Manganese in PDB 6jur: MSDPO4-Dna Complex 5

All present enzymatic activity of MSDPO4-Dna Complex 5:
2.7.7.7;

The structure of MSDPO4-Dna Complex 5, PDB code: 6jur was solved by D.T.Nair, M.K.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.26 / 2.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.670, 80.240, 210.770, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.7

The binding sites of Manganese atom in the MSDPO4-Dna Complex 5 (pdb code 6jur). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the MSDPO4-Dna Complex 5, PDB code: 6jur:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the MSDPO4-Dna Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of MSDPO4-Dna Complex 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:73.9 occ:1.00 O1A A:2TM401 1.8 51.2 1.0 OD2 A:ASP9 1.9 37.3 1.0 OD2 A:ASP107 2.4 42.2 1.0 OE2 A:GLU108 2.4 47.3 1.0 OD1 A:ASP107 2.6 33.0 1.0 PA A:2TM401 2.7 87.5 1.0 CG A:ASP107 2.8 37.2 1.0 CG A:ASP9 2.9 30.3 1.0 CD A:GLU108 3.0 35.9 1.0 CG A:GLU108 3.0 41.5 1.0 OD1 A:ASP9 3.1 25.6 1.0 MN A:MN403 3.2 52.5 1.0 O5' A:2TM401 3.7 59.8 1.0 C1 A:2TM401 3.7 75.0 1.0 O A:HOH566 4.0 39.0 1.0 OE1 A:GLU108 4.1 32.4 1.0 O3' C:DC873 4.2 47.8 1.0 NZ A:LYS152 4.2 37.3 1.0 CB A:ASP107 4.2 35.6 1.0 CB A:ASP9 4.3 27.1 1.0 O2A A:2TM401 4.3 44.4 1.0 C5' A:2TM401 4.4 63.6 1.0 C3' C:DC873 4.4 45.4 1.0 CB A:GLU108 4.5 37.0 1.0 O A:ASP107 4.5 29.7 1.0 C A:ASP107 4.6 33.9 1.0 O2B A:2TM401 4.8 58.3 1.0 CA A:ASP107 4.9 36.2 1.0 PB A:2TM401 4.9 84.0 1.0 CA A:ASP9 5.0 26.7 1.0 N A:GLU108 5.0 33.6 1.0

Manganese binding site 2 out of 4 in the MSDPO4-Dna Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of MSDPO4-Dna Complex 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:52.5 occ:1.00 OD2 A:ASP107 2.1 42.2 1.0 OD1 A:ASP9 2.4 25.6 1.0 O A:LEU10 2.4 27.1 1.0 O2B A:2TM401 2.5 58.3 1.0 O2G A:2TM401 2.7 50.6 1.0 C1 A:2TM401 3.1 75.0 1.0 PB A:2TM401 3.2 84.0 1.0 MN A:MN402 3.2 73.9 1.0 CG A:ASP107 3.3 37.2 1.0 CG A:ASP9 3.4 30.3 1.0 OD2 A:ASP9 3.5 37.3 1.0 C A:LEU10 3.6 28.1 1.0 NZ A:LYS159 3.6 30.5 1.0 PA A:2TM401 3.6 87.5 1.0 PG A:2TM401 3.6 48.4 1.0 O3B A:2TM401 3.7 54.5 1.0 O5' A:2TM401 4.0 59.8 1.0 O3G A:2TM401 4.0 57.5 1.0 CB A:ASP107 4.1 35.6 1.0 O1A A:2TM401 4.2 51.2 1.0 OD1 A:ASP107 4.2 33.0 1.0 N A:GLN12 4.2 28.5 1.0 N A:LEU10 4.3 27.4 1.0 CE A:LYS159 4.3 31.6 1.0 CA A:ASP11 4.4 27.9 1.0 CA A:LEU10 4.4 28.4 1.0 N A:PHE13 4.4 33.0 1.0 N A:ASP11 4.4 25.6 1.0 C A:ASP11 4.5 32.3 1.0 C A:ASP9 4.6 28.1 1.0 CB A:PHE13 4.7 32.0 1.0 CB A:ASP9 4.7 27.1 1.0 O1B A:2TM401 4.7 79.9 1.0 O A:ASP107 4.9 29.7 1.0 O A:ASP9 4.9 25.6 1.0 CB A:LEU10 5.0 30.5 1.0 O1G A:2TM401 5.0 52.3 1.0 CA A:GLN12 5.0 28.6 1.0

