Magnesium in PDB 6jul: MSDPO4-Dna Complex 1

All present enzymatic activity of MSDPO4-Dna Complex 1:
2.7.7.7;

The structure of MSDPO4-Dna Complex 1, PDB code: 6jul 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)	70.17 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.960, 80.780, 210.520, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.9

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

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:32.1 occ:1.00 OE2 F:GLU108 2.2 47.9 1.0 O3' H:DC873 2.2 30.7 1.0 OD2 F:ASP107 2.2 31.4 1.0 OD2 F:ASP9 2.3 27.9 1.0 O2A F:0KX401 2.3 25.5 1.0 CG F:ASP107 3.2 29.4 1.0 CD F:GLU108 3.2 45.5 1.0 C3' H:DC873 3.3 30.4 1.0 PA F:0KX401 3.3 26.1 1.0 CG F:ASP9 3.4 26.0 1.0 CG F:GLU108 3.5 40.9 1.0 MG F:MG403 3.5 25.3 1.0 CB F:ASP107 3.7 32.6 1.0 O5' F:0KX401 3.8 26.4 1.0 O1A F:0KX401 3.8 25.5 1.0 O F:HOH546 3.9 25.2 1.0 OD1 F:ASP9 3.9 26.3 1.0 C5' F:0KX401 4.0 28.7 1.0 O F:HOH565 4.1 43.5 1.0 OD1 F:ASP107 4.1 26.1 1.0 CB F:GLU108 4.2 37.0 1.0 C4' H:DC873 4.2 31.5 1.0 O F:HOH577 4.3 37.5 1.0 OE1 F:GLU108 4.3 46.1 1.0 NZ F:LYS152 4.4 39.6 1.0 C2' H:DC873 4.5 31.6 1.0 C5' H:DC873 4.5 31.9 1.0 CB F:ASP9 4.6 24.3 1.0 O5' H:DC873 4.7 34.1 1.0 O1G F:0KX401 4.7 27.2 1.0 N3A F:0KX401 4.8 26.5 1.0 C F:ASP107 4.8 34.6 1.0 O F:ASP107 4.9 32.7 1.0 O1B F:0KX401 4.9 27.9 1.0 N F:GLU108 4.9 36.5 1.0 CA F:ASP107 5.0 32.6 1.0

