Magnesium in PDB 6jun: MSDPO4-Dna Complex 3

All present enzymatic activity of MSDPO4-Dna Complex 3:
2.7.7.7;

The structure of MSDPO4-Dna Complex 3, PDB code: 6jun 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)	75.84 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.920, 81.320, 210.210, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.7

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

Magnesium binding site 1 out of 4 in the MSDPO4-Dna Complex 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MSDPO4-Dna Complex 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:17.9 occ:1.00 OE2 F:GLU108 1.9 71.1 1.0 O3' H:DC873 1.9 33.4 1.0 OD2 F:ASP107 2.1 56.2 1.0 OD2 F:ASP9 2.1 22.3 1.0 CD F:GLU108 2.7 43.8 1.0 O1A F:0KX401 2.8 39.6 1.0 CG F:GLU108 2.9 49.4 1.0 CG F:ASP107 3.0 42.8 1.0 C3' H:DC873 3.1 35.8 1.0 CG F:ASP9 3.2 34.0 1.0 CB F:ASP107 3.4 34.5 1.0 PA F:0KX401 3.5 35.7 1.0 MG F:MG403 3.5 13.0 1.0 O2A F:0KX401 3.7 53.5 1.0 OD1 F:ASP9 3.7 40.6 1.0 O5' F:0KX401 3.7 50.0 1.0 C4' H:DC873 3.8 38.0 1.0 OE1 F:GLU108 3.9 62.4 1.0 OD1 F:ASP107 4.0 55.8 1.0 O F:HOH514 4.0 30.4 1.0 C5' H:DC873 4.1 55.5 1.0 C5' F:0KX401 4.2 45.2 1.0 C2' H:DC873 4.3 34.8 1.0 NZ F:LYS152 4.3 38.3 1.0 CB F:GLU108 4.3 32.8 1.0 CB F:ASP9 4.5 40.5 1.0 O5' H:DC873 4.5 56.6 1.0 C F:ASP107 4.5 27.2 1.0 CA F:ASP107 4.6 51.0 1.0 N F:GLU108 4.8 35.0 1.0 O F:ASP107 4.8 41.8 1.0

