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Manganese in PDB 5kg3: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 60S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MN2+ 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 MN2+ 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 MN2+ For 60S, PDB code: 5kg3 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) 19.98 / 1.70
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.210, 98.210, 82.210, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 23.7

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 MN2+ For 60S (pdb code 5kg3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 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 MN2+ For 60S, PDB code: 5kg3:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5kg3

Go back to Manganese Binding Sites List in 5kg3
Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MN2+ 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 MN2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:10.1
occ:1.00
 OP1 P:DA9 2.1 11.4 0.2
OD2 A:ASP13 2.1 10.1 1.0
OD1 A:ASP115 2.2 7.2 1.0
OE2 A:GLU116 2.2 12.0 1.0
O P:HOH216 2.3 10.7 1.0
O1A A:DTP506 2.3 11.8 0.8
O3' P:DT8 2.3 10.3 0.4
O3' P:DT8 2.4 10.0 0.3
O3' P:DT8 2.5 12.0 0.2
P P:DA9 2.8 11.7 0.2
CG A:ASP115 3.1 8.6 1.0
CD A:GLU116 3.2 14.3 1.0
CG A:ASP13 3.2 11.0 1.0
C3' P:DT8 3.2 13.7 0.3
C3' P:DT8 3.3 13.7 0.4
OD2 A:ASP115 3.4 8.0 1.0
PA A:DTP506 3.5 8.0 0.8
MN A:MN502 3.6 9.9 1.0
OD1 A:ASP13 3.6 9.1 1.0
C3' P:DT8 3.6 13.8 0.2
OG A:SER113 3.8 11.3 1.0
OE1 A:GLU116 3.8 15.7 1.0
OP2 P:DA9 3.8 11.8 0.2
O2A A:DTP506 3.9 11.3 0.8
O5' P:DA9 4.0 10.5 0.2
O5' A:DTP506 4.0 9.1 0.8
C4' P:DT8 4.0 14.4 0.2
O A:HOH771 4.1 12.0 0.7
O A:HOH771 4.1 14.7 0.3
C4' P:DT8 4.1 14.3 0.3
C5' A:DTP506 4.1 10.8 0.8
C4' P:DT8 4.1 14.1 0.4
CG A:GLU116 4.1 8.9 1.0
CB A:GLU116 4.1 9.0 1.0
NZ A:LYS224 4.2 13.8 1.0
C5' P:DA9 4.2 10.8 0.2
C5' P:DT8 4.4 16.7 0.2
O P:HOH204 4.4 11.5 0.7
CB A:ASP13 4.5 7.0 1.0
C5' P:DT8 4.5 15.4 0.4
C2' P:DT8 4.5 12.6 0.3
CB A:ASP115 4.5 9.0 1.0
C2' P:DT8 4.6 12.6 0.4
C5' P:DT8 4.6 16.4 0.3
O A:ASP115 4.6 8.2 1.0
C A:ASP115 4.6 9.8 1.0
C2' P:DT8 4.7 13.6 0.2
O1G A:DTP506 4.8 10.5 0.8
O5 A:DPO507 4.8 10.5 0.2
O3A A:DTP506 4.8 11.3 0.8
CB A:SER113 4.8 12.1 1.0
N A:GLU116 4.9 6.4 1.0
O5' P:DT8 4.9 15.9 0.4
O1B A:DTP506 5.0 7.5 0.8