Magnesium binding site 2 out of 4 in the MSDPO4-Dna Complex 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:25.3 occ:1.00 O2A F:0KX401 2.2 25.5 1.0 OD1 F:ASP9 2.2 26.3 1.0 O1B F:0KX401 2.2 27.9 1.0 O1G F:0KX401 2.2 27.2 1.0 O F:LEU10 2.2 25.3 1.0 OD1 F:ASP107 2.3 26.1 1.0 OD2 F:ASP107 2.3 31.4 1.0 CG F:ASP107 2.6 29.4 1.0 CG F:ASP9 3.0 26.0 1.0 OD2 F:ASP9 3.2 27.9 1.0 PB F:0KX401 3.4 26.8 1.0 PA F:0KX401 3.4 26.1 1.0 C F:LEU10 3.4 23.8 1.0 MG F:MG402 3.5 32.1 1.0 N3A F:0KX401 3.6 26.5 1.0 PG F:0KX401 3.6 26.2 1.0 O F:HOH546 3.8 25.2 1.0 O3B F:0KX401 3.8 25.9 1.0 N F:LEU10 3.9 22.6 1.0 NZ F:LYS159 4.0 26.9 1.0 C5' F:0KX401 4.0 28.7 1.0 CA F:LEU10 4.1 24.1 1.0 CB F:ASP107 4.1 32.6 1.0 O3G F:0KX401 4.2 25.8 1.0 C F:ASP9 4.2 23.5 1.0 O5' F:0KX401 4.3 26.4 1.0 CB F:ASP9 4.4 24.3 1.0 N F:ASP11 4.5 21.9 1.0 CB F:LEU10 4.6 24.6 1.0 O1A F:0KX401 4.6 25.5 1.0 CB F:PHE13 4.7 24.1 1.0 O2B F:0KX401 4.7 27.6 1.0 O F:ASP9 4.7 24.5 1.0 CA F:ASP9 4.7 23.2 1.0 O F:ASP107 4.7 32.7 1.0 N F:GLN12 4.7 23.9 1.0 N F:PHE13 4.8 25.6 1.0 CA F:ASP11 4.8 23.6 1.0 O2G F:0KX401 4.9 25.2 1.0 CE F:LYS159 4.9 25.8 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:38.4 occ:1.00 O3' C:DC873 2.2 36.2 1.0 C3' C:DC873 2.3 36.8 1.0 OE2 A:GLU108 2.3 33.1 1.0 OD2 A:ASP107 2.8 35.6 1.0 O2A A:0KX401 2.8 26.0 1.0 O A:HOH567 2.8 29.5 1.0 O5' A:0KX401 3.3 26.2 1.0 OD2 A:ASP9 3.3 27.9 1.0 CD A:GLU108 3.4 28.2 1.0 C4' C:DC873 3.4 36.2 1.0 PA A:0KX401 3.4 25.9 1.0 C2' C:DC873 3.5 36.3 1.0 CG A:ASP107 3.6 30.0 1.0 C5' A:0KX401 3.6 27.8 1.0 O C:HOH903 3.7 30.7 1.0 CG A:GLU108 3.7 26.2 1.0 O1A A:0KX401 3.8 26.1 1.0 C5' C:DC873 3.9 36.6 1.0 CB A:ASP107 3.9 28.6 1.0 MG A:MG403 4.1 27.4 1.0 O A:HOH566 4.3 18.7 1.0 CG A:ASP9 4.3 25.6 1.0 O5' C:DC873 4.4 36.5 1.0 OD1 A:ASP107 4.4 30.8 1.0 OE1 A:GLU108 4.5 28.2 1.0 OD1 A:ASP9 4.5 25.9 1.0 O4' C:DC873 4.6 34.5 1.0 C1' C:DC873 4.7 34.5 1.0 OP1 C:DC873 4.9 40.0 1.0 NZ A:LYS152 4.9 35.8 1.0 CB A:GLU108 4.9 25.7 1.0 N3A A:0KX401 5.0 25.9 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:27.4 occ:1.00 O2A A:0KX401 2.1 26.0 1.0 OD1 A:ASP9 2.2 25.9 1.0 O2G A:0KX401 2.2 27.6 1.0 O A:LEU10 2.2 23.5 1.0 O1B A:0KX401 2.2 26.6 1.0 OD2 A:ASP107 2.2 35.6 1.0 OD1 A:ASP107 2.2 30.8 1.0 CG A:ASP107 2.7 30.0 1.0 CG A:ASP9 3.2 25.6 1.0 PB A:0KX401 3.3 26.1 1.0 C A:LEU10 3.4 23.8 1.0 PA A:0KX401 3.4 25.9 1.0 OD2 A:ASP9 3.5 27.9 1.0 PG A:0KX401 3.6 26.6 1.0 N3A A:0KX401 3.7 25.9 1.0 O3B A:0KX401 3.8 26.8 1.0 NZ A:LYS159 3.9 22.0 1.0 N A:LEU10 3.9 24.8 1.0 C5' A:0KX401 3.9 27.8 1.0 O A:HOH566 4.0 18.7 1.0 MG A:MG402 4.1 38.4 1.0 CA A:LEU10 4.1 24.4 1.0 CB A:ASP107 4.1 28.6 1.0 O5' A:0KX401 4.2 26.2 1.0 O3G A:0KX401 4.3 26.0 1.0 C A:ASP9 4.4 24.7 1.0 N A:ASP11 4.5 24.4 1.0 CB A:ASP9 4.5 25.1 1.0 CB A:PHE13 4.5 24.0 1.0 CB A:LEU10 4.6 24.8 1.0 O1A A:0KX401 4.7 26.1 1.0 O2B A:0KX401 4.7 28.5 1.0 CE A:LYS159 4.7 23.2 1.0 O1G A:0KX401 4.8 28.8 1.0 N A:GLN12 4.8 24.4 1.0 O A:ASP107 4.8 26.4 1.0 CA A:ASP9 4.8 24.6 1.0 N A:PHE13 4.9 25.1 1.0 CA A:ASP11 4.9 24.2 1.0 C A:ASP11 5.0 24.3 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