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Manganese in PDB 5kfh: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S, PDB code: 5kfh 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) 19.86 / 1.72
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.350, 98.350, 81.690, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 21.5

Other elements in 5kfh:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S 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 90S (pdb code 5kfh). 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 90S, PDB code: 5kfh:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5kfh

Go back to Manganese Binding Sites List in 5kfh
Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S


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 90S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:14.9
occ:1.00
 OP1 P:DA9 2.0 14.8 0.3
OD1 A:ASP115 2.1 14.7 1.0
OD2 A:ASP13 2.1 18.9 1.0
OE2 A:GLU116 2.2 16.9 1.0
O P:HOH214 2.2 15.8 1.0
O3' P:DT8 2.3 16.0 0.3
O1A A:DTP508 2.3 14.7 0.7
O3' P:DT8 2.4 15.9 0.7
P P:DA9 2.8 14.8 0.3
CG A:ASP115 3.0 15.3 1.0
CG A:ASP13 3.1 15.6 1.0
CD A:GLU116 3.2 21.1 1.0
C3' P:DT8 3.3 20.4 0.7
OD2 A:ASP115 3.3 15.2 1.0
C3' P:DT8 3.5 20.0 0.3
OD1 A:ASP13 3.5 15.8 1.0
PA A:DTP508 3.5 14.8 0.7
CA A:CA502 3.6 15.6 0.5
MN A:MN503 3.6 15.6 0.6
OG A:SER113 3.8 16.8 1.0
OP2 P:DA9 3.8 17.0 0.3
OE1 A:GLU116 3.9 20.4 1.0
O5' P:DA9 3.9 16.1 0.3
O2A A:DTP508 4.0 16.0 0.7
C4' P:DT8 4.0 20.8 0.3
C4' P:DT8 4.1 20.7 0.7
O5' A:DTP508 4.1 14.7 0.7
CB A:GLU116 4.1 15.8 1.0
CG A:GLU116 4.1 15.2 1.0
C5' A:DTP508 4.2 14.4 0.7
C5' P:DA9 4.2 14.5 0.3
NZ A:LYS224 4.3 10.9 0.5
O A:HOH721 4.3 27.6 1.0
O P:HOH202 4.4 17.8 0.6
CB A:ASP13 4.5 14.0 1.0
CB A:ASP115 4.5 12.3 1.0
C5' P:DT8 4.5 21.7 0.3
C A:ASP115 4.5 14.9 1.0
C2' P:DT8 4.6 18.2 0.7
O A:ASP115 4.6 13.9 1.0
C5' P:DT8 4.7 21.8 0.7
C2' P:DT8 4.7 20.4 0.3
O5 A:DPO509 4.7 15.5 0.3
N A:GLU116 4.8 11.5 1.0
O A:HOH610 4.8 32.0 1.0
CB A:SER113 4.8 16.8 1.0
O3A A:DTP508 4.8 14.7 0.7
O1G A:DTP508 4.9 15.5 0.7
CA A:ASP115 4.9 14.1 1.0

Manganese binding site 2 out of 3 in 5kfh

Go back to Manganese Binding Sites List in 5kfh
Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S


