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Manganese in PDB 5kfk: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S, PDB code: 5kfk 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) 19.93 / 1.70
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.270, 98.270, 82.010, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 21

Other elements in 5kfk:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S (pdb code 5kfk). 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 with 10 Mm MN2+ For 300S, PDB code: 5kfk:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5kfk

Go back to Manganese Binding Sites List in 5kfk
Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S


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 with 10 Mm MN2+ For 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:12.6
occ:1.00
 OP1 P:DA9 2.1 13.7 0.5
OD1 A:ASP115 2.1 10.0 1.0
OE2 A:GLU116 2.2 14.6 1.0
O P:HOH210 2.2 14.1 1.0
OD2 A:ASP13 2.2 13.6 1.0
O1A A:DTP507 2.3 13.7 0.5
O3' P:DT8 2.4 13.3 0.5
O3' P:DT8 2.5 14.2 0.5
P P:DA9 2.8 13.4 0.5
CG A:ASP115 3.1 12.7 1.0
CD A:GLU116 3.2 14.4 1.0
CG A:ASP13 3.2 13.2 1.0
C3' P:DT8 3.3 18.5 0.5
OD2 A:ASP115 3.4 9.6 1.0
PA A:DTP507 3.5 9.9 0.5
OD1 A:ASP13 3.6 12.2 1.0
MN A:MN503 3.6 12.0 0.9
CA A:CA502 3.6 12.0 0.1
C3' P:DT8 3.7 18.9 0.5
OG A:SER113 3.8 14.4 1.0
OP2 P:DA9 3.8 14.4 0.5
OE1 A:GLU116 3.8 19.4 1.0
O2A A:DTP507 4.0 13.8 0.5
O5' P:DA9 4.0 13.3 0.5
C4' P:DT8 4.0 18.2 0.5
C4' P:DT8 4.0 18.0 0.5
O5' A:DTP507 4.0 12.2 0.5
CB A:GLU116 4.1 13.0 1.0
CG A:GLU116 4.1 12.4 1.0
O A:HOH690 4.2 28.6 1.0
NZ A:LYS224 4.2 10.8 0.7
C5' A:DTP507 4.2 12.7 0.5
C5' P:DT8 4.2 22.1 0.5
C5' P:DA9 4.2 12.4 0.5
O P:HOH201 4.3 14.4 0.5
CB A:ASP13 4.5 11.1 1.0
C5' P:DT8 4.5 21.8 0.5
CB A:ASP115 4.5 9.7 1.0
O A:ASP115 4.6 10.1 1.0
C A:ASP115 4.6 10.8 1.0
C2' P:DT8 4.6 16.2 0.5
O5 A:DPO508 4.7 12.6 0.5
C2' P:DT8 4.8 16.5 0.5
N A:GLU116 4.8 8.7 1.0
O1G A:DTP507 4.8 13.0 0.5
CB A:SER113 4.8 13.9 1.0
O3A A:DTP507 4.8 13.2 0.5
O1 A:DPO508 4.9 10.6 0.5
CA A:ASP115 5.0 11.6 1.0

Manganese binding site 2 out of 3 in 5kfk

Go back to Manganese Binding Sites List in 5kfk
Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S


