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Magnesium in PDB 4ecx: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 300 Sec

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 300 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 300 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 300 Sec, PDB code: 4ecx 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 / 1.74
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 (%) 17.8 / 22.5

Other elements in 4ecx:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 300 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 300 Sec (pdb code 4ecx). 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 300 Sec, PDB code: 4ecx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ecx

Go back to Magnesium Binding Sites List in 4ecx
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 300 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 300 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.5
occ:0.30
 OP1 P:DA9 2.0 20.2 0.7
OD2 A:ASP13 2.0 22.3 0.8
O2A P:DTP504 2.1 18.9 0.3
OE2 A:GLU116 2.1 32.0 1.0
O3' P:DT8 2.3 17.0 0.3
OD2 A:ASP115 2.3 16.4 1.0
O A:HOH603 2.3 20.7 1.0
O3' P:DT8 2.4 19.4 0.7
P P:DA9 2.7 20.6 0.7
OD2 A:ASP13 2.9 21.6 0.2
OD1 A:ASP13 2.9 15.0 0.2
C3' P:DT8 3.2 20.2 0.3
CG A:ASP13 3.2 17.6 0.8
CD A:GLU116 3.2 26.8 1.0
CG A:ASP115 3.2 15.2 1.0
CG A:ASP13 3.2 17.9 0.2
PA P:DTP504 3.3 14.6 0.3
CA A:CA502 3.3 11.7 0.1
MG A:MG503 3.3 11.3 0.8
OD1 A:ASP115 3.4 12.9 1.0
OD1 A:ASP13 3.6 22.3 0.8
C3' P:DT8 3.7 22.4 0.7
OP2 P:DA9 3.7 20.1 0.7
O1A P:DTP504 3.8 19.0 0.3
O5' P:DA9 3.9 16.2 0.7
OE1 A:GLU116 3.9 29.8 1.0
O5' P:DTP504 4.0 15.0 0.3
C4' P:DT8 4.0 21.4 0.7
C4' P:DT8 4.0 21.3 0.3
C5' P:DTP504 4.1 14.2 0.3
OG A:SER113 4.1 17.6 1.0
CG A:GLU116 4.1 21.4 1.0
C5' P:DA9 4.1 13.7 0.7
CB A:GLU116 4.2 19.9 1.0
O A:HOH888 4.2 27.9 1.0
C5' P:DT8 4.2 23.9 0.7
C2' P:DT8 4.4 19.2 0.3
CB A:ASP13 4.4 12.5 0.8
O7 P:DPO505 4.6 15.4 0.7
O3G P:DTP504 4.6 15.4 0.3
C A:ASP115 4.6 14.4 1.0
O A:ASP115 4.6 12.0 1.0
CB A:ASP115 4.6 11.2 1.0
NZ A:LYS224 4.6 16.2 0.2
O3A P:DTP504 4.6 17.2 0.3
C5' P:DT8 4.6 24.2 0.3
CB A:ASP13 4.6 12.7 0.2
O1 P:DPO505 4.7 17.1 0.7
O1B P:DTP504 4.7 12.8 0.3
O2 P:DPO505 4.7 12.8 0.7
C2' P:DT8 4.8 19.1 0.7
N A:GLU116 4.8 12.0 1.0
MG P:MG506 5.0 30.2 0.7
CA A:ASP115 5.0 11.7 1.0

