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 200 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 200 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:9.2
occ:0.85
 CA A:CA502 0.0 9.4 0.1
O1B P:DTP504 2.1 13.6 0.5
O7 P:DPO505 2.1 14.6 0.5
O2A P:DTP504 2.1 16.4 0.5
O3G P:DTP504 2.2 14.7 0.5
OD1 A:ASP13 2.2 11.4 0.5
O2 P:DPO505 2.2 13.6 0.5
OD1 A:ASP13 2.2 13.6 0.5
OD1 A:ASP115 2.3 15.0 1.0
O A:MET14 2.3 7.8 1.0
OP1 P:DA9 2.4 16.7 0.5
CG A:ASP13 2.8 12.9 0.5
OD2 A:ASP13 2.9 16.0 0.5
PB P:DTP504 3.2 12.9 0.5
P1 P:DPO505 3.2 12.9 0.5
CG A:ASP115 3.3 16.8 1.0
MG A:MG501 3.3 15.2 0.5
PA P:DTP504 3.3 18.0 0.5
CG A:ASP13 3.4 15.0 0.5
O3A P:DTP504 3.4 15.9 0.5
P2 P:DPO505 3.4 14.9 0.5
PG P:DTP504 3.5 14.9 0.5
O1 P:DPO505 3.5 15.7 0.5
C A:MET14 3.5 8.2 1.0
OD2 A:ASP115 3.6 14.3 1.0
O4 P:DPO505 3.7 16.3 0.5
O3B P:DTP504 3.8 16.4 0.5
P P:DA9 3.9 19.3 0.5
O A:HOH843 3.9 24.8 1.0
C5' P:DTP504 3.9 15.0 0.5
NZ A:LYS231 3.9 11.3 1.0
N A:MET14 4.0 9.3 1.0
O5' P:DTP504 4.1 15.5 0.5
O A:HOH604 4.1 20.4 1.0
O2G P:DTP504 4.1 11.8 0.5
OD2 A:ASP13 4.1 23.1 0.5
O5 P:DPO505 4.2 11.8 0.5
CB A:ASP13 4.3 10.5 0.5
CA A:MET14 4.3 9.9 1.0
C A:ASP13 4.3 9.7 1.0
C5' P:DA9 4.3 14.5 0.5
O5' P:DA9 4.4 15.8 0.5
CB A:ASP13 4.5 10.1 0.5
N A:ASP15 4.5 6.6 1.0
N A:CYS16 4.6 9.9 1.0
O1A P:DTP504 4.6 17.9 0.5
CA A:ASP15 4.6 9.6 1.0
CB A:ASP115 4.6 11.2 1.0
O2B P:DTP504 4.6 12.5 0.5
O3 P:DPO505 4.6 12.2 0.5
O6 P:DPO505 4.6 15.7 0.5
MG P:MG506 4.6 22.3 0.5
O1G P:DTP504 4.7 15.7 0.5
O A:ASP13 4.7 9.9 1.0
C A:ASP15 4.7 14.2 1.0
N A:PHE17 4.8 7.6 1.0
CB A:MET14 4.8 7.8 1.0
CA A:ASP13 4.8 10.7 0.5
O3' P:DT8 4.8 17.6 0.5
CA A:ASP13 4.8 10.7 0.5
OP2 P:DA9 4.8 18.2 0.5
CB A:PHE17 4.8 7.5 1.0
CE A:LYS231 4.9 27.3 1.0
O3' P:DT8 4.9 16.9 0.5
O A:ASP115 4.9 12.0 1.0

Magnesium binding site 3 out of 3 in 4ecu

Go back to Magnesium Binding Sites List in 4ecu
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 200 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 200 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg506

b:22.3
occ:0.50
 O1A P:DTP504 1.8 17.9 0.5
O3A P:DTP504 2.0 15.9 0.5
O1 P:DPO505 2.1 15.7 0.5
OP2 P:DA9 2.2 18.2 0.5
PA P:DTP504 2.3 18.0 0.5
O A:HOH644 2.5 16.4 1.0
O A:HOH601 2.6 18.5 0.5
O A:HOH843 2.9 24.8 1.0
P P:DA9 3.2 19.3 0.5
NH2 A:ARG61 3.2 22.0 0.5
O2A P:DTP504 3.3 16.4 0.5
OP1 P:DA9 3.3 16.7 0.5
PB P:DTP504 3.5 12.9 0.5
P1 P:DPO505 3.6 12.9 0.5
O6 P:DPO505 3.6 15.7 0.5
O5' P:DTP504 3.6 15.5 0.5
O3B P:DTP504 3.7 16.4 0.5
O1G P:DTP504 3.7 15.7 0.5
O7 P:DPO505 3.7 14.6 0.5
O3G P:DTP504 3.7 14.7 0.5
NH1 A:ARG61 3.8 17.6 0.5
O4 P:DPO505 3.9 16.3 0.5
CZ A:ARG61 3.9 20.5 0.5
PG P:DTP504 4.0 14.9 0.5
P2 P:DPO505 4.0 14.9 0.5
O A:HOH602 4.0 17.2 0.5
O5' P:DA9 4.0 15.8 0.5
O A:HOH604 4.1 20.4 1.0
O A:HOH603 4.2 22.1 0.5
O A:HOH712 4.3 18.9 1.0
O2B P:DTP504 4.3 12.5 0.5
O1B P:DTP504 4.4 13.6 0.5
O3' P:DT8 4.5 17.6 0.5
O2 P:DPO505 4.5 13.6 0.5
O3 P:DPO505 4.5 12.2 0.5
MG A:MG503 4.6 9.2 0.8
CA A:CA502 4.7 9.4 0.1
C2' P:DT8 4.7 18.1 0.5
O A:HOH861 4.7 27.6 1.0
O A:HOH754 4.8 28.4 1.0
C3' P:DT8 4.8 20.9 0.5
C5' P:DTP504 4.9 15.0 0.5
O P:HOH212 4.9 30.9 1.0
O3' P:DT8 5.0 16.9 0.5
MG A:MG501 5.0 15.2 0.5

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 14:26:13 2024

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