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 with 10 Mm MN2+ For 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:12.0
occ:0.95
 CA A:CA502 0.0 12.0 0.1
O5 A:DPO508 2.0 12.6 0.5
O1 A:DPO508 2.0 10.6 0.5
O1B A:DTP507 2.1 10.5 0.5
OD2 A:ASP115 2.2 9.6 1.0
O1G A:DTP507 2.3 13.0 0.5
O1A A:DTP507 2.3 13.7 0.5
OD1 A:ASP13 2.3 12.2 1.0
O A:MET14 2.3 10.6 1.0
OP1 P:DA9 2.4 13.7 0.5
PB A:DTP507 3.1 11.8 0.5
CG A:ASP13 3.1 13.2 1.0
P1 A:DPO508 3.2 11.8 0.5
CG A:ASP115 3.2 12.7 1.0
PA A:DTP507 3.3 9.9 0.5
P2 A:DPO508 3.3 13.8 0.5
O3A A:DTP507 3.4 13.2 0.5
PG A:DTP507 3.4 13.7 0.5
OD2 A:ASP13 3.4 13.6 1.0
C A:MET14 3.5 12.9 1.0
O2 A:DPO508 3.6 13.2 0.5
MN A:MN501 3.6 12.6 1.0
O4 A:DPO508 3.6 11.1 0.5
O3B A:DTP507 3.6 11.1 0.5
OD1 A:ASP115 3.7 10.0 1.0
P P:DA9 3.8 13.4 0.5
O A:HOH690 3.9 28.6 1.0
C5' A:DTP507 3.9 12.7 0.5
NZ A:LYS231 3.9 16.1 1.0
O7 A:DPO508 3.9 11.2 0.5
O2G A:DTP507 4.0 11.1 0.5
N A:MET14 4.0 9.3 1.0
O5' A:DTP507 4.1 12.2 0.5
C5' P:DA9 4.1 12.4 0.5
CA A:MET14 4.2 10.8 1.0
O5' P:DA9 4.3 13.3 0.5
C A:ASP13 4.3 10.2 1.0
N A:CYS16 4.4 10.5 1.0
CB A:ASP13 4.4 11.1 1.0
O P:HOH210 4.4 14.1 1.0
N A:ASP15 4.5 8.6 1.0
O2B A:DTP507 4.5 11.9 0.5
O3 A:DPO508 4.5 11.8 0.5
O6 A:DPO508 4.5 14.0 0.5
CB A:ASP115 4.5 9.7 1.0
O2A A:DTP507 4.5 13.8 0.5
CA A:ASP15 4.5 9.3 1.0
O3G A:DTP507 4.6 14.2 0.5
OP2 P:DA9 4.7 14.4 0.5
O A:ASP13 4.7 11.6 1.0
C A:ASP15 4.7 13.0 1.0
CB A:MET14 4.7 12.7 1.0
N A:PHE17 4.7 8.9 1.0
CE A:LYS231 4.7 23.2 1.0
O3' P:DT8 4.8 13.3 0.5
CA A:ASP13 4.9 11.4 1.0
MN P:MN101 4.9 19.4 0.5
CB A:PHE17 4.9 9.2 1.0
O A:ASP115 5.0 10.1 1.0

Manganese binding site 3 out of 3 in 5kfk

Go back to Manganese Binding Sites List in 5kfk
Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S


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 with 10 Mm MN2+ For 300S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:19.4
occ:0.50
 O2A A:DTP507 1.6 13.8 0.5
OP2 P:DA9 2.0 14.4 0.5
O3A A:DTP507 2.2 13.2 0.5
O2 A:DPO508 2.2 13.2 0.5
O A:HOH878 2.2 18.9 0.5
O A:HOH790 2.2 30.6 1.0
PA A:DTP507 2.4 9.9 0.5
NH1 A:ARG61 2.5 20.9 0.5
O A:HOH636 2.8 18.2 1.0
O A:HOH690 2.9 28.6 1.0
P P:DA9 3.1 13.4 0.5
O1A A:DTP507 3.4 13.7 0.5
OP1 P:DA9 3.5 13.7 0.5
CZ A:ARG61 3.6 17.8 0.5
O5' A:DTP507 3.6 12.2 0.5
P1 A:DPO508 3.6 11.8 0.5
PB A:DTP507 3.7 11.8 0.5
O5' P:DA9 3.8 13.3 0.5
NH2 A:ARG61 3.8 16.4 0.5
O A:HOH835 3.8 16.3 0.5
O6 A:DPO508 3.8 14.0 0.5
O5 A:DPO508 4.0 12.6 0.5
O1G A:DTP507 4.0 13.0 0.5
O3B A:DTP507 4.1 11.1 0.5
O4 A:DPO508 4.1 11.1 0.5
O3G A:DTP507 4.1 14.2 0.5
O A:HOH897 4.2 21.3 1.0
P2 A:DPO508 4.2 13.8 0.5
O P:HOH210 4.3 14.1 1.0
O A:HOH866 4.3 32.2 0.5
PG A:DTP507 4.3 13.7 0.5
O P:HOH212 4.3 31.0 1.0
O2B A:DTP507 4.4 11.9 0.5
O P:HOH214 4.4 21.3 1.0
O3' P:DT8 4.4 13.3 0.5
O1 A:DPO508 4.5 10.6 0.5
O3 A:DPO508 4.5 11.8 0.5
O1B A:DTP507 4.7 10.5 0.5
C2' P:DT8 4.7 16.2 0.5
C3' P:DT8 4.8 18.5 0.5
NE A:ARG61 4.8 22.2 0.5
C5' A:DTP507 4.8 12.7 0.5
C8 A:DTP507 4.8 14.9 0.5
C3' P:DT8 4.9 18.9 0.5
CA A:CA502 4.9 12.0 0.1
MN A:MN503 4.9 12.0 0.9
C5' P:DA9 5.0 12.4 0.5
C8 P:DA9 5.0 14.9 0.5

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 01:40:40 2024

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