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Magnesium in PDB 4ect: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 140 Sec

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 140 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 140 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 140 Sec, PDB code: 4ect 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) 28.52 / 1.79
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 (%) 16.6 / 20.8

Other elements in 4ect:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 140 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 140 Sec (pdb code 4ect). 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 140 Sec, PDB code: 4ect:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ect

Go back to Magnesium Binding Sites List in 4ect
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 140 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 140 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.9
occ:0.60
 OD2 A:ASP13 2.1 24.4 0.8
OP1 P:DA9 2.1 16.8 0.4
O2A P:DTP504 2.1 17.0 0.6
OE2 A:GLU116 2.2 31.8 1.0
O A:HOH603 2.3 21.5 1.0
OD2 A:ASP115 2.3 15.0 1.0
O3' P:DT8 2.3 16.5 0.6
O3' P:DT8 2.5 17.3 0.4
OD2 A:ASP13 2.8 12.9 0.2
P P:DA9 2.8 16.2 0.4
OD1 A:ASP13 3.0 20.3 0.2
CG A:ASP13 3.2 15.3 0.8
CG A:ASP115 3.2 14.2 1.0
CG A:ASP13 3.2 17.0 0.2
CD A:GLU116 3.2 31.6 1.0
C3' P:DT8 3.3 19.8 0.6
MG A:MG503 3.3 8.0 0.8
CA A:CA502 3.3 8.3 0.1
PA P:DTP504 3.4 16.7 0.6
OD1 A:ASP115 3.4 12.1 1.0
OD1 A:ASP13 3.6 20.7 0.8
C3' P:DT8 3.7 19.3 0.4
OP2 P:DA9 3.8 16.2 0.4
O1A P:DTP504 3.9 15.7 0.6
O5' P:DTP504 3.9 14.5 0.6
OG A:SER113 4.0 18.1 1.0
O5' P:DA9 4.0 15.3 0.4
OE1 A:GLU116 4.0 30.7 1.0
C4' P:DT8 4.0 19.2 0.4
C5' P:DTP504 4.1 13.8 0.6
CB A:GLU116 4.1 22.9 1.0
CG A:GLU116 4.1 24.9 1.0
C4' P:DT8 4.1 18.8 0.6
C5' P:DA9 4.1 13.4 0.4
C5' P:DT8 4.2 21.8 0.4
O P:HOH201 4.3 22.1 0.6
O A:HOH898 4.4 29.8 1.0
CB A:ASP13 4.4 11.8 0.8
O A:ASP115 4.5 11.6 1.0
C A:ASP115 4.5 14.0 1.0
C2' P:DT8 4.6 18.4 0.6
O3G P:DTP504 4.6 12.0 0.6
O7 P:DPO505 4.6 12.1 0.4
CB A:ASP115 4.6 11.3 1.0
C5' P:DT8 4.6 22.4 0.6
CB A:ASP13 4.7 11.3 0.2
O3A P:DTP504 4.7 15.4 0.6
O1B P:DTP504 4.7 12.5 0.6
NZ A:LYS224 4.7 25.7 0.8
O2 P:DPO505 4.7 12.5 0.4
C2' P:DT8 4.8 15.0 0.4
O1 P:DPO505 4.8 15.3 0.4
N A:GLU116 4.8 11.7 1.0

