Magnesium in PDB 4m0a: Human Dna Polymerase Mu Post-Catalytic Complex

All present enzymatic activity of Human Dna Polymerase Mu Post-Catalytic Complex:
2.7.7.7;

The structure of Human Dna Polymerase Mu Post-Catalytic Complex, PDB code: 4m0a was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.38 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.018, 68.670, 110.444, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20

The structure of Human Dna Polymerase Mu Post-Catalytic Complex also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Human Dna Polymerase Mu Post-Catalytic Complex (pdb code 4m0a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Mu Post-Catalytic Complex, PDB code: 4m0a:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Mu Post-Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Mu Post-Catalytic Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:5.6 occ:1.00 OD1 A:ASP330 2.1 6.6 0.5 O A:HOH601 2.1 7.9 1.0 O12 A:PPV503 2.1 1.2 0.5 OD2 A:ASP332 2.1 4.7 1.0 OP1 P:DT5 2.1 3.2 1.0 OD2 A:ASP330 2.3 6.8 0.5 O A:HOH900 2.4 13.4 1.0 CG A:ASP330 3.1 8.0 0.5 CG A:ASP332 3.2 4.4 1.0 P2 A:PPV503 3.3 6.5 0.8 MN A:MN505 3.3 15.4 1.0 CG A:ASP330 3.5 8.5 0.5 O22 A:PPV503 3.5 9.8 0.8 P P:DT5 3.5 4.4 1.0 OD1 A:ASP332 3.5 4.9 1.0 OD2 A:ASP330 3.5 8.2 0.5 OPP A:PPV503 4.0 9.4 0.8 O5' P:DT5 4.0 2.3 1.0 C5' P:DT5 4.0 1.5 1.0 OD1 A:ASP330 4.0 10.5 0.5 O A:ASP330 4.1 5.3 0.5 MG A:MG506 4.2 22.7 1.0 O A:ASP330 4.2 5.3 0.5 O A:HOH617 4.3 3.9 1.0 N A:GLY320 4.3 1.8 1.0 OP2 P:DT5 4.4 4.6 1.0 CB A:ASP330 4.4 6.0 0.5 O A:HOH730 4.5 17.8 1.0 CA A:GLY319 4.5 2.4 1.0 O32 A:PPV503 4.5 2.9 0.8 C A:ASP330 4.5 5.7 0.5 CB A:ASP332 4.5 2.2 1.0 O A:HOH665 4.5 19.2 1.0 C A:ASP330 4.5 5.7 0.5 O P:HOH208 4.5 13.9 1.0 O3' P:DA4 4.5 4.3 1.0 CB A:ASP330 4.7 5.9 0.5 O P:HOH218 4.7 21.4 1.0 O11 A:PPV503 4.9 15.1 0.5 N A:ASP332 4.9 2.1 1.0 P1 A:PPV503 4.9 15.4 0.5 C A:GLY319 5.0 2.1 1.0 CA A:ASP330 5.0 6.2 0.5 CA A:ASP330 5.0 6.2 0.5

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Mu Post-Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Mu Post-Catalytic Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:10.8 occ:1.00 O A:VAL246 2.4 10.2 1.0 O A:ILE243 2.4 8.3 1.0 O P:HOH202 2.4 12.1 1.0 O A:THR241 2.4 11.5 1.0 O A:HOH737 2.5 17.2 1.0 OP1 P:DT3 2.6 7.9 1.0 C A:ILE243 3.4 9.0 1.0 C A:VAL246 3.4 9.5 1.0 C A:THR241 3.4 14.2 1.0 N A:VAL246 3.6 10.4 1.0 P P:DT3 3.7 8.6 1.0 O P:HOH213 3.9 24.9 1.0 OP2 P:DT3 3.9 5.4 1.0 CA A:VAL246 4.0 10.3 1.0 N A:ILE243 4.0 12.1 1.0 N A:PHE244 4.1 7.4 1.0 N A:GLY245 4.1 7.1 1.0 O A:HOH858 4.1 26.9 1.0 C A:GLN242 4.1 16.9 1.0 CA A:THR241 4.2 11.5 1.0 CA A:PHE244 4.2 8.5 1.0 O P:HOH219 4.3 28.9 1.0 CA A:ILE243 4.3 8.4 1.0 CB A:VAL246 4.3 9.8 1.0 N A:GLN242 4.4 10.4 1.0 N A:GLY247 4.5 7.4 1.0 O A:GLN242 4.5 14.7 1.0 C A:PHE244 4.5 10.3 1.0 O3' P:DG2 4.6 8.8 1.0 CA A:GLN242 4.6 12.3 1.0 C A:GLY245 4.7 10.5 1.0 O A:PHE240 4.7 9.2 1.0 CA A:GLY247 4.8 10.3 1.0 CB A:THR241 4.8 12.5 1.0 O5' P:DT3 4.9 5.7 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Mu Post-Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Mu Post-Catalytic Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:22.7 occ:1.00 O22 A:PPV503 1.9 9.8 0.8 O11 A:PPV503 1.9 15.1 0.5 O A:HOH900 2.1 13.4 1.0 O A:HOH843 2.2 19.7 1.0 O P:HOH218 2.2 21.4 1.0 P1 A:PPV503 3.2 15.4 0.5 P2 A:PPV503 3.2 6.5 0.8 O A:HOH665 3.5 19.2 1.0 OPP A:PPV503 3.5 9.4 0.8 O A:HOH683 3.9 15.5 1.0 OD2 A:ASP330 4.0 8.2 0.5 O12 A:PPV503 4.0 1.2 0.5 O31 A:PPV503 4.0 16.9 0.8 OP2 P:DT5 4.1 4.6 1.0 O21 A:PPV503 4.1 17.5 0.5 MG A:MG501 4.2 5.6 1.0 O A:HOH746 4.3 21.2 1.0 O32 A:PPV503 4.3 2.9 0.8 OP1 P:DT5 4.4 3.2 1.0 P P:DT5 4.7 4.4 1.0 CG A:ASP330 4.9 8.0 0.5 OD1 A:ASP330 4.9 6.6 0.5 O A:HOH609 4.9 6.2 1.0

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Sustained Active Site Rigidity During Synthesis By Human Dna Polymerase Mu. Nat.Struct.Mol.Biol. V. 21 253 2014.
ISSN: ISSN 1545-9993
PubMed: 24487959
DOI: 10.1038/NSMB.2766