Manganese in PDB 6juq: Mutant Poliv-Dna Incoming Nucleotide Complex 2

All present enzymatic activity of Mutant Poliv-Dna Incoming Nucleotide Complex 2:
2.7.7.7;

The structure of Mutant Poliv-Dna Incoming Nucleotide Complex 2, PDB code: 6juq 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)	86.01 / 2.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.151, 57.244, 110.793, 90.00, 92.26, 90.00
R / Rfree (%)	22.6 / 27.1

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

Manganese binding site 1 out of 4 in the Mutant Poliv-Dna Incoming Nucleotide Complex 2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mutant Poliv-Dna Incoming Nucleotide Complex 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn402 b:82.3 occ:1.00 O F:MET9 1.9 67.7 1.0 OD1 F:ASP8 2.1 79.7 1.0 O1B F:2TM401 2.1 86.4 1.0 OD2 F:ASP103 2.2 83.9 1.0 O1G F:2TM401 2.3 91.6 1.0 O1A F:2TM401 2.3 89.1 1.0 CG F:ASP8 3.0 73.1 1.0 C F:MET9 3.1 71.8 1.0 OD2 F:ASP8 3.2 75.6 1.0 PB F:2TM401 3.3 89.7 1.0 MN F:MN403 3.4 80.8 1.0 O F:HOH502 3.4 59.2 1.0 PG F:2TM401 3.5 90.4 1.0 CG F:ASP103 3.5 78.3 1.0 PA F:2TM401 3.6 90.0 1.0 O2G F:2TM401 3.8 82.8 1.0 N F:MET9 3.8 68.2 1.0 O3B F:2TM401 3.8 84.1 1.0 C1 F:2TM401 3.9 90.8 1.0 CA F:MET9 4.0 71.2 1.0 O5' F:2TM401 4.1 74.5 1.0 C5' F:2TM401 4.1 72.5 1.0 N F:ASP10 4.1 75.6 1.0 C F:ASP8 4.1 68.9 1.0 N F:CYS11 4.2 88.1 1.0 CA F:ASP10 4.3 75.6 1.0 OD1 F:ASP103 4.3 78.7 1.0 CB F:ASP8 4.3 68.5 1.0 CB F:ASP103 4.4 76.2 1.0 C F:ASP10 4.5 72.5 1.0 CB F:MET9 4.5 72.6 1.0 O2B F:2TM401 4.5 92.0 1.0 O F:ASP8 4.6 68.4 1.0 CA F:ASP8 4.6 68.8 1.0 O3G F:2TM401 4.7 83.4 1.0 O F:HOH501 4.8 83.4 1.0 N F:PHE12 4.8 91.3 1.0 O2A F:2TM401 4.8 72.8 1.0 CB F:PHE12 4.9 93.7 1.0 CA F:CYS11 4.9 93.2 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mutant Poliv-Dna Incoming Nucleotide Complex 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn403 b:80.8 occ:1.00 OD1 F:ASP103 2.2 78.7 1.0 OD2 F:ASP103 2.2 83.9 1.0 OE1 F:GLU104 2.2 79.2 1.0 OD2 F:ASP8 2.3 75.6 1.0 CG F:GLU104 2.5 74.7 1.0 CG F:ASP103 2.6 78.3 1.0 O1A F:2TM401 2.6 89.1 1.0 CD F:GLU104 2.7 78.2 1.0 O F:HOH501 3.0 83.4 1.0 C3' H:DC873 3.3 65.3 1.0 O3' H:DC873 3.3 66.5 1.0 MN F:MN402 3.4 82.3 1.0 CG F:ASP8 3.4 73.1 1.0 O5' F:2TM401 3.4 74.5 1.0 PA F:2TM401 3.5 90.0 1.0 OD1 F:ASP8 3.9 79.7 1.0 O F:HOH502 4.0 59.2 1.0 CB F:GLU104 4.0 69.5 1.0 OE2 F:GLU104 4.0 73.9 1.0 O2A F:2TM401 4.1 72.8 1.0 CB F:ASP103 4.1 76.2 1.0 C5' F:2TM401 4.1 72.5 1.0 C4' H:DC873 4.2 65.3 1.0 OG F:SER101 4.4 83.6 1.0 N F:GLU104 4.4 71.6 1.0 C F:ASP103 4.4 75.4 1.0 C2' H:DC873 4.5 67.7 1.0 C5' H:DC873 4.5 65.3 1.0 O1B F:2TM401 4.6 86.4 1.0 CB F:ASP8 4.6 68.5 1.0 O F:ASP103 4.6 80.7 1.0 CA F:GLU104 4.7 72.5 1.0 CA F:ASP103 4.8 76.2 1.0 O1G F:2TM401 4.8 91.6 1.0 O5' H:DC873 4.9 68.7 1.0 C1 F:2TM401 4.9 90.8 1.0 O F:MET9 5.0 67.7 1.0