Magnesium binding site 2 out of 4 in the MSDPO4-Dna Complex 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MSDPO4-Dna Complex 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:13.0 occ:1.00 O1A F:0KX401 2.0 39.6 1.0 OD1 F:ASP9 2.1 40.6 1.0 O F:LEU10 2.2 32.4 1.0 OD1 F:ASP107 2.3 55.8 1.0 O2B F:0KX401 2.4 58.6 1.0 OD2 F:ASP107 2.5 56.2 1.0 O1G F:0KX401 2.7 51.3 1.0 CG F:ASP107 2.7 42.8 1.0 CG F:ASP9 3.0 34.0 1.0 OD2 F:ASP9 3.2 22.3 1.0 C F:LEU10 3.4 37.9 1.0 PA F:0KX401 3.4 35.7 1.0 MG F:MG402 3.5 17.9 1.0 PB F:0KX401 3.7 36.7 1.0 N F:LEU10 3.8 36.7 1.0 C5' F:0KX401 3.8 45.2 1.0 NZ F:LYS159 3.8 39.5 1.0 O F:HOH514 3.9 30.4 1.0 PG F:0KX401 4.0 38.4 1.0 N3A F:0KX401 4.0 42.2 1.0 O5' F:0KX401 4.1 50.0 1.0 CB F:ASP107 4.1 34.5 1.0 CA F:LEU10 4.1 40.7 1.0 O3B F:0KX401 4.3 36.1 1.0 CB F:ASP9 4.3 40.5 1.0 C F:ASP9 4.4 41.7 1.0 N F:ASP11 4.5 30.3 1.0 O2A F:0KX401 4.5 53.5 1.0 O2G F:0KX401 4.6 34.3 1.0 CB F:LEU10 4.6 35.6 1.0 CE F:LYS159 4.7 38.1 1.0 CA F:ASP11 4.7 42.2 1.0 CB F:PHE13 4.8 35.2 1.0 N F:GLN12 4.8 48.4 1.0 O3' H:DC873 4.8 33.4 1.0 CA F:ASP9 4.8 46.0 1.0 N F:PHE13 4.8 43.9 1.0 O1B F:0KX401 4.8 35.2 1.0 C F:ASP11 4.9 40.6 1.0 O F:ASP107 5.0 41.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of MSDPO4-Dna Complex 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:13.4 occ:1.00 OD2 A:ASP107 1.9 62.6 1.0 O1A A:0KX902 2.0 25.9 1.0 OD1 A:ASP9 2.0 45.0 1.0 O2B A:0KX902 2.3 49.3 1.0 O1G A:0KX902 2.4 54.6 1.0 O A:LEU10 2.4 34.9 1.0 CG A:ASP107 2.6 60.8 1.0 OD1 A:ASP107 2.8 82.5 1.0 CG A:ASP9 2.9 52.5 1.0 OD2 A:ASP9 3.1 32.8 1.0 PA A:0KX902 3.4 38.8 1.0 PB A:0KX902 3.6 36.7 1.0 C A:LEU10 3.6 48.5 1.0 MG A:MG903 3.6 19.7 1.0 PG A:0KX902 3.8 41.8 1.0 N3A A:0KX902 3.9 42.8 1.0 NZ A:LYS159 4.0 40.5 1.0 CB A:ASP107 4.0 46.4 1.0 N A:LEU10 4.0 50.6 1.0 C5' A:0KX902 4.0 36.6 1.0 O A:HOH1026 4.1 36.3 1.0 O3B A:0KX902 4.1 38.1 1.0 O5' A:0KX902 4.2 38.4 1.0 CB A:ASP9 4.3 40.8 1.0 CA A:LEU10 4.3 57.8 1.0 C A:ASP9 4.4 44.9 1.0 O2G A:0KX902 4.4 38.0 1.0 O2A A:0KX902 4.5 47.9 1.0 O A:HOH1007 4.5 39.5 1.0 N A:ASP11 4.6 46.2 1.0 N A:GLN12 4.7 46.2 1.0 N A:PHE13 4.7 51.2 1.0 CB A:PHE13 4.7 41.4 1.0 CA A:ASP9 4.7 40.9 1.0 O1B A:0KX902 4.8 48.9 1.0 O3' C:DC873 4.8 37.0 1.0 CA A:ASP11 4.8 48.3 1.0 CB A:LEU10 4.9 48.0 1.0 CE A:LYS159 4.9 40.7 1.0 O3G A:0KX902 4.9 36.0 1.0 C A:ASP11 4.9 42.8 1.0 O A:ASP9 4.9 41.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of MSDPO4-Dna Complex 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:19.7 occ:1.00 O3' C:DC873 1.8 37.0 1.0 OE2 A:GLU108 1.8 65.2 1.0 OD2 A:ASP9 2.1 32.8 1.0 O A:HOH1007 2.2 39.5 1.0 CD A:GLU108 2.6 50.5 1.0 O1A A:0KX902 2.8 25.9 1.0 CG A:GLU108 2.8 65.1 1.0 C3' C:DC873 3.1 52.1 1.0 CG A:ASP9 3.3 52.5 1.0 CB A:ASP107 3.3 46.4 1.0 CG A:ASP107 3.4 60.8 1.0 OD2 A:ASP107 3.5 62.6 1.0 PA A:0KX902 3.6 38.8 1.0 MG A:MG901 3.6 13.4 1.0 O2A A:0KX902 3.6 47.9 1.0 O5' A:0KX902 3.8 38.4 1.0 OE1 A:GLU108 3.8 47.1 1.0 OD1 A:ASP9 3.8 45.0 1.0 C4' C:DC873 3.9 58.2 1.0 OD1 A:ASP107 3.9 82.5 1.0 O A:HOH1004 3.9 56.1 1.0 O A:HOH1026 4.2 36.3 1.0 C2' C:DC873 4.2 48.1 1.0 CB A:GLU108 4.2 35.1 1.0 C5' C:DC873 4.3 62.1 1.0 C5' A:0KX902 4.3 36.6 1.0 NZ A:LYS152 4.4 54.2 1.0 CB A:ASP9 4.5 40.8 1.0 CA A:ASP107 4.6 63.9 1.0 C A:ASP107 4.6 44.3 1.0 N A:GLU108 4.7 54.5 1.0 O5' C:DC873 4.7 50.6 1.0 O A:HOH1015 4.8 50.0 1.0 CA A:GLU108 5.0 47.9 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