Sodium in PDB 4yd2: Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate

All present enzymatic activity of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate:
2.7.7.7;

The structure of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate, PDB code: 4yd2 was solved by A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.61 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.083, 68.700, 114.977, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.2

The structure of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate (pdb code 4yd2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate, PDB code: 4yd2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:18.6 occ:1.00 OD2 A:ASP418 2.4 27.7 1.0 OP1 P:DT5 2.4 45.1 1.0 OD1 A:ASP332 2.5 16.4 1.0 OD1 A:ASP330 2.5 32.5 1.0 O3' P:DA4 2.5 40.5 0.9 P P:DT5 2.9 46.6 1.0 CG A:ASP330 3.1 32.9 1.0 CG A:ASP418 3.4 26.2 1.0 CG A:ASP332 3.4 15.9 1.0 OD2 A:ASP330 3.5 38.1 1.0 OD2 A:ASP332 3.7 16.7 1.0 C3' P:DA4 3.7 40.4 0.9 OP2 P:DT5 3.7 46.5 1.0 NA A:NA504 3.9 30.6 1.0 C4' P:DA4 3.9 41.6 0.9 C5' P:DA4 3.9 40.7 0.9 CB A:ASP330 4.0 27.3 1.0 CB A:ASP418 4.2 22.0 1.0 O5' P:DA4 4.3 39.1 0.9 O5' P:DT5 4.3 34.4 1.0 OD1 A:ASP418 4.3 28.3 1.0 NH2 A:ARG416 4.4 25.7 1.0 C5' P:DT5 4.6 33.2 1.0 OP1 P:DA4 4.7 41.9 0.9 CB A:ASP332 4.8 16.0 1.0 C2' P:DA4 4.9 39.9 0.9 CZ3 A:TRP434 5.0 35.0 1.0

Sodium binding site 2 out of 3 in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:30.6 occ:1.00 OP1 P:DT5 2.4 45.1 1.0 O A:HOH632 2.4 41.1 1.0 OD1 A:ASP330 2.5 32.5 1.0 O32 A:PPV507 2.5 28.2 0.8 OD2 A:ASP332 2.7 16.7 1.0 OD2 A:ASP330 2.7 38.1 1.0 O22 A:PPV507 2.8 38.0 0.8 CG A:ASP330 2.9 32.9 1.0 P2 A:PPV507 3.0 29.9 0.8 OPP A:PPV507 3.3 33.0 0.8 O A:HOH733 3.3 28.6 1.0 CG A:ASP332 3.7 15.9 1.0 P P:DT5 3.8 46.6 1.0 NA A:NA501 3.9 18.6 1.0 OD1 A:ASP332 4.1 16.4 1.0 O A:ASP330 4.1 19.3 1.0 N A:GLY320 4.3 15.6 1.0 CB A:ASP330 4.3 27.3 1.0 C A:ASP330 4.4 19.8 1.0 O5' P:DT5 4.4 34.4 1.0 O12 A:PPV507 4.5 29.8 0.8 OP2 P:DT5 4.5 46.5 1.0 C5' P:DT5 4.5 33.2 1.0 O A:HOH636 4.6 8.8 1.0 CA A:ASP330 4.7 23.4 1.0 N A:ASP330 4.7 25.5 1.0 CA A:GLY319 4.7 15.9 1.0 O3' P:DA4 4.9 40.5 0.9 N A:VAL331 5.0 17.2 1.0 O P:HOH101 5.0 54.7 1.0

Sodium binding site 3 out of 3 in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:37.4 occ:1.00 O A:THR241 2.5 31.7 1.0 O P:HOH102 2.5 32.5 1.0 O A:ILE243 2.5 30.6 1.0 OP1 P:DT3 2.9 44.9 1.0 O A:HOH659 3.0 24.8 1.0 O A:VAL246 3.2 30.3 1.0 C A:ILE243 3.3 30.1 1.0 O P:HOH103 3.5 33.4 1.0 C A:THR241 3.5 31.7 1.0 C A:GLN242 3.7 30.9 0.6 C A:GLN242 3.7 30.9 0.4 N A:ILE243 3.7 31.1 1.0 N A:PHE244 4.0 28.4 1.0 CA A:GLN242 4.0 30.6 0.4 CA A:GLN242 4.0 30.6 0.6 O A:GLN242 4.0 30.5 0.6 CA A:PHE244 4.1 26.1 1.0 O A:GLN242 4.1 30.5 0.4 CA A:ILE243 4.2 30.7 1.0 N A:GLN242 4.2 31.5 0.6 N A:GLN242 4.2 31.5 0.4 P P:DT3 4.2 44.7 1.0 C A:VAL246 4.2 31.5 1.0 N A:VAL246 4.3 30.7 1.0 N A:GLY245 4.4 27.9 1.0 CA A:THR241 4.6 33.5 1.0 OP2 P:DT3 4.7 42.4 1.0 C A:PHE244 4.7 28.2 1.0 CA A:VAL246 4.8 31.4 1.0

A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Creative Template-Dependent Synthesis By Human Polymerase Mu. Proc.Natl.Acad.Sci.Usa V. 112 E4530 2015.
ISSN: ESSN 1091-6490
PubMed: 26240373
DOI: 10.1073/PNAS.1505798112