Magnesium in PDB 6jum: MSDPO4-Dna Complex 2

All present enzymatic activity of MSDPO4-Dna Complex 2:
2.7.7.7;

The structure of MSDPO4-Dna Complex 2, PDB code: 6jum was solved by D.T.Nair, M.J.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.96 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.020, 80.960, 211.610, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.4

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

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.9 occ:1.00 OD2 A:ASP107 2.1 22.3 1.0 O2G A:0KX401 2.2 25.7 1.0 O1A A:0KX401 2.2 26.1 1.0 OD1 A:ASP9 2.3 20.3 1.0 O2B A:0KX401 2.3 25.9 1.0 O A:LEU10 2.3 20.9 1.0 CG A:ASP9 3.1 20.7 1.0 CG A:ASP107 3.2 21.5 1.0 PB A:0KX401 3.2 26.8 1.0 OD2 A:ASP9 3.2 21.4 1.0 PG A:0KX401 3.4 27.0 1.0 PA A:0KX401 3.4 26.9 1.0 C A:LEU10 3.4 21.8 1.0 N3A A:0KX401 3.5 26.7 1.0 O3B A:0KX401 3.5 27.2 1.0 OD1 A:ASP107 3.6 20.5 1.0 MG A:MG403 3.6 22.1 1.0 O A:HOH547 3.9 20.9 1.0 NZ A:LYS159 3.9 22.4 1.0 N A:LEU10 4.0 21.4 1.0 O3G A:0KX401 4.0 27.7 1.0 CA A:LEU10 4.1 22.1 1.0 C5' A:0KX401 4.2 26.9 1.0 O5' A:0KX401 4.3 26.1 1.0 C A:ASP9 4.3 20.6 1.0 CB A:ASP9 4.3 20.1 1.0 N A:ASP11 4.5 23.0 1.0 CB A:ASP107 4.5 22.5 1.0 CB A:LEU10 4.6 23.1 1.0 O1B A:0KX401 4.6 27.5 1.0 O2A A:0KX401 4.7 27.1 1.0 O1G A:0KX401 4.7 27.8 1.0 O A:HOH609 4.7 20.7 1.0 CA A:ASP11 4.7 23.2 1.0 N A:GLN12 4.7 22.1 1.0 N A:PHE13 4.7 22.5 1.0 CB A:PHE13 4.7 22.7 1.0 CE A:LYS159 4.8 23.2 1.0 CA A:ASP9 4.8 20.1 1.0 O A:ASP9 4.8 20.3 1.0 C A:ASP11 4.9 22.7 1.0 O A:ASP107 5.0 21.1 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:22.1 occ:1.00 OD2 A:ASP9 2.1 21.4 1.0 OD1 A:ASP107 2.2 20.5 1.0 O1A A:0KX401 2.3 26.1 1.0 OE1 A:GLU108 2.3 20.4 1.0 O3' C:DC873 2.3 27.9 1.0 O A:HOH609 2.4 20.7 1.0 CG A:ASP107 3.2 21.5 1.0 CD A:GLU108 3.3 22.6 1.0 CG A:ASP9 3.3 20.7 1.0 PA A:0KX401 3.3 26.9 1.0 C3' C:DC873 3.5 30.3 1.0 OD2 A:ASP107 3.5 22.3 1.0 MG A:MG402 3.6 23.9 1.0 OD1 A:ASP9 3.7 20.3 1.0 O5' A:0KX401 3.7 26.1 1.0 O2A A:0KX401 3.7 27.1 1.0 O A:HOH547 3.9 20.9 1.0 CG A:GLU108 4.0 22.8 1.0 O C:HOH913 4.1 26.6 1.0 C5' A:0KX401 4.1 26.9 1.0 C4' C:DC873 4.2 29.3 1.0 OE2 A:GLU108 4.2 20.6 1.0 CB A:GLU108 4.4 22.0 1.0 C5' C:DC873 4.4 29.6 1.0 NZ A:LYS152 4.5 23.1 1.0 CB A:ASP9 4.5 20.1 1.0 CB