Magnesium in PDB 4xrp: Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex

The structure of Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex, PDB code: 4xrp was solved by R.H.Huang, P.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.21 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.160, 179.201, 114.333, 90.00, 103.70, 90.00
R / Rfree (%)	17.5 / 23.8

The binding sites of Magnesium atom in the Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex (pdb code 4xrp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex, PDB code: 4xrp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:58.7 occ:1.00 OD2 A:ASP288 1.9 67.7 1.0 O A:ASP185 2.3 74.8 1.0 OD2 A:ASP183 2.5 63.4 1.0 CG A:ASP288 3.0 68.5 1.0 OD1 A:ASP288 3.4 70.2 1.0 C A:ASP185 3.5 79.4 1.0 CG A:ASP183 3.5 71.8 1.0 CB A:ARG289 3.9 69.9 1.0 OD1 A:ASP183 3.9 78.3 1.0 OD1 A:ASP287 4.0 71.3 1.0 CB A:ASP185 4.2 87.8 1.0 N A:ARG289 4.2 69.1 1.0 CA A:ASP185 4.3 80.2 1.0 CB A:ASP288 4.4 66.5 1.0 N A:GLY186 4.6 81.6 1.0 CD A:ARG289 4.6 76.7 1.0 CA A:ARG289 4.7 66.7 1.0 N A:ASP185 4.7 75.5 1.0 CA A:GLY186 4.8 77.0 1.0 OG1 A:THR187 4.8 60.8 1.0 NZ A:LYS268 4.8 67.1 1.0 CG A:ARG289 4.8 72.0 1.0 CB A:ASP183 4.9 53.8 1.0 OD2 A:ASP264 4.9 0.8 1.0 N A:ASP288 4.9 61.5 1.0 CE1 A:PHE312 5.0 83.7 1.0 CA A:ASP288 5.0 65.9 1.0 C A:ASP288 5.0 68.7 1.0

Magnesium binding site 2 out of 4 in the Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:42.6 occ:1.00 OE2 B:GLU43 2.6 81.3 1.0 O4 B:SO4403 3.4 71.6 1.0 CD B:GLU43 3.7 74.2 1.0 OE1 B:GLU34 4.1 96.4 1.0 OE1 B:GLU43 4.2 72.3 1.0 S B:SO4403 4.8 73.8 1.0 CD2 B:LEU46 4.9 43.4 1.0 OE2 B:GLU34 4.9 0.2 1.0 CD B:GLU34 4.9 93.9 1.0 CG B:GLU43 5.0 66.6 1.0

Magnesium binding site 3 out of 4 in the Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:41.1 occ:1.00 O B:LYS60 3.0 55.9 1.0 OE1 B:GLU120 3.3 75.8 1.0 CA B:LYS61 3.7 51.3 1.0 C B:LYS60 3.9 52.9 1.0 CD1 B:PHE234 4.0 47.2 1.0 CD B:LYS61 4.0 52.2 1.0 N B:TYR62 4.1 55.1 1.0 OE1 B:GLU59 4.1 73.8 1.0 N B:LYS61 4.2 50.7 1.0 CD B:GLU120 4.3 69.8 1.0 CG B:PHE234 4.4 42.9 1.0 C B:LYS61 4.4 51.7 1.0 CE1 B:PHE234 4.5 47.3 1.0 CG2 B:VAL297 4.6 53.1 1.0 CB B:LYS61 4.6 48.7 1.0 CB B:PHE234 4.6 41.7 1.0 CB B:GLU59 4.7 42.8 1.0 CG B:GLU120 4.7 60.3 1.0 CG B:LYS61 4.9 51.4 1.0

Magnesium binding site 4 out of 4 in the Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the PNKP1/Rnl/HEN1 Rna Repair Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:43.5 occ:1.00 OD2 D:ASP183 2.0 66.3 1.0 OD1 D:ASP288 2.2 57.9 1.0 O D:ASP185 2.4 56.1 1.0 CG D:ASP183 3.0 69.3 1.0 CG D:ASP288 3.4 61.2 1.0 OD1 D:ASP287 3.5 85.0 1.0 OD1 D:ASP183 3.5 76.7 1.0 C D:ASP185 3.6 63.3 1.0 NZ D:LYS268 3.9 60.4 1.0 OD2 D:ASP288 3.9 62.5 1.0 CB D:ARG289 4.1 69.2 1.0 N D:ARG289 4.3 61.9 1.0 CB D:ASP183 4.3 63.5 1.0 CB D:ASP185 4.4 73.2 1.0 CA D:ASP185 4.4 68.3 1.0 CG D:ASP287 4.5 78.8 1.0 OG1 D:THR187 4.5 61.2 1.0 N D:ASP185 4.6 73.4 1.0 CB D:ASP288 4.6 62.8 1.0 N D:GLY186 4.7 63.5 1.0 OD2 D:ASP287 4.7 79.2 1.0 N D:ASP288 4.7 62.1 1.0 CA D:ARG289 4.8 61.2 1.0 CA D:GLY186 5.0 61.2 1.0

P.Wang, K.Selvadurai, R.H.Huang. Reconstitution and Structure of A Bacterial PNKP1-Rnl-HEN1 Rna Repair Complex. Nat Commun V. 6 6876 2015.
ISSN: ESSN 2041-1723
PubMed: 25882814
DOI: 10.1038/NCOMMS7876