Magnesium in PDB 6juo: MSDPO4-Dna Complex 4

All present enzymatic activity of MSDPO4-Dna Complex 4:
2.7.7.7;

The structure of MSDPO4-Dna Complex 4, PDB code: 6juo 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)	70.18 / 2.16
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.100, 81.030, 210.530, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.5

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

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:41.8 occ:1.00 O3' C:DC873 2.4 33.5 1.0 OD1 A:ASP107 2.4 41.4 1.0 O1A A:0KX401 2.5 26.6 1.0 OE2 A:GLU108 2.6 33.6 1.0 OD2 A:ASP9 2.7 36.6 1.0 CG A:ASP107 3.2 34.7 1.0 CG A:GLU108 3.3 28.7 1.0 C3' C:DC873 3.3 38.5 1.0 CD A:GLU108 3.3 32.1 1.0 OD2 A:ASP107 3.3 35.9 1.0 PA A:0KX401 3.4 29.0 1.0 MG A:MG403 3.6 24.0 1.0 O5' A:0KX401 3.7 29.5 1.0 CG A:ASP9 3.8 31.5 1.0 O2A A:0KX401 3.9 26.6 1.0 C5' A:0KX401 3.9 31.2 1.0 O A:HOH552 4.1 27.6 1.0 OD1 A:ASP9 4.2 35.5 1.0 C4' C:DC873 4.2 38.8 1.0 C5' C:DC873 4.4 40.5 1.0 OE1 A:GLU108 4.5 30.7 1.0 C2' C:DC873 4.5 39.3 1.0 O A:ASP107 4.6 27.8 1.0 CB A:ASP107 4.7 33.1 1.0 C A:ASP107 4.7 29.1 1.0 CB A:GLU108 4.7 28.5 1.0 O A:HOH634 4.8 41.5 1.0 O1G A:0KX401 4.8 32.8 1.0 O5' C:DC873 4.9 40.1 1.0 N3A A:0KX401 4.9 28.2 1.0 N A:GLU108 5.0 27.3 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:24.0 occ:1.00 O1A A:0KX401 2.0 26.6 1.0 OD2 A:ASP107 2.1 35.9 1.0 OD1 A:ASP9 2.2 35.5 1.0 O1G A:0KX401 2.2 32.8 1.0 O2B A:0KX401 2.3 28.5 1.0 O A:LEU10 2.5 23.9 1.0 CG A:ASP9 3.0 31.5 1.0 OD2 A:ASP9 3.2 36.6 1.0 CG A:ASP107 3.3 34.7 1.0 PB A:0KX401 3.3 27.4 1.0 PA A:0KX401 3.4 29.0 1.0 MG A:MG402 3.6 41.8 1.0 C A:LEU10 3.6 26.0 1.0 PG A:0KX401 3.6 29.1 1.0 N3A A:0KX401 3.7 28.2 1.0 O A:HOH552 3.7 27.6 1.0 OD1 A:ASP107 3.8 41.4 1.0 O3B A:0KX401 3.9 30.1 1.0 NZ A:LYS159 3.9 27.8 1.0 C5' A:0KX401 4.0 31.2 1.0 N A:LEU10 4.0 26.7 1.0 O2G A:0KX401 4.2 27.2 1.0 O5' A:0KX401 4.2 29.5 1.0 CA A:LEU10 4.3 28.3 1.0 CB A:ASP9 4.4 29.3 1.0 C A:ASP9 4.4 28.1 1.0 CB A:ASP107 4.5 33.1 1.0 CE A:LYS159 4.6 28.2 1.0 O2A A:0KX401 4.6 26.6 1.0 O3G A:0KX401 4.6 29.1 1.0 N A:ASP11 4.6 27.0 1.0 CB A:PHE13 4.7 29.0 1.0 O A:ASP107 4.7 27.8 1.0 O1B A:0KX401 4.8 32.5 1.0 CB A:LEU10 4.8 29.6 1.0 CA A:ASP9 4.9 27.4 1.0 N A:GLN12 4.9 26.6 1.0 CA A:ASP11 4.9 26.4 1.0 N A:PHE13 4.9 27.6 1.0 O A:ASP9 4.9 26.2 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:45.1 occ:1.00 OE1 F:GLU108 2.1 53.8 1.0 OD1 F:ASP107 2.2 50.5 1.0 OD2 F:ASP9 2.5 37.7 1.0 O3' H:DC873 2.5 33.9 1.0 O F:HOH554 2.7 38.1 1.0 O1A F:0KX401 2.7 28.6 1.0 CG F:ASP107 3.1 40.4 1.0 CD F:GLU108 3.2 47.9 1.0 C3' H:DC873 3.3 38.0 1.0 CG F:ASP9 3.5 32.9 1.0 MG F:MG403 3.7 25.0 1.0 PA F:0KX401 3.7 31.1 1.0 OD2 F:ASP107 3.8 40.5 1.0 CG F:GLU108 3.9 42.3 1.0 CB F:ASP107 3.9 39.5 1.0 OD1 F:ASP9 3.9 31.7 1.0 O F:HOH574 3.9 22.0 1.0 CB F:GLU108 4.0 41.4 1.0 O5' F:0KX401 4.1 32.8 1.0 O2A F:0KX401 4.2 32.0 1.0 OE2 F:GLU108 4.2 50.6 1.0 C5' F:0KX401 4.2 35.2 1.0 C4' H:DC873 4.2 38.8 1.0 C5' H:DC873 4.4 42.1 1.0 C2' H:DC873 4.5 38.0 1.0 O5' H:DC873 4.6 46.0 1.0 CB F:ASP9 4.7 30.2 1.0 C F:ASP107 4.8 34.8 1.0 O F:ASP107 4.8 33.4 1.0 CA F:ASP107 5.0 35.1 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:25.0 occ:1.00 OD2 F:ASP107 2.0 40.5 1.0 OD1 F:ASP9 2.1 31.7 1.0 O1A F:0KX401 2.2 28.6 1.0 O F:LEU10 2.4 24.1 1.0 O2B F:0KX401 2.4 29.1 1.0 O1G F:0KX401 2.5 33.4 1.0 CG F:ASP107 2.8 40.4 1.0 OD1 F:ASP107 3.0 50.5 1.0 CG F:ASP9 3.1 32.9 1.0 PB F:0KX401 3.3 30.0 1.0 OD2 F:ASP9 3.3 37.7 1.0 PA F:0KX401 3.4 31.1 1.0 C F:LEU10 3.6 27.6 1.0 PG F:0KX401 3.6 33.3 1.0 MG F:MG402 3.7 45.1 1.0 O3B F:0KX401 3.7 31.9 1.0 N3A F:0KX401 3.7 30.1 1.0 O F:HOH574 3.7 22.0 1.0 NZ F:LYS159 3.8 33.0 1.0 N F:LEU10 3.9 26.0 1.0 C5' F:0KX401 4.1 35.2 1.0 CB F:ASP107 4.2 39.5 1.0 CA F:LEU10 4.2 27.6 1.0 C F:ASP9 4.3 26.8 1.0 O2G F:0KX401 4.3 30.9 1.0 O5' F:0KX401 4.4 32.8 1.0 CB F:ASP9 4.4 30.2 1.0 O F:HOH554 4.5 38.1 1.0 O2A F:0KX401 4.6 32.0 1.0 O1B F:0KX401 4.7 33.0 1.0 N F:ASP11 4.7 26.9 1.0 CB F:PHE13 4.7 28.5 1.0 CB F:LEU10 4.7 27.8 1.0 CE F:LYS159 4.7 31.5 1.0 O F:ASP107 4.7 33.4 1.0 CA F:ASP9 4.7 26.6 1.0 N F:PHE13 4.8 29.0 1.0 N F:GLN12 4.8 27.3 1.0 O F:ASP9 4.8 28.2 1.0 O3G F:0KX401 4.9 32.1 1.0 CA F:ASP11 4.9 27.0 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