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Manganese in PDB 5kg5: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm CD2+ For 60S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm CD2+ 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 CD2+ 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 CD2+ For 60S, PDB code: 5kg5 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) 19.95 / 1.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.210, 98.210, 82.090, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 21.9

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 CD2+ For 60S (pdb code 5kg5). 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 CD2+ For 60S, PDB code: 5kg5:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5kg5

Go back to Manganese Binding Sites List in 5kg5
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 CD2+ 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 CD2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:10.1
occ:1.00
 OP1 P:DA9 2.0 11.2 0.1
OD2 A:ASP13 2.1 12.7 1.0
OE2 A:GLU116 2.2 13.3 1.0
O A:HOH799 2.2 11.7 1.0
OD1 A:ASP115 2.2 10.2 1.0
O1A A:DTP506 2.2 10.9 0.8
O3' P:DT8 2.4 11.2 0.8
O3' P:DT8 2.5 12.7 0.1
P P:DA9 2.7 12.9 0.1
CG A:ASP115 3.2 10.1 1.0
CD A:GLU116 3.2 14.3 1.0
CG A:ASP13 3.2 10.7 1.0
C3' P:DT8 3.3 15.6 0.8
PA A:DTP506 3.4 10.4 0.8
OD2 A:ASP115 3.4 10.2 1.0
OD1 A:ASP13 3.6 11.3 1.0
MN A:MN502 3.6 10.3 1.0
C3' P:DT8 3.7 15.6 0.1
OP2 P:DA9 3.8 14.1 0.1
OE1 A:GLU116 3.8 16.0 1.0
OG A:SER113 3.8 12.6 1.0
O2A A:DTP506 3.9 14.2 0.8
O5' P:DA9 3.9 11.8 0.1
O5' A:DTP506 3.9 11.0 0.8
O A:HOH764 4.1 14.4 0.8
CG A:GLU116 4.1 8.9 1.0
C4' P:DT8 4.1 16.8 0.1
C4' P:DT8 4.1 16.0 0.8
CB A:GLU116 4.2 9.8 1.0
NZ A:LYS224 4.2 14.6 1.0
C5' A:DTP506 4.2 13.0 0.8
C5' P:DA9 4.2 12.1 0.1
O P:HOH204 4.4 14.6 1.0
O A:HOH764 4.4 13.2 0.2
CB A:ASP13 4.5 8.4 1.0
C5' P:DT8 4.5 23.3 0.1
C2' P:DT8 4.6 14.3 0.8
CB A:ASP115 4.6 11.0 1.0
O5 A:DPO507 4.6 11.2 0.1
C5' P:DT8 4.7 22.8 0.8
C A:ASP115 4.7 9.6 1.0
O A:ASP115 4.7 10.7 1.0
O1G A:DTP506 4.7 11.2 0.8
O3A A:DTP506 4.8 11.6 0.8
CB A:SER113 4.8 12.5 1.0
N A:GLU116 4.9 8.9 1.0
C2' P:DT8 4.9 15.3 0.1
O1B A:DTP506 4.9 9.7 0.8
O2 A:DPO507 4.9 11.9 0.1

