Manganese in PDB 5kfy: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 4 Degree

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 4 Degree:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 4 Degree, PDB code: 5kfy 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)	19.76 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.590, 98.590, 82.340, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 22.8

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 5 Mm MN2+ For 60S at 4 Degree (pdb code 5kfy). 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 5 Mm MN2+ For 60S at 4 Degree, PDB code: 5kfy:
Jump to Manganese binding site number: 1; 2;

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 5 Mm MN2+ For 60S at 4 Degree


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 5 Mm MN2+ For 60S at 4 Degree within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:10.3 occ:1.00 OD2 A:ASP13 2.1 12.8 1.0 OE2 A:GLU116 2.2 9.9 1.0 OD1 A:ASP115 2.2 8.0 1.0 O A:HOH829 2.2 8.8 1.0 O1A A:DTP505 2.3 10.7 1.0 O3' P:DT8 2.3 9.1 1.0 CG A:ASP115 3.1 6.3 1.0 CD A:GLU116 3.2 11.2 1.0 CG A:ASP13 3.2 8.8 1.0 C3' P:DT8 3.2 9.6 1.0 OD2 A:ASP115 3.4 6.1 1.0 PA A:DTP505 3.5 11.1 1.0 MN A:MN502 3.6 10.5 1.0 OD1 A:ASP13 3.7 10.7 1.0 OG A:SER113 3.8 10.3 1.0 O2A A:DTP505 3.8 9.5 1.0 OE1 A:GLU116 3.8 16.2 1.0 O5' A:DTP505 4.0 7.7 1.0 C4' P:DT8 4.0 11.6 1.0 CG A:GLU116 4.1 9.2 1.0 CB A:GLU116 4.1 9.6 1.0 C5' A:DTP505 4.2 9.0 1.0 NZ A:LYS224 4.2 7.0 0.6 O P:HOH101 4.3 11.7 1.0 O A:HOH728 4.3 15.3 1.0 C5' P:DT8 4.4 17.0 0.4 CB A:ASP13 4.5 6.5 1.0 CB A:ASP115 4.6 9.4 1.0 C2' P:DT8 4.6 10.9 1.0 C5' P:DT8 4.6 17.6 0.6 C A:ASP115 4.6 10.4 1.0 O A:ASP115 4.7 9.1 1.0 O3A A:DTP505 4.8 10.0 1.0 O1G A:DTP505 4.8 10.4 1.0 CB A:SER113 4.8 11.3 1.0 N A:GLU116 4.8 7.4 1.0 O1B A:DTP505 5.0 10.1 1.0

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 5 Mm MN2+ For 60S at 4 Degree


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 5 Mm MN2+ For 60S at 4 Degree within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:10.5 occ:1.00 OD2 A:ASP115 2.2 6.1 1.0 O1B A:DTP505 2.2 10.1 1.0 OD1 A:ASP13 2.2 10.7 1.0 O1G A:DTP505 2.2 10.4 1.0 O A:MET14 2.3 7.8 1.0 O1A A:DTP505 2.3 10.7 1.0 CG A:ASP13 3.1 8.8 1.0 PB A:DTP505 3.2 9.2 1.0 CG A:ASP115 3.3 6.3 1.0 OD2 A:ASP13 3.3 12.8 1.0 C A:MET14 3.4 9.1 1.0 PA A:DTP505 3.4 11.1 1.0 PG A:DTP505 3.4 10.5 1.0 O3A A:DTP505 3.5 10.0 1.0 MN A:MN501 3.6 10.3 1.0 OD1 A:ASP115 3.7 8.0 1.0 O3B A:DTP505 3.7 9.1 1.0 O A:HOH728 4.0 15.3 1.0 N A:MET14 4.0 6.2 1.0 NZ A:LYS231 4.0 11.0 0.3 O2G A:DTP505 4.0 7.3 1.0 C5' A:DTP505 4.0 9.0 1.0 CA A:MET14 4.2 5.6 1.0 O5' A:DTP505 4.3 7.7 1.0 C A:ASP13 4.3 6.3 1.0 O A:HOH829 4.4 8.8 1.0 CB A:ASP13 4.4 6.5 1.0 N A:ASP15 4.4 8.1 1.0 N A:CYS16 4.5 7.4 1.0 CB A:ASP115 4.5 9.4 1.0 O2B A:DTP505 4.6 8.8 1.0 CA A:ASP15 4.6 8.3 1.0 O2A A:DTP505 4.6 9.5 1.0 CE A:LYS231 4.6 16.4 0.3 O3G A:DTP505 4.7 10.6 1.0 O A:ASP13 4.7 9.2 1.0 CB A:MET14 4.7 11.9 1.0 C A:ASP15 4.7 10.2 1.0 CA A:ASP13 4.8 8.8 1.0 N A:PHE17 4.8 7.5 1.0 CB A:PHE17 4.9 7.1 1.0 O A:ASP115 4.9 9.1 1.0

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