Manganese in PDB 7kti: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN), PDB code: 7kti was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.99 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.965, 68.716, 110.586, 90, 90, 90
R / Rfree (%)	16.2 / 17.9

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN) (pdb code 7kti). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN), PDB code: 7kti:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:20.6 occ:0.87 O21 A:PPV501 2.1 20.0 0.8 OD1 A:ASP330 2.1 25.7 1.0 O32 A:PPV501 2.2 23.4 0.7 OD2 A:ASP332 2.2 22.5 1.0 O A:HOH716 2.3 22.6 1.0 OP1 P:8OG5 2.3 34.0 0.9 CG A:ASP330 3.2 29.1 1.0 P1 A:PPV501 3.2 22.7 0.8 CG A:ASP332 3.2 20.4 1.0 P2 A:PPV501 3.4 26.6 0.6 O31 A:PPV501 3.5 24.8 0.7 MN A:MN503 3.6 19.6 0.7 OD1 A:ASP332 3.6 22.5 1.0 OD2 A:ASP330 3.7 34.4 1.0 OPP A:PPV501 3.7 23.9 0.7 P P:8OG5 3.7 29.9 0.9 O A:HOH809 4.0 38.2 1.0 O5' P:8OG5 4.1 31.0 0.9 O A:ASP330 4.1 19.7 1.0 O12 A:PPV501 4.1 33.8 1.0 C5' P:8OG5 4.1 32.9 0.9 N A:GLY320 4.3 13.5 1.0 C A:ASP330 4.3 20.5 1.0 O A:HOH608 4.4 17.9 1.0 O A:HOH744 4.4 31.9 1.0 CB A:ASP330 4.5 24.0 1.0 OP2 P:8OG5 4.5 30.7 0.9 O A:HOH602 4.5 29.8 1.0 O11 A:PPV501 4.5 23.5 0.9 CA A:GLY319 4.6 14.5 1.0 O22 A:PPV501 4.6 28.5 0.8 CB A:ASP332 4.6 15.1 1.0 N A:ASP330 4.8 19.5 1.0 CA A:ASP330 4.8 21.1 1.0 O3' P:DA4 4.8 27.7 1.0 N A:VAL331 4.9 19.0 1.0 N A:ASP332 4.9 14.2 1.0

Manganese binding site 2 out of 3 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:19.6 occ:0.72 OD2 A:ASP330 1.9 34.4 1.0 OP1 P:8OG5 2.1 34.0 0.9 OD2 A:ASP418 2.1 22.8 1.0 OD1 A:ASP332 2.2 22.5 1.0 O A:HOH602 2.3 29.8 1.0 O3' P:DA4 2.7 27.7 1.0 P P:8OG5 2.8 29.9 0.9 CG A:ASP330 2.9 29.1 1.0 CG A:ASP418 3.1 18.6 1.0 CG A:ASP332 3.1 20.4 1.0 OD1 A:ASP330 3.2 25.7 1.0 OD2 A:ASP332 3.5 22.5 1.0 MN A:MN502 3.6 20.6 0.9 OP2 P:8OG5 3.8 30.7 0.9 C3' P:DA4 3.8 25.7 1.0 CB A:ASP418 3.8 15.9 1.0 C4' P:DA4 4.0 24.5 1.0 C5' P:DA4 4.0 23.6 1.0 O5' P:8OG5 4.1 31.0 0.9 OD1 A:ASP418 4.1 18.7 1.0 O A:HOH809 4.1 38.2 1.0 CB A:ASP330 4.2 24.0 1.0 C5' P:8OG5 4.3 32.9 0.9 CB A:ASP332 4.5 15.1 1.0 NH2 A:ARG416 4.5 19.9 1.0 OP1 P:DA4 4.7 24.1 1.0 CZ3 A:TRP434 4.7 20.4 1.0 O32 A:PPV501 4.8 23.4 0.7 O5' P:DA4 4.8 23.6 1.0 O A:VAL331 4.9 15.2 1.0 N A:ASP418 5.0 15.0 1.0

Manganese binding site 3 out of 3 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN) within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:21.7 occ:0.40 O A:HOH842 2.1 26.5 1.0 O31 A:PPV501 2.3 24.8 0.7 O A:HOH660 2.3 42.4 1.0 O8 P:8OG5 2.3 38.2 0.9 OP2 P:8OG5 2.4 30.7 0.9 O5' P:8OG5 3.1 31.0 0.9 P P:8OG5 3.3 29.9 0.9 C8 P:8OG5 3.5 36.7 0.9 P1 A:PPV501 3.7 22.7 0.8 O A:HOH753 3.9 18.5 1.0 O P:HOH213 4.0 52.5 1.0 OP1 P:8OG5 4.1 34.0 0.9 N7 P:8OG5 4.2 36.4 0.9 O22 A:PPV501 4.2 28.5 0.8 C3' P:8OG5 4.2 35.2 0.9 O11 A:PPV501 4.3 23.5 0.9 OPP A:PPV501 4.4 23.9 0.7 C5' P:8OG5 4.5 32.9 0.9 O32 A:PPV501 4.5 23.4 0.7 O3' P:DA4 4.6 27.7 1.0 N9 P:8OG5 4.7 34.0 0.9 O21 A:PPV501 4.7 20.0 0.8 P2 A:PPV501 4.7 26.6 0.6 O A:HOH809 4.8 38.2 1.0 CB A:LYS438 4.8 16.7 1.0 C3' P:DA4 4.8 25.7 1.0 C4' P:8OG5 4.8 33.8 0.9 O A:HOH752 4.9 34.5 1.0 C2' P:8OG5 4.9 36.1 0.9 O4' P:8OG5 5.0 31.6 0.9

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6