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Magnesium in PDB 5kg4: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S, PDB code: 5kg4 was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 1.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.270, 98.270, 82.050, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.3

Other elements in 5kg4:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S (pdb code 5kg4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S, PDB code: 5kg4:

Magnesium binding site 1 out of 1 in 5kg4

Go back to Magnesium Binding Sites List in 5kg4
Magnesium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S


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 First with 1 Mm MN2+ For 1800S Then with 10 Mm MG2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:18.5
occ:0.30
 O2A A:DTP506 1.9 14.2 0.7
O P:HOH222 2.0 21.5 0.3
OP2 P:DA9 2.2 15.5 0.3
O2 A:DPO507 2.4 12.3 0.3
O A:HOH620 2.4 27.2 1.0
NH1 A:ARG61 2.4 23.9 0.7
O3A A:DTP506 2.5 11.9 0.7
O A:HOH760 2.5 16.7 0.3
O A:HOH638 2.6 18.7 1.0
PA A:DTP506 2.7 10.5 0.7
P P:DA9 3.5 15.0 0.3
CZ A:ARG61 3.5 21.6 0.7
NH2 A:ARG61 3.7 17.1 0.7
O A:HOH694 3.8 29.4 0.6
O1A A:DTP506 3.8 13.1 0.7
P1 A:DPO507 3.8 12.5 0.3
O5' A:DTP506 3.8 11.0 0.7
O A:HOH781 3.9 17.0 0.3
PB A:DTP506 3.9 11.4 0.7
O A:HOH918 3.9 21.6 1.0
O6 A:DPO507 3.9 12.5 0.3
O3G A:DTP506 4.0 12.1 0.7
OP1 P:DA9 4.0 13.0 0.3
O A:HOH760 4.0 13.4 0.7
O5' P:DA9 4.1 13.0 0.3
O4 A:DPO507 4.2 10.6 0.3
O3B A:DTP506 4.2 10.3 0.7
O5 A:DPO507 4.2 11.7 0.3
O1G A:DTP506 4.3 11.6 0.7
O P:HOH221 4.3 23.2 1.0
P2 A:DPO507 4.4 12.3 0.3
O P:HOH212 4.4 15.0 1.0
PG A:DTP506 4.5 12.2 0.7
O3 A:DPO507 4.6 11.0 0.3
O2B A:DTP506 4.6 10.8 0.7
C2' P:DT8 4.7 15.0 0.7
NE A:ARG61 4.7 19.5 0.7
O3' P:DT8 4.7 13.8 0.3
C3' P:DT8 4.7 17.1 0.3
O A:HOH778 4.8 27.2 1.0
O1 A:DPO507 4.8 10.7 0.3
NE A:ARG61 4.8 27.5 0.3
C3' P:DT8 4.9 16.4 0.7
C8 A:DTP506 4.9 13.4 0.7
O1B A:DTP506 5.0 10.1 0.7

Reference:

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633
Page generated: Sun Sep 29 19:07:25 2024

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