Calcium 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:

Manganese	(Mn)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Dna Polymerase Mu Reactant Complex, MN2+ (4 Min), PDB code: 5tyu:

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca506 b:25.8 occ:0.60 MN A:MN502 0.0 26.0 0.4 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

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