Manganese binding site 2 out of 3 in 5kg3

Go back to Manganese Binding Sites List in 5kg3
Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MN2+ 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 MN2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:9.9
occ:1.00
 O1B A:DTP506 2.1 7.5 0.8
O1G A:DTP506 2.1 10.5 0.8
OD2 A:ASP115 2.1 8.0 1.0
O5 A:DPO507 2.2 10.5 0.2
OD1 A:ASP13 2.2 9.1 1.0
O A:MET14 2.3 9.1 1.0
O1 A:DPO507 2.3 8.7 0.2
O1A A:DTP506 2.4 11.8 0.8
OP1 P:DA9 2.5 11.4 0.2
CG A:ASP13 3.1 11.0 1.0
PB A:DTP506 3.1 10.0 0.8
CG A:ASP115 3.2 8.6 1.0
PG A:DTP506 3.3 10.5 0.8
P1 A:DPO507 3.4 10.3 0.2
C A:MET14 3.4 9.7 1.0
PA A:DTP506 3.4 8.0 0.8
OD2 A:ASP13 3.4 10.1 1.0
P2 A:DPO507 3.4 10.5 0.2
O3A A:DTP506 3.5 11.3 0.8
MN A:MN501 3.6 10.1 1.0
O3B A:DTP506 3.6 7.6 0.8
OD1 A:ASP115 3.7 7.2 1.0
O2 A:DPO507 3.7 10.9 0.2
O4 A:DPO507 3.8 7.9 0.2
NZ A:LYS231 3.8 14.6 1.0
O A:HOH771 3.9 12.0 0.7
N A:MET14 3.9 7.2 1.0
P P:DA9 3.9 11.7 0.2
O2G A:DTP506 4.0 10.2 0.8
O7 A:DPO507 4.0 10.3 0.2
C5' A:DTP506 4.1 10.8 0.8
CA A:MET14 4.1 10.9 1.0
C5' P:DA9 4.2 10.8 0.2
C A:ASP13 4.2 6.5 1.0
O5' A:DTP506 4.2 9.1 0.8
O A:HOH771 4.3 14.7 0.3
N A:ASP15 4.4 8.8 1.0
N A:CYS16 4.4 7.1 1.0
CB A:ASP13 4.4 7.0 1.0
O5' P:DA9 4.5 10.5 0.2
O2B A:DTP506 4.5 9.7 0.8
O P:HOH216 4.5 10.7 1.0
CA A:ASP15 4.5 8.2 1.0
CB A:ASP115 4.5 9.0 1.0
O3G A:DTP506 4.6 10.0 0.8
O2A A:DTP506 4.6 11.3 0.8
CE A:LYS231 4.6 16.0 1.0
O6 A:DPO507 4.6 10.1 0.2
O A:ASP13 4.6 9.0 1.0
CB A:MET14 4.6 10.9 1.0
C A:ASP15 4.7 9.3 1.0
O3 A:DPO507 4.7 9.6 0.2
OP2 P:DA9 4.7 11.8 0.2
N A:PHE17 4.7 6.7 1.0
CA A:ASP13 4.8 9.6 1.0
O A:ASP115 4.9 8.2 1.0
CB A:PHE17 4.9 6.5 1.0
O3' P:DT8 5.0 12.0 0.2

Manganese binding site 3 out of 3 in 5kg3

Go back to Manganese Binding Sites List in 5kg3
Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 60S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:18.0
occ:0.25
 O2A A:DTP506 1.8 11.3 0.8
OP2 P:DA9 2.0 11.8 0.2
O A:HOH679 2.2 15.7 0.3
O2 A:DPO507 2.2 10.9 0.2
O3A A:DTP506 2.3 11.3 0.8
O A:HOH771 2.4 14.7 0.3
O A:HOH652 2.5 16.2 1.0
PA A:DTP506 2.6 8.0 0.8
NH1 A:ARG61 2.8 23.0 0.7
O P:HOH205 3.0 24.2 1.0
P P:DA9 3.2 11.7 0.2
NH2 A:ARG61 3.5 13.9 0.7
CZ A:ARG61 3.6 18.7 0.7
O1A A:DTP506 3.6 11.8 0.8
P1 A:DPO507 3.7 10.3 0.2
O5' A:DTP506 3.7 9.1 0.8
OP1 P:DA9 3.7 11.4 0.2
PB A:DTP506 3.8 10.0 0.8
O A:HOH769 3.8 12.8 0.3
O A:HOH607 3.8 23.9 0.5
O5' P:DA9 3.8 10.5 0.2
O A:HOH867 3.9 16.4 1.0
O3G A:DTP506 3.9 10.0 0.8
O6 A:DPO507 4.0 10.1 0.2
O A:HOH771 4.0 12.0 0.7
O3B A:DTP506 4.1 7.6 0.8
O4 A:DPO507 4.1 7.9 0.2
O5 A:DPO507 4.1 10.5 0.2
O1G A:DTP506 4.3 10.5 0.8
P2 A:DPO507 4.3 10.5 0.2
PG A:DTP506 4.4 10.5 0.8
O2B A:DTP506 4.4 9.7 0.8
O3 A:DPO507 4.5 9.6 0.2
O P:HOH216 4.5 10.7 1.0
O3' P:DT8 4.5 12.0 0.2
O P:HOH224 4.5 24.3 1.0
O1 A:DPO507 4.6 8.7 0.2
C2' P:DT8 4.7 12.6 0.3
C2' P:DT8 4.7 12.6 0.4
C3' P:DT8 4.8 13.8 0.2
NE A:ARG61 4.8 19.6 0.7
NE A:ARG61 4.8 24.9 0.3
O1B A:DTP506 4.9 7.5 0.8
C8 A:DTP506 4.9 12.0 0.8
C5' P:DA9 5.0 10.8 0.2
C3' P:DT8 5.0 13.7 0.4
C3' P:DT8 5.0 13.7 0.3
O P:HOH218 5.0 25.8 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 01:43:06 2024

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