Manganese binding site 3 out of 4 in the Mutant Poliv-Dna Incoming Nucleotide Complex 2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mutant Poliv-Dna Incoming Nucleotide Complex 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:0.2 occ:1.00 O1G A:2TM401 2.0 0.3 1.0 O1B A:2TM401 2.0 0.8 1.0 OD1 A:ASP8 2.1 0.7 1.0 O A:MET9 2.1 0.8 1.0 O1A A:2TM401 2.1 0.1 1.0 OD2 A:ASP103 2.1 0.1 1.0 MN A:MN403 2.9 0.2 1.0 CG A:ASP8 3.1 0.4 1.0 OD2 A:ASP8 3.3 1.0 1.0 C A:MET9 3.4 0.5 1.0 PB A:2TM401 3.4 0.3 1.0 PG A:2TM401 3.4 0.6 1.0 CG A:ASP103 3.4 0.1 1.0 PA A:2TM401 3.5 0.4 1.0 NZ A:LYS157 3.7 0.5 1.0 O2G A:2TM401 3.8 0.3 1.0 O3B A:2TM401 3.9 0.4 1.0 N A:MET9 3.9 0.2 1.0 C1 A:2TM401 4.0 0.3 1.0 OD1 A:ASP103 4.1 0.9 1.0 CA A:MET9 4.2 0.4 1.0 C5' A:2TM401 4.2 0.2 1.0 O5' A:2TM401 4.3 1.0 1.0 C A:ASP8 4.3 1.0 1.0 N A:ASP10 4.4 0.4 1.0 CB A:ASP8 4.4 0.2 1.0 CB A:ASP103 4.5 0.4 1.0 N A:CYS11 4.5 0.1 1.0 CA A:ASP10 4.5 0.4 1.0 OE1 A:GLU104 4.6 0.4 1.0 N A:PHE12 4.6 0.2 1.0 O2B A:2TM401 4.6 0.3 1.0 O3G A:2TM401 4.7 0.4 1.0 CB A:PHE12 4.7 0.4 1.0 O2A A:2TM401 4.7 0.6 1.0 C A:ASP10 4.7 0.2 1.0 CE A:LYS157 4.8 0.1 1.0 CA A:ASP8 4.8 0.5 1.0 O A:ASP8 4.8 1.0 1.0 CB A:MET9 4.9 0.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mutant Poliv-Dna Incoming Nucleotide Complex 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:0.2 occ:1.00 OD2 A:ASP8 2.1 1.0 1.0 OD2 A:ASP103 2.1 0.1 1.0 OE1 A:GLU104 2.1 0.4 1.0 OD1 A:ASP103 2.2 0.9 1.0 O1A A:2TM401 2.3 0.1 1.0 CG A:ASP103 2.6 0.1 1.0 CG A:GLU104 2.9 0.7 1.0 MN A:MN402 2.9 0.2 1.0 CD A:GLU104 2.9 0.6 1.0 CG A:ASP8 3.0 0.4 1.0 OD1 A:ASP8 3.2 0.7 1.0 O3' C:DC873 3.3 0.2 1.0 PA A:2TM401 3.5 0.4 1.0 C3' C:DC873 3.7 0.8 1.0 O5' A:2TM401 3.9 1.0 1.0 OE2 A:GLU104 4.1 0.5 1.0 CB A:ASP103 4.1 0.4 1.0 O1G A:2TM401 4.2 0.3 1.0 O2A A:2TM401 4.2 0.6 1.0 CB A:ASP8 4.2 0.2 1.0 CB A:GLU104 4.2 0.2 1.0 O1B A:2TM401 4.3 0.8 1.0 O A:ASP103 4.3 0.9 1.0 C5' A:2TM401 4.3 0.2 1.0 C A:ASP103 4.4 0.4 1.0 O A:MET9 4.6 0.8 1.0 C2' C:DC873 4.6 0.1 1.0 N A:GLU104 4.7 0.0 1.0 OG A:SER101 4.7 0.1 1.0 CA A:ASP8 4.7 0.5 1.0 CA A:ASP103 4.8 0.6 1.0 C4' C:DC873 4.9 0.5 1.0 C1 A:2TM401 4.9 0.3 1.0 N A:MET9 5.0 0.2 1.0 CA A:GLU104 5.0 0.9 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