Manganese binding site 2 out of 3 in 5kg5

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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 CD2+ 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 CD2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:10.3
occ:1.00
 OD1 A:ASP13 2.1 11.3 1.0
OD2 A:ASP115 2.1 10.2 1.0
O1G A:DTP506 2.1 11.2 0.8
O5 A:DPO507 2.2 11.2 0.1
O1B A:DTP506 2.2 9.7 0.8
O A:MET14 2.3 10.8 1.0
O1A A:DTP506 2.3 10.9 0.8
O1 A:DPO507 2.4 10.4 0.1
OP1 P:DA9 2.6 11.2 0.1
CG A:ASP13 3.1 10.7 1.0
PB A:DTP506 3.2 10.8 0.8
CG A:ASP115 3.2 10.1 1.0
PA A:DTP506 3.4 10.4 0.8
P1 A:DPO507 3.4 11.2 0.1
C A:MET14 3.4 10.6 1.0
PG A:DTP506 3.4 11.9 0.8
P2 A:DPO507 3.4 12.0 0.1
OD2 A:ASP13 3.4 12.7 1.0
O3A A:DTP506 3.5 11.6 0.8
O2 A:DPO507 3.6 11.9 0.1
MN A:MN501 3.6 10.1 1.0
O3B A:DTP506 3.6 10.0 0.8
OD1 A:ASP115 3.6 10.2 1.0
NZ A:LYS231 3.8 14.8 1.0
O4 A:DPO507 3.8 10.6 0.1
N A:MET14 3.9 9.2 1.0
O A:HOH764 3.9 14.4 0.8
O7 A:DPO507 3.9 11.8 0.1
P P:DA9 3.9 12.9 0.1
O2G A:DTP506 4.0 11.7 0.8
C5' A:DTP506 4.0 13.0 0.8
CA A:MET14 4.1 10.3 1.0
C5' P:DA9 4.1 12.1 0.1
O5' A:DTP506 4.2 11.0 0.8
C A:ASP13 4.2 9.8 1.0
CB A:ASP13 4.3 8.4 1.0
O A:HOH764 4.4 13.2 0.2
N A:ASP15 4.4 9.6 1.0
O A:HOH799 4.4 11.7 1.0
N A:CYS16 4.4 8.9 1.0
CB A:ASP115 4.5 11.0 1.0
O5' P:DA9 4.5 11.8 0.1
CE A:LYS231 4.5 19.4 1.0
O2B A:DTP506 4.5 11.1 0.8
CA A:ASP15 4.6 9.6 1.0
O2A A:DTP506 4.6 14.2 0.8
O3G A:DTP506 4.6 11.8 0.8
O6 A:DPO507 4.6 12.1 0.1
CB A:MET14 4.6 12.1 1.0
O A:ASP13 4.6 11.2 1.0
O3 A:DPO507 4.7 11.2 0.1
OP2 P:DA9 4.7 14.1 0.1
C A:ASP15 4.7 10.2 1.0
N A:PHE17 4.8 8.6 1.0
CA A:ASP13 4.8 11.1 1.0
O A:ASP115 4.9 10.7 1.0
CB A:PHE17 4.9 8.6 1.0

Manganese binding site 3 out of 3 in 5kg5

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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 CD2+ 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 CD2+ For 60S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:17.3
occ:0.15
 O2A A:DTP506 1.8 14.2 0.8
O P:HOH215 2.0 18.6 0.1
OP2 P:DA9 2.0 14.1 0.1
O3A A:DTP506 2.4 11.6 0.8
O A:HOH764 2.4 13.2 0.2
O2 A:DPO507 2.5 11.9 0.1
NH1 A:ARG61 2.6 24.8 0.8
PA A:DTP506 2.6 10.4 0.8
O A:HOH667 2.7 18.7 1.0
O A:HOH712 2.9 23.8 1.0
P P:DA9 3.3 12.9 0.1
CZ A:ARG61 3.6 23.3 0.8
O1A A:DTP506 3.6 10.9 0.8
NH2 A:ARG61 3.7 18.6 0.8
O5' A:DTP506 3.7 11.0 0.8
PB A:DTP506 3.8 10.8 0.8
P1 A:DPO507 3.8 11.2 0.1
OP1 P:DA9 3.9 11.2 0.1
O A:HOH627 3.9 28.3 0.6
O A:HOH764 3.9 14.4 0.8
O5' P:DA9 4.0 11.8 0.1
O6 A:DPO507 4.0 12.1 0.1
O A:HOH906 4.0 19.9 1.0
O A:HOH656 4.0 16.4 0.1
O4 A:DPO507 4.0 10.6 0.1
O5 A:DPO507 4.0 11.2 0.1
O3G A:DTP506 4.0 11.8 0.8
O3B A:DTP506 4.1 10.0 0.8
P2 A:DPO507 4.2 12.0 0.1
O1G A:DTP506 4.3 11.2 0.8
O A:HOH799 4.4 11.7 1.0
PG A:DTP506 4.4 11.9 0.8
O P:HOH222 4.4 29.8 1.0
O3' P:DT8 4.5 12.7 0.1
O2B A:DTP506 4.5 11.1 0.8
C2' P:DT8 4.6 14.3 0.8
O3 A:DPO507 4.6 11.2 0.1
C3' P:DT8 4.6 15.6 0.1
NE A:ARG61 4.8 19.1 0.8
NE A:ARG61 4.8 26.4 0.2
O1 A:DPO507 4.8 10.4 0.1
O1B A:DTP506 4.9 9.7 0.8
C3' P:DT8 4.9 15.6 0.8
C8 A:DTP506 4.9 13.0 0.8
C2' P:DT8 4.9 15.3 0.1
O A:HOH815 4.9 26.6 1.0
C8 P:DA9 5.0 13.3 0.1
C5' A:DTP506 5.0 13.0 0.8

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 01:44:45 2024

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