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Magnesium in PDB 4ecw: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 250 Sec

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 250 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 250 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 250 Sec, PDB code: 4ecw 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 / 1.90
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 / 21.5

Other elements in 4ecw:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 250 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 250 Sec (pdb code 4ecw). 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 250 Sec, PDB code: 4ecw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ecw

Go back to Magnesium Binding Sites List in 4ecw
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 250 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 250 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:14.0
occ:0.40
 OD2 A:ASP13 2.0 21.0 0.8
OP1 P:DA9 2.1 18.2 0.6
O A:HOH604 2.2 21.3 1.0
OE2 A:GLU116 2.2 28.4 1.0
O2A P:DTP504 2.2 18.0 0.4
O3' P:DT8 2.3 17.2 0.4
OD2 A:ASP115 2.3 15.4 1.0
O3' P:DT8 2.5 17.1 0.6
P P:DA9 2.8 20.8 0.6
OD1 A:ASP13 2.9 14.0 0.2
OD2 A:ASP13 3.0 20.1 0.2
CD A:GLU116 3.1 25.9 1.0
CG A:ASP13 3.2 16.0 0.8
CG A:ASP13 3.3 16.9 0.2
CG A:ASP115 3.3 14.8 1.0
C3' P:DT8 3.3 21.7 0.4
MG A:MG503 3.4 11.6 0.8
PA P:DTP504 3.4 17.2 0.4
CA A:CA502 3.4 11.9 0.1
OD1 A:ASP115 3.6 12.9 1.0
C3' P:DT8 3.7 23.1 0.6
OD1 A:ASP13 3.7 16.0 0.8
OP2 P:DA9 3.8 18.5 0.6
O1A P:DTP504 3.9 18.5 0.4
OE1 A:GLU116 3.9 23.5 1.0
CG A:GLU116 4.0 23.6 1.0
C4' P:DT8 4.0 23.1 0.6
O5' P:DA9 4.0 16.9 0.6
OG A:SER113 4.0 19.7 1.0
CB A:GLU116 4.1 22.1 1.0
O5' P:DTP504 4.1 16.5 0.4
C4' P:DT8 4.1 23.3 0.4
C5' P:DTP504 4.2 15.6 0.4
C5' P:DA9 4.2 14.7 0.6
C5' P:DT8 4.2 23.9 0.6
O A:HOH984 4.3 27.4 1.0
CB A:ASP13 4.4 10.4 0.8
O A:ASP115 4.5 11.9 1.0
C A:ASP115 4.5 12.9 1.0
C2' P:DT8 4.6 19.3 0.4
NZ A:LYS224 4.6 23.0 0.8
O3G P:DTP504 4.6 16.2 0.4
O7 P:DPO505 4.7 16.2 0.6
CB A:ASP13 4.7 11.0 0.2
CB A:ASP115 4.7 9.6 1.0
C5' P:DT8 4.7 24.1 0.4
N A:GLU116 4.7 12.0 1.0
O3A P:DTP504 4.7 17.1 0.4
C2' P:DT8 4.8 20.9 0.6
O1B P:DTP504 4.8 13.9 0.4
O1 P:DPO505 4.8 17.1 0.6
O2 P:DPO505 4.9 13.9 0.6