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 90S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:15.6
occ:0.55
 CA A:CA502 0.0 15.6 0.5
O5 A:DPO509 2.2 15.5 0.3
O1B A:DTP508 2.2 13.0 0.7
OD1 A:ASP13 2.2 15.8 1.0
OD2 A:ASP115 2.3 15.2 1.0
O1A A:DTP508 2.3 14.7 0.7
O1 A:DPO509 2.3 13.5 0.3
O1G A:DTP508 2.3 15.5 0.7
O A:MET14 2.3 13.5 1.0
OP1 P:DA9 2.4 14.8 0.3
CG A:ASP13 3.1 15.6 1.0
PB A:DTP508 3.2 15.1 0.7
CG A:ASP115 3.4 15.3 1.0
P2 A:DPO509 3.4 16.1 0.3
P1 A:DPO509 3.4 15.3 0.3
PA A:DTP508 3.4 14.8 0.7
O3A A:DTP508 3.5 14.7 0.7
OD2 A:ASP13 3.5 18.9 1.0
PG A:DTP508 3.5 15.7 0.7
C A:MET14 3.5 13.6 1.0
MN A:MN501 3.6 14.9 1.0
O3B A:DTP508 3.7 14.5 0.7
O2 A:DPO509 3.8 14.8 0.3
O4 A:DPO509 3.8 14.6 0.3
OD1 A:ASP115 3.8 14.7 1.0
P P:DA9 3.9 14.8 0.3
C1 A:GOL507 3.9 12.5 0.5
O7 A:DPO509 4.0 14.6 0.3
O A:HOH721 4.0 27.6 1.0
O2G A:DTP508 4.0 14.1 0.7
N A:MET14 4.0 13.3 1.0
C5' A:DTP508 4.1 14.4 0.7
C5' P:DA9 4.2 14.5 0.3
O5' A:DTP508 4.2 14.7 0.7
CA A:MET14 4.3 13.9 1.0
C A:ASP13 4.3 11.8 1.0
O P:HOH214 4.3 15.8 1.0
C3 A:GOL507 4.4 21.9 0.5
N A:CYS16 4.4 13.2 1.0
CB A:ASP13 4.4 14.0 1.0
N A:ASP15 4.4 11.4 1.0
O5' P:DA9 4.5 16.1 0.3
O2B A:DTP508 4.5 12.8 0.7
CA A:ASP15 4.6 13.2 1.0
O6 A:DPO509 4.6 16.3 0.3
CB A:ASP115 4.6 12.3 1.0
O2A A:DTP508 4.6 16.0 0.7
C A:ASP15 4.7 15.7 1.0
OP2 P:DA9 4.7 17.0 0.3
O3 A:DPO509 4.7 13.2 0.3
O A:ASP13 4.7 12.8 1.0
N A:PHE17 4.7 11.5 1.0
O3G A:DTP508 4.7 16.3 0.7
C2 A:GOL507 4.7 14.5 0.5
CB A:MET14 4.8 16.4 1.0
O3' P:DT8 4.8 16.0 0.3
O1 A:GOL507 4.8 18.7 0.5
CA A:ASP13 4.8 14.0 1.0
CB A:PHE17 4.9 11.7 1.0
MN P:MN101 5.0 19.5 0.3

Manganese binding site 3 out of 3 in 5kfh

Go back to Manganese Binding Sites List in 5kfh
Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 90S


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 90S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:19.5
occ:0.35
 O2A A:DTP508 1.7 16.0 0.7
OP2 P:DA9 2.0 17.0 0.3
O A:HOH844 2.1 16.1 0.3
O3A A:DTP508 2.2 14.7 0.7
O2 A:DPO509 2.3 14.8 0.3
O A:HOH695 2.3 27.8 1.0
PA A:DTP508 2.4 14.8 0.7
O A:HOH622 2.8 19.6 1.0
NH1 A:ARG61 2.8 23.6 0.7
O A:HOH721 3.1 27.6 1.0
P P:DA9 3.2 14.8 0.3
O1A A:DTP508 3.5 14.7 0.7
O5' A:DTP508 3.6 14.7 0.7
OP1 P:DA9 3.6 14.8 0.3
P1 A:DPO509 3.7 15.3 0.3
PB A:DTP508 3.7 15.1 0.7
CZ A:ARG61 3.8 21.2 0.7
NH2 A:ARG61 3.8 17.6 0.7
O6 A:DPO509 3.8 16.3 0.3
O5 A:DPO509 3.9 15.5 0.3
O5' P:DA9 3.9 16.1 0.3
O1G A:DTP508 4.0 15.5 0.7
O4 A:DPO509 4.1 14.6 0.3
O A:HOH702 4.1 17.5 0.3
O3B A:DTP508 4.1 14.5 0.7
P2 A:DPO509 4.2 16.1 0.3
O3G A:DTP508 4.2 16.3 0.7
O P:HOH214 4.3 15.8 1.0
O A:HOH925 4.3 23.4 1.0
PG A:DTP508 4.4 15.7 0.7
O3' P:DT8 4.4 16.0 0.3
O2B A:DTP508 4.4 12.8 0.7
O A:HOH879 4.4 31.1 0.7
O P:HOH215 4.5 23.0 1.0
O1 A:DPO509 4.5 13.5 0.3
C2' P:DT8 4.6 18.2 0.7
C3' P:DT8 4.6 20.0 0.3
O3 A:DPO509 4.6 13.2 0.3
O1B A:DTP508 4.7 13.0 0.7
C3' P:DT8 4.8 20.4 0.7
O P:HOH216 4.8 27.7 1.0
C5' A:DTP508 4.9 14.4 0.7
C8 A:DTP508 4.9 17.6 0.7
CA A:CA502 4.9 15.6 0.5
MN A:MN503 5.0 15.6 0.6

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 01:39:58 2024

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