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Manganese 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:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where 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:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5kg4

Go back to Manganese Binding Sites List in 5kg4
Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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
A:Mn501

b:12.5
occ:1.00
 OP1 P:DA9 1.9 13.0 0.3
OD2 A:ASP13 2.1 12.1 1.0
OD1 A:ASP115 2.1 11.0 1.0
OE2 A:GLU116 2.2 13.5 1.0
O3' P:DT8 2.3 13.8 0.3
O1A A:DTP506 2.3 13.1 0.7
O P:HOH212 2.3 15.0 1.0
O3' P:DT8 2.3 12.8 0.7
P P:DA9 2.7 15.0 0.3
CG A:ASP115 3.1 11.9 1.0
CG A:ASP13 3.1 10.8 1.0
CD A:GLU116 3.2 14.2 1.0
C3' P:DT8 3.2 16.4 0.7
OD2 A:ASP115 3.4 12.5 1.0
PA A:DTP506 3.5 10.5 0.7
C3' P:DT8 3.5 17.1 0.3
OD1 A:ASP13 3.5 11.7 1.0
MN A:MN502 3.6 11.6 1.0
OG A:SER113 3.8 13.5 1.0
OP2 P:DA9 3.8 15.5 0.3
OE1 A:GLU116 3.8 17.9 1.0
O5' P:DA9 3.9 13.0 0.3
O2A A:DTP506 3.9 14.2 0.7
O5' A:DTP506 4.0 11.0 0.7
C4' P:DT8 4.1 16.6 0.7
O A:HOH760 4.1 16.7 0.3
C4' P:DT8 4.1 17.5 0.3
CG A:GLU116 4.1 9.2 1.0
NZ A:LYS224 4.2 9.2 0.7
CB A:GLU116 4.2 12.2 1.0
C5' A:DTP506 4.2 11.8 0.7
O A:HOH760 4.2 13.4 0.7
C5' P:DA9 4.2 11.8 0.3
CB A:ASP13 4.4 9.8 1.0
O P:HOH204 4.5 11.0 0.7
C2' P:DT8 4.5 15.0 0.7
C5' P:DT8 4.5 20.6 0.3
CB A:ASP115 4.5 10.1 1.0
C A:ASP115 4.6 11.7 1.0
O A:ASP115 4.6 11.7 1.0
C5' P:DT8 4.7 19.8 0.7
O5 A:DPO507 4.7 11.7 0.3
C2' P:DT8 4.7 18.8 0.3
O1G A:DTP506 4.8 11.6 0.7
O3A A:DTP506 4.8 11.9 0.7
CB A:SER113 4.8 14.7 1.0
N A:GLU116 4.9 9.0 1.0
O1B A:DTP506 4.9 10.1 0.7
O A:HOH738 5.0 24.9 1.0

Manganese binding site 2 out of 2 in 5kg4

Go back to Manganese Binding Sites List in 5kg4
Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn binding site number 2 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
A:Mn502

b:11.6
occ:1.00
 O5 A:DPO507 2.1 11.7 0.3
O1B A:DTP506 2.1 10.1 0.7
OD1 A:ASP13 2.1 11.7 1.0
OD2 A:ASP115 2.2 12.5 1.0
O1G A:DTP506 2.2 11.6 0.7
O1A A:DTP506 2.3 13.1 0.7
O1 A:DPO507 2.3 10.7 0.3
O A:MET14 2.3 12.1 1.0
OP1 P:DA9 2.5 13.0 0.3
CG A:ASP13 3.1 10.8 1.0
PB A:DTP506 3.1 11.4 0.7
CG A:ASP115 3.2 11.9 1.0
P1 A:DPO507 3.3 12.5 0.3
PA A:DTP506 3.4 10.5 0.7
P2 A:DPO507 3.4 12.3 0.3
PG A:DTP506 3.4 12.2 0.7
C A:MET14 3.4 12.3 1.0
OD2 A:ASP13 3.4 12.1 1.0
O3A A:DTP506 3.4 11.9 0.7
MN A:MN501 3.6 12.5 1.0
O3B A:DTP506 3.6 10.3 0.7
O2 A:DPO507 3.6 12.3 0.3
OD1 A:ASP115 3.7 11.0 1.0
O4 A:DPO507 3.8 10.6 0.3
NZ A:LYS231 3.8 17.4 1.0
P P:DA9 3.9 15.0 0.3
O A:HOH760 3.9 13.4 0.7
N A:MET14 3.9 10.8 1.0
O7 A:DPO507 4.0 12.5 0.3
C5' A:DTP506 4.0 11.8 0.7
O2G A:DTP506 4.0 12.4 0.7
O A:HOH760 4.1 16.7 0.3
CA A:MET14 4.1 12.8 1.0
C5' P:DA9 4.2 11.8 0.3
O5' A:DTP506 4.2 11.0 0.7
C A:ASP13 4.2 8.9 1.0
CB A:ASP13 4.3 9.8 1.0
O P:HOH212 4.4 15.0 1.0
N A:ASP15 4.4 10.0 1.0
N A:CYS16 4.5 9.8 1.0
O5' P:DA9 4.5 13.0 0.3
O2B A:DTP506 4.5 10.8 0.7
CE A:LYS231 4.5 20.3 1.0
CB A:ASP115 4.5 10.1 1.0
O6 A:DPO507 4.6 12.5 0.3
O2A A:DTP506 4.6 14.2 0.7
CA A:ASP15 4.6 9.1 1.0
O A:ASP13 4.6 11.6 1.0
O3G A:DTP506 4.6 12.1 0.7
O3 A:DPO507 4.7 11.0 0.3
CB A:MET14 4.7 15.4 1.0
N A:PHE17 4.7 9.7 1.0
C A:ASP15 4.7 10.6 1.0
CA A:ASP13 4.8 11.2 1.0
OP2 P:DA9 4.8 15.5 0.3
O3' P:DT8 4.8 13.8 0.3
CB A:PHE17 4.9 11.2 1.0
O A:ASP115 4.9 11.7 1.0

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 Oct 6 01:43:40 2024

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