Magnesium binding site 2 out of 3 in 4ecw

Go back to Magnesium Binding Sites List in 4ecw
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 250 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 250 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:11.6
occ:0.85
 CA A:CA502 0.1 11.9 0.1
O1B P:DTP504 2.1 13.9 0.4
O3G P:DTP504 2.1 16.2 0.4
OD1 A:ASP13 2.2 16.0 0.8
O7 P:DPO505 2.2 16.2 0.6
O2A P:DTP504 2.2 18.0 0.4
O2 P:DPO505 2.2 13.9 0.6
OD1 A:ASP13 2.2 14.0 0.2
O A:MET14 2.3 11.5 1.0
OD1 A:ASP115 2.3 12.9 1.0
OP1 P:DA9 2.4 18.2 0.6
CG A:ASP13 2.9 16.0 0.8
OD2 A:ASP13 3.0 21.0 0.8
PB P:DTP504 3.2 14.2 0.4
P1 P:DPO505 3.2 14.2 0.6
CG A:ASP115 3.3 14.8 1.0
PA P:DTP504 3.3 17.2 0.4
MG A:MG501 3.4 14.0 0.4
PG P:DTP504 3.4 17.1 0.4
P2 P:DPO505 3.4 17.1 0.6
O3A P:DTP504 3.4 17.1 0.4
CG A:ASP13 3.5 16.9 0.2
O1 P:DPO505 3.5 17.1 0.6
C A:MET14 3.5 10.3 1.0
OD2 A:ASP115 3.6 15.4 1.0
O4 P:DPO505 3.7 14.4 0.6
O3B P:DTP504 3.8 14.5 0.4
P P:DA9 3.9 20.8 0.6
NZ A:LYS231 3.9 13.1 1.0
N A:MET14 4.0 10.4 1.0
C5' P:DTP504 4.0 15.6 0.4
O2G P:DTP504 4.0 15.6 0.4
O A:HOH984 4.0 27.4 1.0
O5 P:DPO505 4.1 15.6 0.6
O5' P:DTP504 4.2 16.5 0.4
OD2 A:ASP13 4.2 20.1 0.2
O A:HOH604 4.2 21.3 1.0
CA A:MET14 4.3 11.7 1.0
C A:ASP13 4.3 8.4 1.0
CB A:ASP13 4.3 10.4 0.8
C5' P:DA9 4.3 14.7 0.6
O5' P:DA9 4.4 16.9 0.6
CB A:ASP13 4.4 11.0 0.2
N A:ASP15 4.5 8.6 1.0
N A:CYS16 4.5 10.4 1.0
CA A:ASP15 4.6 11.9 1.0
O1A P:DTP504 4.6 18.5 0.4
O2B P:DTP504 4.6 14.0 0.4
O3 P:DPO505 4.6 13.9 0.6
O6 P:DPO505 4.6 17.1 0.6
CB A:ASP115 4.6 9.6 1.0
O1G P:DTP504 4.7 17.2 0.4
C A:ASP15 4.7 14.3 1.0
O A:ASP13 4.7 8.0 1.0
CA A:ASP13 4.7 11.7 0.2
CB A:MET14 4.7 9.0 1.0
N A:PHE17 4.8 8.5 1.0
OP2 P:DA9 4.8 18.5 0.6
CA A:ASP13 4.8 11.7 0.8
O3' P:DT8 4.8 17.1 0.6
MG P:MG506 4.8 26.5 0.6
CE A:LYS231 4.9 28.2 1.0
O A:ASP115 4.9 11.9 1.0
CB A:PHE17 4.9 8.0 1.0
O3' P:DT8 5.0 17.2 0.4

Magnesium binding site 3 out of 3 in 4ecw

Go back to Magnesium Binding Sites List in 4ecw
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 250 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 250 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg506

b:26.5
occ:0.60
 O1A P:DTP504 1.7 18.5 0.4
O3A P:DTP504 2.1 17.1 0.4
OP2 P:DA9 2.1 18.5 0.6
O A:HOH603 2.2 19.8 0.6
O1 P:DPO505 2.2 17.1 0.6
PA P:DTP504 2.3 17.2 0.4
O A:HOH672 2.6 20.9 1.0
O A:HOH984 2.7 27.4 1.0
NH1 A:ARG61 2.9 22.6 0.4
P P:DA9 3.1 20.8 0.6
O2A P:DTP504 3.4 18.0 0.4
OP1 P:DA9 3.4 18.2 0.6
O5' P:DTP504 3.5 16.5 0.4
P1 P:DPO505 3.6 14.2 0.6
PB P:DTP504 3.7 14.2 0.4
O5' P:DA9 3.8 16.9 0.6
O6 P:DPO505 3.8 17.1 0.6
O3G P:DTP504 3.9 16.2 0.4
O3B P:DTP504 3.9 14.5 0.4
CZ A:ARG61 3.9 20.9 0.4
O1G P:DTP504 3.9 17.2 0.4
O7 P:DPO505 4.0 16.2 0.6
O A:HOH602 4.0 16.7 0.6
O4 P:DPO505 4.0 14.4 0.6
NH2 A:ARG61 4.0 17.5 0.4
O A:HOH604 4.2 21.3 1.0
O A:HOH601 4.2 23.8 0.4
PG P:DTP504 4.2 17.1 0.4
P2 P:DPO505 4.2 17.1 0.6
O A:HOH676 4.3 23.2 1.0
O A:HOH775 4.3 29.6 1.0
O2B P:DTP504 4.4 14.0 0.4
O3' P:DT8 4.5 17.1 0.6
O3 P:DPO505 4.5 13.9 0.6
C2' P:DT8 4.5 19.3 0.4
O1B P:DTP504 4.6 13.9 0.4
O2 P:DPO505 4.6 13.9 0.6
C3' P:DT8 4.6 21.7 0.4
O A:HOH994 4.7 30.3 1.0
MG A:MG503 4.8 11.6 0.8
C5' P:DTP504 4.8 15.6 0.4
CA A:CA502 4.8 11.9 0.1
O3' P:DT8 4.9 17.2 0.4
C8 P:DTP504 5.0 18.4 0.4
C3' P:DT8 5.0 23.1 0.6

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 14:27:15 2024

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