Manganese binding site 3 out of 4 in the MSDPO4-Dna Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of MSDPO4-Dna Complex 5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn402 b:63.1 occ:1.00 O1A F:2TM401 1.7 44.9 1.0 OE2 F:GLU108 2.0 43.7 1.0 OD2 F:ASP9 2.2 37.1 1.0 OD1 F:ASP107 2.5 37.5 1.0 CD F:GLU108 2.7 37.2 1.0 OD2 F:ASP107 2.7 42.6 1.0 CG F:GLU108 2.9 39.2 1.0 CG F:ASP107 3.0 38.4 1.0 PA F:2TM401 3.0 85.2 1.0 CG F:ASP9 3.1 29.6 1.0 OD1 F:ASP9 3.4 23.4 1.0 MN F:MN403 3.5 44.3 1.0 O3' H:DC873 3.6 42.2 1.0 O5' F:2TM401 3.7 49.2 1.0 OE1 F:GLU108 3.8 40.5 1.0 C1 F:2TM401 3.8 65.1 1.0 O F:HOH512 3.9 26.9 1.0 NZ F:LYS152 3.9 38.9 1.0 C3' H:DC873 4.0 45.3 1.0 O F:HOH529 4.0 38.6 1.0 C5' F:2TM401 4.0 60.8 1.0 CB F:GLU108 4.2 35.9 1.0 O2A F:2TM401 4.2 44.2 1.0 CB F:ASP107 4.4 36.2 1.0 CB F:ASP9 4.5 25.8 1.0 C F:ASP107 4.6 33.8 1.0 O F:ASP107 4.7 34.7 1.0 C2' H:DC873 4.8 41.9 1.0 N F:GLU108 4.9 32.1 1.0 CA F:GLU108 5.0 34.0 1.0

Manganese binding site 4 out of 4 in the MSDPO4-Dna Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of MSDPO4-Dna Complex 5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn403 b:44.3 occ:1.00 OD2 F:ASP107 2.0 42.6 1.0 OD1 F:ASP9 2.2 23.4 1.0 O2B F:2TM401 2.4 45.2 1.0 O F:LEU10 2.5 27.8 1.0 C1 F:2TM401 2.7 65.1 1.0 O2G F:2TM401 2.8 41.8 1.0 PB F:2TM401 2.9 60.1 1.0 CG F:ASP107 3.2 38.4 1.0 CG F:ASP9 3.3 29.6 1.0 MN F:MN402 3.5 63.1 1.0 O1A F:2TM401 3.5 44.9 1.0 O F:HOH512 3.5 26.9 1.0 OD2 F:ASP9 3.6 37.1 1.0 NZ F:LYS159 3.6 36.3 1.0 O3B F:2TM401 3.7 44.8 1.0 C F:LEU10 3.7 31.9 1.0 PG F:2TM401 3.7 42.7 1.0 PA F:2TM401 3.8 85.2 1.0 O5' F:2TM401 3.9 49.2 1.0 OD1 F:ASP107 4.0 37.5 1.0 CB F:ASP107 4.1 36.2 1.0 N F:LEU10 4.2 27.4 1.0 O1B F:2TM401 4.3 73.3 1.0 N F:GLN12 4.4 32.6 1.0 O3G F:2TM401 4.4 49.6 1.0 CE F:LYS159 4.4 35.7 1.0 CA F:LEU10 4.5 31.6 1.0 N F:PHE13 4.6 30.8 1.0 C F:ASP9 4.6 27.1 1.0 N F:ASP11 4.6 29.0 1.0 CB F:ASP9 4.6 25.8 1.0 CA F:ASP11 4.6 30.3 1.0 CB F:PHE13 4.7 28.3 1.0 C F:ASP11 4.7 32.3 1.0 C5' F:2TM401 4.9 60.8 1.0 O F:ASP107 4.9 34.7 1.0

M.K.Johnson, J.Kottur, D.T.Nair. A Polar Filter in Dna Polymerases Prevents Ribonucleotide Incorporation. Nucleic Acids Res. V. 47 10693 2019.
ISSN: ESSN 1362-4962
PubMed: 31544946
DOI: 10.1093/NAR/GKZ792