Magnesium binding site 2 out of 3 in 4ecx

Go back to Magnesium Binding Sites List in 4ecx
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 300 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 300 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:11.3
occ:0.85
 CA A:CA502 0.0 11.7 0.1
O1B P:DTP504 2.1 12.8 0.3
O2 P:DPO505 2.1 12.8 0.7
O2A P:DTP504 2.1 18.9 0.3
O3G P:DTP504 2.1 15.4 0.3
O7 P:DPO505 2.1 15.4 0.7
OD1 A:ASP13 2.2 15.0 0.2
OD1 A:ASP13 2.2 22.3 0.8
O A:MET14 2.3 11.7 1.0
OD1 A:ASP115 2.3 12.9 1.0
OP1 P:DA9 2.4 20.2 0.7
CG A:ASP13 3.0 17.6 0.8
OD2 A:ASP13 3.1 22.3 0.8
PB P:DTP504 3.2 15.0 0.3
P1 P:DPO505 3.2 15.0 0.7
CG A:ASP115 3.3 15.2 1.0
PA P:DTP504 3.3 14.6 0.3
MG A:MG501 3.3 13.5 0.3
O3A P:DTP504 3.4 17.2 0.3
P2 P:DPO505 3.4 15.1 0.7
PG P:DTP504 3.4 15.1 0.3
C A:MET14 3.4 13.1 1.0
CG A:ASP13 3.4 17.9 0.2
O1 P:DPO505 3.5 17.1 0.7
OD2 A:ASP115 3.6 16.4 1.0
O4 P:DPO505 3.7 16.1 0.7
O3B P:DTP504 3.7 16.0 0.3
P P:DA9 3.9 20.6 0.7
NZ A:LYS231 3.9 12.9 1.0
N A:MET14 4.0 10.2 1.0
C5' P:DTP504 4.0 14.2 0.3
O2G P:DTP504 4.0 15.5 0.3
O5 P:DPO505 4.1 15.5 0.7
O5' P:DTP504 4.1 15.0 0.3
O A:HOH888 4.1 27.9 1.0
OD2 A:ASP13 4.1 21.6 0.2
CA A:MET14 4.2 11.0 1.0
C5' P:DA9 4.2 13.7 0.7
C A:ASP13 4.3 9.9 1.0
O A:HOH603 4.3 20.7 1.0
CB A:ASP13 4.4 12.5 0.8
O5' P:DA9 4.4 16.2 0.7
N A:ASP15 4.4 9.1 1.0
N A:CYS16 4.5 12.1 1.0
CB A:ASP13 4.5 12.7 0.2
O1A P:DTP504 4.5 19.0 0.3
CA A:ASP15 4.5 10.5 1.0
O2B P:DTP504 4.5 15.4 0.3
CB A:ASP115 4.5 11.2 1.0
O3 P:DPO505 4.6 15.4 0.7
O6 P:DPO505 4.6 16.5 0.7
O1G P:DTP504 4.6 16.7 0.3
C A:ASP15 4.6 12.2 1.0
CB A:MET14 4.7 10.2 1.0
N A:PHE17 4.7 9.9 1.0
O A:ASP13 4.7 10.4 1.0
OP2 P:DA9 4.8 20.1 0.7
CA A:ASP13 4.8 12.2 0.2
CA A:ASP13 4.8 12.2 0.8
O3' P:DT8 4.8 19.4 0.7
CE A:LYS231 4.8 27.0 1.0
O A:ASP115 4.9 12.0 1.0
CB A:PHE17 4.9 8.6 1.0
MG P:MG506 4.9 30.2 0.7
O3' P:DT8 5.0 17.0 0.3

Magnesium binding site 3 out of 3 in 4ecx

Go back to Magnesium Binding Sites List in 4ecx
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 300 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 300 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg506

b:30.2
occ:0.70
 O1A P:DTP504 1.6 19.0 0.3
OP2 P:DA9 2.0 20.1 0.7
O A:HOH602 2.1 19.4 0.7
O3A P:DTP504 2.1 17.2 0.3
O A:HOH943 2.1 25.7 0.5
O1 P:DPO505 2.2 17.1 0.7
O A:HOH888 2.3 27.9 1.0
PA P:DTP504 2.3 14.6 0.3
O A:HOH665 2.7 20.8 1.0
NH2 A:ARG61 2.9 23.5 0.3
P P:DA9 3.1 20.6 0.7
OP1 P:DA9 3.4 20.2 0.7
O5' P:DTP504 3.4 15.0 0.3
O2A P:DTP504 3.4 18.9 0.3
NH1 A:ARG61 3.6 17.8 0.3
P1 P:DPO505 3.7 15.0 0.7
CZ A:ARG61 3.7 20.3 0.3
PB P:DTP504 3.7 15.0 0.3
NH2 A:ARG61 3.7 33.2 0.7
O5' P:DA9 3.8 16.2 0.7
O A:HOH601 3.9 17.7 0.7
O6 P:DPO505 3.9 16.5 0.7
O3G P:DTP504 4.0 15.4 0.3
O7 P:DPO505 4.1 15.4 0.7
O3B P:DTP504 4.1 16.0 0.3
O4 P:DPO505 4.1 16.1 0.7
O1G P:DTP504 4.1 16.7 0.3
O A:HOH670 4.1 20.8 1.0
O A:HOH733 4.1 26.4 1.0
O A:HOH603 4.2 20.7 1.0
P2 P:DPO505 4.3 15.1 0.7
O2B P:DTP504 4.3 15.4 0.3
PG P:DTP504 4.3 15.1 0.3
C2' P:DT8 4.4 19.2 0.3
O3' P:DT8 4.4 19.4 0.7
O3 P:DPO505 4.5 15.4 0.7
O P:HOH213 4.6 32.1 1.0
C3' P:DT8 4.6 20.2 0.3
O2 P:DPO505 4.6 12.8 0.7
O1B P:DTP504 4.6 12.8 0.3
C5' P:DTP504 4.8 14.2 0.3
C8 P:DTP504 4.8 17.9 0.3
MG A:MG503 4.9 11.3 0.8
CA A:CA502 4.9 11.7 0.1
C3' P:DT8 4.9 22.4 0.7
O3' P:DT8 4.9 17.0 0.3
O A:HOH994 4.9 33.0 1.0
NE A:ARG61 4.9 20.1 0.3
MG A:MG501 5.0 13.5 0.3
CZ A:ARG61 5.0 32.4 0.7

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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