Atomistry » Manganese » PDB 5jqk-5kg4 » 5kg4
Atomistry »
  Manganese »
    PDB 5jqk-5kg4 »
      5kg4 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy