Magnesium in PDB 6jup: Mutant Poliv-Dna Incoming Nucleotide Complex

All present enzymatic activity of Mutant Poliv-Dna Incoming Nucleotide Complex:
2.7.7.7;

The structure of Mutant Poliv-Dna Incoming Nucleotide Complex, PDB code: 6jup 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)	69.71 / 2.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.184, 56.974, 111.136, 90.00, 92.90, 90.00
R / Rfree (%)	22.1 / 24.5

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

Magnesium binding site 1 out of 4 in the Mutant Poliv-Dna Incoming Nucleotide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant Poliv-Dna Incoming Nucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:58.6 occ:1.00 O2B F:0KX401 1.7 97.2 1.0 OD1 F:ASP8 2.0 0.8 1.0 O F:MET9 2.0 72.4 1.0 O1G F:0KX401 2.3 0.5 1.0 O2A F:0KX401 2.3 85.1 1.0 OD2 F:ASP103 2.3 81.4 1.0 PB F:0KX401 3.1 68.7 1.0 CG F:ASP8 3.1 81.2 1.0 C F:MET9 3.2 76.2 1.0 MG F:MG403 3.3 56.8 1.0 PA F:0KX401 3.5 69.3 1.0 PG F:0KX401 3.5 77.0 1.0 CG F:ASP103 3.6 65.2 1.0 N3A F:0KX401 3.7 75.6 1.0 O3B F:0KX401 3.7 77.4 1.0 OD2 F:ASP8 3.8 89.2 1.0 C5' F:0KX401 3.8 64.7 1.0 N F:MET9 3.8 66.9 1.0 CA F:MET9 4.0 81.1 1.0 O5' F:0KX401 4.1 61.2 1.0 O3G F:0KX401 4.1 80.7 1.0 O1B F:0KX401 4.2 79.4 1.0 N F:ASP10 4.2 81.0 1.0 C F:ASP8 4.2 71.0 1.0 CB F:ASP8 4.3 81.8 1.0 CA F:ASP10 4.4 84.0 1.0 CB F:ASP103 4.4 69.0 1.0 OD1 F:ASP103 4.4 0.2 1.0 NZ F:LYS157 4.5 81.8 1.0 CB F:MET9 4.5 78.9 1.0 N F:CYS11 4.6 79.2 1.0 CA F:ASP8 4.6 83.7 1.0 O2G F:0KX401 4.7 66.6 1.0 C F:ASP10 4.7 72.6 1.0 O1A F:0KX401 4.7 60.1 1.0 O F:ASP8 4.8 78.2 1.0 N F:PHE12 4.8 76.9 1.0 CB F:PHE12 4.8 77.8 1.0 O F:ASP103 5.0 73.8 1.0

Magnesium binding site 2 out of 4 in the Mutant Poliv-Dna Incoming Nucleotide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant Poliv-Dna Incoming Nucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:56.8 occ:1.00 OE1 F:GLU104 1.9 98.2 1.0 OD2 F:ASP103 2.4 81.4 1.0 O2A F:0KX401 2.5 85.1 1.0 OD1 F:ASP103 2.6 0.2 1.0 OD2 F:ASP8 2.6 89.2 1.0 OD1 F:ASP8 2.7 0.8 1.0 CG F:ASP103 2.8 65.2 1.0 CG F:ASP8 2.9 81.2 1.0 CD F:GLU104 3.1 81.4 1.0 O3' H:DC873 3.3 83.7 1.0 MG F:MG402 3.3 58.6 1.0 C3' H:DC873 3.4 73.7 1.0 PA F:0KX401 3.6 69.3 1.0 O5' F:0KX401 3.7 61.2 1.0 CB F:GLU104 3.8 71.8 1.0 CG F:GLU104 3.9 70.5 1.0 OE2 F:GLU104 4.0 82.4 1.0 O1A F:0KX401 4.2 60.1 1.0 C5' F:0KX401 4.2 64.7 1.0 OG F:SER101 4.3 80.2 1.0 CB F:ASP103 4.3 69.0 1.0 CB F:ASP8 4.3 81.8 1.0 C4' H:DC873 4.3 81.7 1.0 O F:ASP103 4.3 73.8 1.0 O2B F:0KX401 4.4 97.2 1.0 C2' H:DC873 4.5 92.7 1.0 C F:ASP103 4.5 81.4 1.0 C5' H:DC873 4.6 75.8 1.0 CA F:GLU104 4.7 76.5 1.0 O1G F:0KX401 4.7 0.5 1.0 CA F:ASP8 4.8 83.7 1.0 N F:GLU104 4.9 77.2 1.0 O F:MET9 5.0 72.4 1.0 O5' H:DC873 5.0 84.4 1.0

Magnesium binding site 3 out of 4 in the Mutant Poliv-Dna Incoming Nucleotide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutant Poliv-Dna Incoming Nucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:85.0 occ:1.00 O2B A:0KX401 1.8 94.8 1.0 OD1 A:ASP8 1.9 1.0 1.0 OD2 A:ASP103 2.0 0.7 1.0 O A:MET9 2.1 93.9 1.0 O1A A:0KX401 2.1 97.9 1.0 O1G A:0KX401 2.2 0.1 1.0 CG A:ASP8 3.0 0.9 1.0 MG A:MG403 3.1 0.4 1.0 PB A:0KX401 3.1 91.5 1.0 C A:MET9 3.2 97.1 1.0 CG A:ASP103 3.3 0.1 1.0 PA A:0KX401 3.3 92.6 1.0 OD2 A:ASP8 3.4 0.4 1.0 PG A:0KX401 3.5 91.8 1.0 N A:MET9 3.7 1.0 1.0 N3A A:0KX401 3.7 93.4 1.0 O3B A:0KX401 3.8 95.8 1.0 C5' A:0KX401 3.8 93.5 1.0 OD1 A:ASP103 3.9 98.2 1.0 O5' A:0KX401 4.0 92.9 1.0 CA A:MET9 4.0 0.1 1.0 O2G A:0KX401 4.1 0.7 1.0 CB A:ASP8 4.2 0.1 1.0 O1B A:0KX401 4.3 93.9 1.0 N A:ASP10 4.3 0.2 1.0 C A:ASP8 4.3 99.1 1.0 CB A:ASP103 4.3 0.2 1.0 N A:CYS11 4.4 0.3 1.0 CA A:ASP10 4.5 0.1 1.0 O2A A:0KX401 4.5 89.5 1.0 N A:PHE12 4.6 0.5 1.0 CB A:MET9 4.6 0.5 1.0 CA A:ASP8 4.6 0.3 1.0 O3G A:0KX401 4.7 97.4 1.0 CB A:PHE12 4.7 0.1 1.0 C A:ASP10 4.8 0.3 1.0 NZ A:LYS157 4.8 0.1 1.0 OE1 A:GLU104 4.9 0.7 1.0 O A:ASP103 4.9 0.4 1.0

Magnesium binding site 4 out of 4 in the Mutant Poliv-Dna Incoming Nucleotide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mutant Poliv-Dna Incoming Nucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:0.4 occ:1.00 OE1 A:GLU104 2.1 0.7 1.0 OD2 A:ASP8 2.3 0.4 1.0 OD1 A:ASP103 2.3 98.2 1.0 O1A A:0KX401 2.3 97.9 1.0 CG A:GLU104 2.5 0.4 1.0 OD1 A:ASP8 2.5 1.0 1.0 CG A:ASP8 2.6 0.9 1.0 OD2 A:ASP103 2.6 0.7 1.0 CD A:GLU104 2.6 0.4 1.0 CG A:ASP103 2.8 0.1 1.0 MG A:MG402 3.1 85.0 1.0 O3' C:DC873 3.2 98.2 1.0 PA A:0KX401 3.4 92.6 1.0 C3' C:DC873 3.6 97.7 1.0 O5' A:0KX401 3.7 92.9 1.0 OE2 A:GLU104 3.9 1.0 1.0 O2A A:0KX401 3.9 89.5 1.0 CB A:GLU104 3.9 98.5 1.0 CB A:ASP8 3.9 0.1 1.0 O A:ASP103 4.1 0.4 1.0 C5' A:0KX401 4.2 93.5 1.0 C A:ASP103 4.2 0.9 1.0 CB A:ASP103 4.2 0.2 1.0 O2B A:0KX401 4.4 94.8 1.0 O1G A:0KX401 4.4 0.1 1.0 CA A:ASP8 4.4 0.3 1.0 N A:GLU104 4.5 0.3 1.0 CA A:GLU104 4.6 1.0 1.0 C2' C:DC873 4.6 98.4 1.0 N A:MET9 4.8 1.0 1.0 C4' C:DC873 4.8 99.5 1.0 O A:MET9 4.8 93.9 1.0 CA A:ASP103 4.8 0.9 1.0 OG A:SER101 4.9 99.2 1.0 N3A A:0KX401 4.9 93.4 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