Manganese in PDB 6jus: MSDPO4-Dna Complex 6

All present enzymatic activity of MSDPO4-Dna Complex 6:
2.7.7.7;

The structure of MSDPO4-Dna Complex 6, PDB code: 6jus 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)	44.60 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.730, 80.340, 208.720, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.4

The binding sites of Manganese atom in the MSDPO4-Dna Complex 6 (pdb code 6jus). 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 6, PDB code: 6jus:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the MSDPO4-Dna Complex 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:89.6 occ:1.00 OE1 A:GLU108 2.1 69.2 1.0 OD2 A:ASP9 2.3 64.9 1.0 O1A A:2TM401 2.3 68.1 1.0 OD2 A:ASP107 2.6 72.1 1.0 OD1 A:ASP107 2.8 71.1 1.0 CD A:GLU108 3.0 61.7 1.0 CG A:ASP107 3.1 62.5 1.0 CG A:ASP9 3.2 56.7 1.0 PA A:2TM401 3.4 62.9 1.0 MN A:MN403 3.6 0.1 1.0 CG A:GLU108 3.7 57.6 1.0 OD1 A:ASP9 3.7 74.5 1.0 O5' A:2TM401 3.7 61.0 1.0 C3' C:DC873 3.8 64.7 1.0 OE2 A:GLU108 3.9 70.2 1.0 CB A:GLU108 3.9 51.3 1.0 O3' C:DC873 4.0 71.8 1.0 O2A A:2TM401 4.1 59.5 1.0 C5' A:2TM401 4.1 65.9 1.0 N A:GLU108 4.4 49.4 1.0 CB A:ASP9 4.4 51.2 1.0 NZ A:LYS152 4.5 46.6 1.0 CB A:ASP107 4.6 61.5 1.0 C1 A:2TM401 4.6 69.7 1.0 CA A:GLU108 4.7 49.1 1.0 O2B A:2TM401 4.7 71.7 1.0 C2' C:DC873 4.7 65.6 1.0 O1G A:2TM401 4.9 55.4 1.0 C5' C:DC873 4.9 62.9 1.0 C4' C:DC873 4.9 61.2 1.0 O5' C:DC873 4.9 70.4 1.0

Manganese binding site 2 out of 4 in the MSDPO4-Dna Complex 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:0.1 occ:1.00 O2B A:2TM401 1.4 71.7 1.0 OD1 A:ASP9 2.2 74.5 1.0 OD2 A:ASP107 2.2 72.1 1.0 O A:LEU10 2.5 49.9 1.0 O1A A:2TM401 2.8 68.1 1.0 PB A:2TM401 2.8 71.8 1.0 NZ A:LYS159 3.0 54.5 1.0 CG A:ASP9 3.1 56.7 1.0 O1G A:2TM401 3.1 55.4 1.0 OD2 A:ASP9 3.3 64.9 1.0 C1 A:2TM401 3.4 69.7 1.0 CG A:ASP107 3.5 62.5 1.0 MN A:MN402 3.6 89.6 1.0 PG A:2TM401 3.6 53.6 1.0 PA A:2TM401 3.7 62.9 1.0 O3B A:2TM401 3.7 62.1 1.0 O3G A:2TM401 3.7 56.8 1.0 C A:LEU10 3.7 45.4 1.0 C5' A:2TM401 3.8 65.9 1.0 O1B A:2TM401 4.1 69.3 1.0 CB A:ASP107 4.2 61.5 1.0 O5' A:2TM401 4.2 61.0 1.0 N A:LEU10 4.3 44.4 1.0 OD1 A:ASP107 4.4 71.1 1.0 CB A:ASP9 4.4 51.2 1.0 CE A:LYS159 4.5 43.9 1.0 N A:GLN12 4.5 40.3 1.0 CA A:LEU10 4.5 45.7 1.0 C A:ASP9 4.5 44.3 1.0 N A:ASP11 4.6 39.8 1.0 CA A:ASP11 4.6 40.3 1.0 N A:PHE13 4.7 41.3 1.0 CB A:PHE13 4.7 44.6 1.0 C A:ASP11 4.8 41.5 1.0 CA A:ASP9 4.9 46.9 1.0

