Manganese in PDB 5tyu: Dna Polymerase Mu Reactant Complex, MN2+ (4 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, MN2+ (4 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Reactant Complex, MN2+ (4 Min), PDB code: 5tyu 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)	33.37 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.155, 62.223, 118.588, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The structure of Dna Polymerase Mu Reactant Complex, MN2+ (4 Min) also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min) (pdb code 5tyu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min), PDB code: 5tyu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min)


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 Reactant Complex, MN2+ (4 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:26.0 occ:0.40 CA A:CA506 0.0 25.8 0.6 OD2 A:ASP330 1.9 35.6 1.0 OD2 A:ASP418 2.0 25.2 1.0 OP1 P:DT5 2.0 25.8 0.4 OD1 A:ASP332 2.1 24.4 1.0 O3' P:DA4 2.4 29.0 0.4 O3' P:DA4 2.5 28.0 0.6 O P:HOH202 2.5 35.1 1.0 P P:DT5 2.7 26.1 0.4 O2A A:TTP501 2.7 25.8 0.6 CG A:ASP330 2.9 25.5 1.0 CG A:ASP332 3.1 23.8 1.0 CG A:ASP418 3.1 21.2 1.0 OD1 A:ASP330 3.2 24.5 1.0 OD2 A:ASP332 3.4 24.3 1.0 C3' P:DA4 3.6 29.7 0.4 C3' P:DA4 3.6 29.9 0.6 PA A:TTP501 3.6 26.7 0.6 MN A:MN503 3.6 28.1 1.0 OP2 P:DT5 3.7 27.3 0.4 O1A A:TTP501 3.7 28.9 0.6 O5' A:TTP501 3.8 26.9 0.6 C4' P:DA4 3.8 29.8 0.4 CB A:ASP418 3.8 20.7 1.0 C5' P:DA4 3.9 33.0 0.4 C5' P:DA4 3.9 33.0 0.6 C4' P:DA4 3.9 29.9 0.6 O5' P:DT5 3.9 26.8 0.4 OD1 A:ASP418 4.1 24.5 1.0 C5' A:TTP501 4.1 24.8 0.6 C5' P:DT5 4.2 24.7 0.4 CB A:ASP330 4.3 23.2 1.0 O P:HOH212 4.4 27.9 0.4 CB A:ASP332 4.5 23.8 1.0 CE1 A:HIS329 4.5 30.1 0.6 NH2 A:ARG416 4.5 28.2 1.0 O5' P:DA4 4.5 33.0 0.4 O5' P:DA4 4.6 33.1 0.6 CZ3 A:TRP434 4.6 27.3 1.0 OP1 P:DA4 4.6 30.6 0.6 OP1 P:DA4 4.7 30.6 0.4 C2' P:DA4 4.8 29.0 0.4 O2G A:TTP501 4.9 31.1 0.6 C2' P:DA4 4.9 29.2 0.6 NE2 A:HIS329 4.9 29.1 0.6 O32 A:PPV507 5.0 31.1 0.3 MN P:MN101 5.0 36.2 0.3

Manganese binding site 2 out of 4 in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min)


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 Reactant Complex, MN2+ (4 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:28.1 occ:1.00 O2A A:TTP501 1.8 25.8 0.6 O2G A:TTP501 2.1 31.1 0.6 OD1 A:ASP330 2.1 24.5 1.0 O A:HOH718 2.1 26.0 1.0 O1B A:TTP501 2.1 24.7 0.6 OD2 A:ASP332 2.2 24.3 1.0 O32 A:PPV507 2.2 31.1 0.3 O21 A:PPV507 2.3 25.1 0.4 OP1 P:DT5 2.4 25.8 0.4 PA A:TTP501 3.1 26.7 0.6 PB A:TTP501 3.2 26.4 0.6 P1 A:PPV507 3.2 27.2 0.4 O31 A:PPV507 3.2 30.4 0.4 CG A:ASP330 3.2 25.5 1.0 CG A:ASP332 3.3 23.8 1.0 PG A:TTP501 3.3 37.1 0.6 P2 A:PPV507 3.5 36.1 0.3 O3A A:TTP501 3.5 31.8 0.6 MN A:MN502 3.6 26.0 0.4 CA A:CA506 3.6 25.8 0.6 OD1 A:ASP332 3.7 24.4 1.0 OD2 A:ASP330 3.7 35.6 1.0 O3B A:TTP501 3.7 36.9 0.6 OPP A:PPV507 3.8 36.6 0.4 P P:DT5 3.8 26.1 0.4 O A:ASP330 3.9 27.3 1.0 O3G A:TTP501 4.0 32.7 0.6 O5' A:TTP501 4.1 26.9 0.6 C5' A:TTP501 4.1 24.8 0.6 O22 A:PPV507 4.1 33.2 0.3 O1A A:TTP501 4.1 28.9 0.6 O5' P:DT5 4.2 26.8 0.4 CE1 A:HIS329 4.2 30.1 0.6 C A:ASP330 4.3 24.4 1.0 ND1 A:HIS329 4.3 29.8 0.6 N A:GLY320 4.3 24.6 1.0 O A:HOH620 4.4 22.0 1.0 C5' P:DT5 4.4 24.7 0.4 O P:HOH212 4.5 27.9 0.4 O1G A:TTP501 4.5 32.9 0.6 O2B A:TTP501 4.5 26.1 0.6 CB A:ASP330 4.5 23.2 1.0 O11 A:PPV507 4.6 26.5 0.4 O A:HOH625 4.6 33.4 1.0 CB A:ASP332 4.6 23.8 1.0 CA A:GLY319 4.6 22.6 1.0 N A:ASP330 4.6 23.4 1.0 MN P:MN101 4.6 36.2 0.3 O12 A:PPV507 4.7 32.9 0.4 OP2 P:DT5 4.7 27.3 0.4 CA A:ASP330 4.7 22.5 1.0 O P:HOH202 4.8 35.1 1.0 O3' P:DA4 4.8 29.0 0.4 N A:VAL331 4.9 22.9 1.0 N A:ASP332 4.9 22.4 1.0