A:ASP107 4.5 22.5 1.0 O2G A:0KX401 4.6 25.7 1.0 C2' C:DC873 4.6 30.6 1.0 O A:HOH658 4.6 25.1 1.0 N3A A:0KX401 4.7 26.7 1.0 C A:ASP107 4.7 22.2 1.0 O A:ASP107 4.8 21.1 1.0 O5' C:DC873 4.9 29.8 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:18.2 occ:1.00 OD2 F:ASP107 2.1 23.7 1.0 O1G F:0KX401 2.1 22.1 1.0 OD1 F:ASP9 2.2 19.8 1.0 O1B F:0KX401 2.3 21.5 1.0 O F:LEU10 2.3 17.7 1.0 O2A F:0KX401 2.3 20.0 1.0 CG F:ASP9 3.1 20.3 1.0 PB F:0KX401 3.2 21.8 1.0 CG F:ASP107 3.2 23.3 1.0 PA F:0KX401 3.4 21.4 1.0 PG F:0KX401 3.4 21.3 1.0 C F:LEU10 3.4 19.7 1.0 OD2 F:ASP9 3.5 20.8 1.0 O3B F:0KX401 3.6 21.3 1.0 MG F:MG403 3.6 17.6 1.0 N3A F:0KX401 3.6 21.5 1.0 OD1 F:ASP107 3.7 25.6 1.0 NZ F:LYS159 3.7 20.6 1.0 O F:HOH588 3.9 21.1 1.0 N F:LEU10 3.9 19.0 1.0 O3G F:0KX401 4.0 21.9 1.0 CA F:LEU10 4.2 19.6 1.0 C5' F:0KX401 4.2 23.0 1.0 O5' F:0KX401 4.4 21.6 1.0 C F:ASP9 4.4 18.5 1.0 CB F:ASP9 4.5 19.3 1.0 N F:ASP11 4.5 20.1 1.0 O2B F:0KX401 4.5 21.8 1.0 CB F:ASP107 4.5 23.5 1.0 O1A F:0KX401 4.6 21.3 1.0 N F:GLN12 4.6 22.1 1.0 O F:HOH555 4.6 17.6 1.0 N F:PHE13 4.6 22.1 1.0 CB F:LEU10 4.6 20.2 1.0 CE F:LYS159 4.7 21.5 1.0 CA F:ASP11 4.7 20.7 1.0 CB F:PHE13 4.7 22.8 1.0 O2G F:0KX401 4.7 21.1 1.0 O F:ASP9 4.8 18.1 1.0 O F:ASP107 4.8 20.1 1.0 C F:ASP11 4.8 21.0 1.0 CA F:ASP9 4.9 19.3 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:17.6 occ:1.00 OD1 F:ASP107 2.2 25.6 1.0 OD2 F:ASP9 2.2 20.8 1.0 O3' H:DC873 2.2 21.0 1.0 O2A F:0KX401 2.3 20.0 1.0 O F:HOH555 2.3 17.6 1.0 OE1 F:GLU108 2.3 23.6 1.0 CG F:ASP107 3.1 23.3 1.0 CG F:ASP9 3.2 20.3 1.0 C3' H:DC873 3.3 21.9 1.0 PA F:0KX401 3.4 21.4 1.0 OD2 F:ASP107 3.4 23.7 1.0 CD F:GLU108 3.4 22.8 1.0 O1A F:0KX401 3.5 21.3 1.0 OD1 F:ASP9 3.6 19.8 1.0 MG F:MG402 3.6 18.2 1.0 O5' F:0KX401 3.8 21.6 1.0 CG F:GLU108 4.0 22.1 1.0 O F:HOH588 4.0 21.1 1.0 CB F:GLU108 4.0 21.6 1.0 C4' H:DC873 4.1 22.2 1.0 C5' F:0KX401 4.1 23.0 1.0 NZ F:LYS152 4.2 22.4 1.0 OE2 F:GLU108 4.2 23.8 1.0 C5' H:DC873 4.3 22.5 1.0 O H:HOH915 4.3 14.9 1.0 CB F:ASP107 4.4 23.5 1.0 CB F:ASP9 4.5 19.3 1.0 C2' H:DC873 4.5 22.4 1.0 O F:ASP107 4.6 20.1 1.0 O1G F:0KX401 4.6 22.1 1.0 C F:ASP107 4.7 21.1 1.0 O5' H:DC873 4.8 24.0 1.0 O F:HOH695 4.8 21.0 1.0 N3A F:0KX401 4.8 21.5 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