Manganese binding site 3 out of 4 in the MSDPO4-Dna Complex 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn402 b:47.4 occ:1.00 O F:HOH501 2.0 39.6 1.0 OD2 F:ASP9 2.1 38.9 1.0 OD1 F:ASP107 2.4 47.3 1.0 OE2 F:GLU108 2.4 54.1 1.0 O1A F:2TM401 2.6 55.5 1.0 CD F:GLU108 2.7 46.0 1.0 O3' H:DC873 2.7 44.6 1.0 OE1 F:GLU108 3.0 55.4 1.0 OD2 F:ASP107 3.1 54.0 1.0 CG F:ASP107 3.1 44.0 1.0 C3' H:DC873 3.2 44.6 1.0 CG F:ASP9 3.4 37.6 1.0 CG F:GLU108 3.5 41.4 1.0 PA F:2TM401 3.6 55.3 1.0 MN F:MN403 3.7 55.1 1.0 CB F:GLU108 3.7 38.3 1.0 C5' F:2TM401 3.9 55.2 1.0 O5' F:2TM401 3.9 54.3 1.0 OD1 F:ASP9 4.0 43.4 1.0 NZ F:LYS152 4.1 39.2 1.0 O2A F:2TM401 4.2 53.1 1.0 C4' H:DC873 4.2 48.8 1.0 C2' H:DC873 4.3 49.0 1.0 O F:HOH502 4.4 23.8 1.0 O H:HOH902 4.4 41.8 1.0 CB F:ASP9 4.5 34.9 1.0 CB F:ASP107 4.6 43.8 1.0 C5' H:DC873 4.6 54.8 1.0 C F:ASP107 4.7 42.2 1.0 O F:ASP107 4.7 42.1 1.0 O5' H:DC873 4.7 59.4 1.0 N F:GLU108 4.8 37.5 1.0 O2B F:2TM401 4.9 59.4 1.0 CA F:GLU108 4.9 37.1 1.0 C1 F:2TM401 5.0 56.4 1.0

Manganese binding site 4 out of 4 in the MSDPO4-Dna Complex 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn403 b:55.1 occ:1.00 O2B F:2TM401 1.7 59.4 1.0 OD2 F:ASP107 2.0 54.0 1.0 OD1 F:ASP9 2.0 43.4 1.0 O1A F:2TM401 2.4 55.5 1.0 O F:LEU10 2.5 33.6 1.0 O1G F:2TM401 2.7 43.4 1.0 CG F:ASP9 2.7 37.6 1.0 OD2 F:ASP9 2.9 38.9 1.0 PB F:2TM401 3.1 54.2 1.0 CG F:ASP107 3.2 44.0 1.0 PA F:2TM401 3.6 55.3 1.0 C1 F:2TM401 3.6 56.4 1.0 C F:LEU10 3.6 33.1 1.0 MN F:MN402 3.7 47.4 1.0 O F:HOH502 3.7 23.8 1.0 PG F:2TM401 3.7 40.3 1.0 O F:HOH501 3.7 39.6 1.0 NZ F:LYS159 3.8 35.9 1.0 O3B F:2TM401 3.9 46.7 1.0 OD1 F:ASP107 3.9 47.3 1.0 C5' F:2TM401 3.9 55.2 1.0 O3G F:2TM401 3.9 42.1 1.0 N F:LEU10 4.0 33.2 1.0 CB F:ASP9 4.1 34.9 1.0 CB F:ASP107 4.2 43.8 1.0 O1B F:2TM401 4.2 50.2 1.0 O5' F:2TM401 4.3 54.3 1.0 CA F:LEU10 4.3 34.0 1.0 C F:ASP9 4.3 33.1 1.0 CE F:LYS159 4.5 34.6 1.0 N F:ASP11 4.6 38.5 1.0 CA F:ASP9 4.7 32.6 1.0 O F:ASP107 4.7 42.1 1.0 CB F:LEU10 4.8 36.1 1.0 CA F:ASP11 4.8 37.9 1.0 N F:GLN12 4.9 37.4 1.0 N F:PHE13 4.9 36.5 1.0 CB F:PHE13 4.9 34.5 1.0 O2A F:2TM401 4.9 53.1 1.0 O F:ASP9 5.0 33.3 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