Magnesium binding site 2 out of 3 in 4ect

Go back to Magnesium Binding Sites List in 4ect
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 140 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 140 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:8.0
occ:0.85
 CA A:CA502 0.0 8.3 0.1
O1B P:DTP504 2.1 12.5 0.6
O2 P:DPO505 2.1 12.5 0.4
O3G P:DTP504 2.1 12.0 0.6
O2A P:DTP504 2.2 17.0 0.6
O7 P:DPO505 2.2 12.1 0.4
OD1 A:ASP115 2.3 12.1 1.0
OD2 A:ASP13 2.3 12.9 0.2
OD1 A:ASP13 2.3 20.7 0.8
O A:MET14 2.3 10.6 1.0
OP1 P:DA9 2.4 16.8 0.4
OD2 A:ASP13 2.9 24.4 0.8
CG A:ASP13 2.9 15.3 0.8
PB P:DTP504 3.2 13.6 0.6
P1 P:DPO505 3.2 13.6 0.4
MG A:MG501 3.3 16.9 0.6
CG A:ASP115 3.3 14.2 1.0
PA P:DTP504 3.3 16.7 0.6
PG P:DTP504 3.4 13.6 0.6
P2 P:DPO505 3.4 13.5 0.4
O3A P:DTP504 3.5 15.4 0.6
O1 P:DPO505 3.5 15.3 0.4
CG A:ASP13 3.5 17.0 0.2
C A:MET14 3.5 11.3 1.0
OD2 A:ASP115 3.7 15.0 1.0
O4 P:DPO505 3.7 12.2 0.4
O3B P:DTP504 3.7 12.2 0.6
P P:DA9 3.9 16.2 0.4
C5' P:DTP504 4.0 13.8 0.6
NZ A:LYS231 4.0 17.3 1.0
O2G P:DTP504 4.1 11.3 0.6
N A:MET14 4.1 9.3 1.0
O5 P:DPO505 4.1 11.3 0.4
O5' P:DTP504 4.1 14.5 0.6
O A:HOH898 4.2 29.8 1.0
OD1 A:ASP13 4.3 20.3 0.2
O A:HOH603 4.3 21.5 1.0
C5' P:DA9 4.3 13.4 0.4
CA A:MET14 4.3 10.5 1.0
C A:ASP13 4.3 7.8 1.0
CB A:ASP13 4.3 11.8 0.8
O5' P:DA9 4.4 15.3 0.4
CB A:ASP13 4.5 11.3 0.2
N A:ASP15 4.5 10.2 1.0
O3 P:DPO505 4.5 12.6 0.4
O1A P:DTP504 4.6 15.7 0.6
N A:CYS16 4.6 10.4 1.0
O2B P:DTP504 4.6 12.6 0.6
O6 P:DPO505 4.6 15.0 0.4
CA A:ASP15 4.6 11.0 1.0
CB A:ASP115 4.6 11.3 1.0
O1G P:DTP504 4.6 15.0 0.6
C A:ASP15 4.7 11.6 1.0
O A:ASP13 4.7 10.0 1.0
N A:PHE17 4.7 9.1 1.0
CB A:MET14 4.7 10.7 1.0
O3' P:DT8 4.8 17.3 0.4
CA A:ASP13 4.8 11.7 0.2
CE A:LYS231 4.8 35.1 1.0
OP2 P:DA9 4.8 16.2 0.4
MG P:MG506 4.9 23.9 0.4
O A:ASP115 4.9 11.6 1.0
CA A:ASP13 4.9 11.8 0.8
CB A:PHE17 4.9 6.8 1.0
O3' P:DT8 4.9 16.5 0.6

Magnesium binding site 3 out of 3 in 4ect

Go back to Magnesium Binding Sites List in 4ect
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 140 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 140 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg506

b:23.9
occ:0.40
 O1A P:DTP504 1.6 15.7 0.6
O3A P:DTP504 2.1 15.4 0.6
O1 P:DPO505 2.1 15.3 0.4
OP2 P:DA9 2.1 16.2 0.4
O A:HOH601 2.2 18.4 0.4
PA P:DTP504 2.3 16.7 0.6
O A:HOH1033 2.4 33.2 1.0
NH1 A:ARG61 2.8 24.2 0.6
O A:HOH652 2.8 18.4 1.0
O A:HOH898 3.0 29.8 1.0
P P:DA9 3.1 16.2 0.4
OP1 P:DA9 3.4 16.8 0.4
O2A P:DTP504 3.4 17.0 0.6
O5' P:DTP504 3.5 14.5 0.6
P1 P:DPO505 3.6 13.6 0.4
PB P:DTP504 3.6 13.6 0.6
NH2 A:ARG61 3.7 15.4 0.6
CZ A:ARG61 3.7 21.7 0.6
O5' P:DA9 3.8 15.3 0.4
O A:HOH1067 3.8 41.2 1.0
O A:HOH602 3.8 14.8 0.4
O6 P:DPO505 3.9 15.0 0.4
O3B P:DTP504 3.9 12.2 0.6
O1G P:DTP504 3.9 15.0 0.6
O4 P:DPO505 3.9 12.2 0.4
O3G P:DTP504 4.0 12.0 0.6
O7 P:DPO505 4.0 12.1 0.4
O A:HOH667 4.0 18.5 1.0
O A:HOH797 4.0 29.6 1.0
PG P:DTP504 4.2 13.6 0.6
P2 P:DPO505 4.2 13.5 0.4
O A:HOH603 4.3 21.5 1.0
O2B P:DTP504 4.3 12.6 0.6
O3 P:DPO505 4.4 12.6 0.4
O3' P:DT8 4.5 17.3 0.4
O2 P:DPO505 4.5 12.5 0.4
O1B P:DTP504 4.6 12.5 0.6
C2' P:DT8 4.6 18.4 0.6
C3' P:DT8 4.7 19.8 0.6
O P:HOH216 4.7 33.9 1.0
C5' P:DTP504 4.8 13.8 0.6
C8 P:DTP504 4.8 17.0 0.6
CA A:CA502 4.8 8.3 0.1
MG A:MG503 4.9 8.0 0.8
NE A:ARG61 4.9 26.6 0.4
O3' P:DT8 4.9 16.5 0.6
NE A:ARG61 5.0 24.4 0.6
C3' P:DT8 5.0 19.3 0.4

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 14:26:10 2024

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