Manganese binding site 3 out of 4 in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min)


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 Reactant Complex, MN2+ (4 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:93.9 occ:1.00 NE2 A:HIS219 2.2 57.0 1.0 OE1 A:GLU218 3.0 65.3 1.0 CD2 A:HIS219 3.1 54.6 1.0 CE1 A:HIS219 3.3 58.5 1.0 CD A:GLU218 4.2 63.2 1.0 CG A:HIS219 4.3 50.5 1.0 ND1 A:HIS219 4.3 59.2 1.0 CB A:GLU218 4.7 47.8 1.0

Manganese binding site 4 out of 4 in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Mu Reactant Complex, MN2+ (4 Min) within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:36.2 occ:0.35 O1A A:TTP501 1.3 28.9 0.6 OP2 P:DT5 1.9 27.3 0.4 PA A:TTP501 2.1 26.7 0.6 O3A A:TTP501 2.2 31.8 0.6 O31 A:PPV507 2.4 30.4 0.4 O P:HOH212 2.5 27.9 0.4 P P:DT5 2.9 26.1 0.4 O5' A:TTP501 3.2 26.9 0.6 O2A A:TTP501 3.2 25.8 0.6 O5' P:DT5 3.4 26.8 0.4 OP1 P:DT5 3.4 25.8 0.4 O A:HOH611 3.6 44.4 1.0 CE1 A:HIS329 3.6 30.1 0.6 PB A:TTP501 3.7 26.4 0.6 C7 P:DT5 3.8 29.0 0.4 O P:HOH202 3.9 35.1 1.0 P1 A:PPV507 3.9 27.2 0.4 C5M A:TTP501 3.9 29.2 0.6 O32 A:PPV507 4.0 31.1 0.3 O2G A:TTP501 4.0 31.1 0.6 O1G A:TTP501 4.1 32.9 0.6 O3B A:TTP501 4.2 36.9 0.6 O12 A:PPV507 4.2 32.9 0.4 O3' P:DA4 4.3 29.0 0.4 PG A:TTP501 4.3 37.1 0.6 ND1 A:HIS329 4.3 29.8 0.6 OPP A:PPV507 4.4 36.6 0.4 P2 A:PPV507 4.4 36.1 0.3 O1B A:TTP501 4.5 24.7 0.6 NE2 A:HIS329 4.5 29.1 0.6 C5' A:TTP501 4.5 24.8 0.6 O2B A:TTP501 4.6 26.1 0.6 MN A:MN503 4.6 28.1 1.0 C6 A:TTP501 4.7 27.2 0.6 O11 A:PPV507 4.7 26.5 0.4 C6 P:DT5 4.7 27.2 0.4 C3' P:DA4 4.8 29.7 0.4 C5' P:DT5 4.8 24.7 0.4 C5 P:DT5 4.8 27.8 0.4 O A:HOH677 4.8 23.9 1.0 O21 A:PPV507 4.8 25.1 0.4 C5 A:TTP501 4.8 27.7 0.6 O3' P:DA4 4.9 28.0 0.6 MN A:MN502 5.0 26.0 0.4 CA A:CA506 5.0 25.8 0.6

J.A.Jamsen, W.A.Beard, L.C.Pedersen, D.D.Shock, A.F.Moon, J.M.Krahn, K.Bebenek, T.A.Kunkel, S.H.Wilson. Time-Lapse Crystallography Snapshots of A Double-Strand Break Repair Polymerase in Action. Nat Commun V. 8 253 2017.
ISSN: ESSN 2041-1723
PubMed: 28811466
DOI: 10.1038/S41467-017-00271-7