Magnesium in PDB 4xru: Structure of PNKP1/Rnl/HEN1 Complex

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

Resolution Low / High (Å)	42.93 / 3.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.483, 187.245, 111.999, 90.00, 106.04, 90.00
R / Rfree (%)	17.6 / 23.3

The binding sites of Magnesium atom in the Structure of PNKP1/Rnl/HEN1 Complex (pdb code 4xru). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of PNKP1/Rnl/HEN1 Complex, PDB code: 4xru:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of PNKP1/Rnl/HEN1 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 PNKP1/Rnl/HEN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:54.4 occ:1.00 OD2 A:ASP288 2.2 76.7 1.0 OD2 A:ASP183 2.3 72.2 1.0 O A:ASP185 2.3 82.2 1.0 OD1 A:ASP288 2.8 80.9 1.0 CG A:ASP288 2.8 76.9 1.0 O A:HOH506 3.1 53.6 1.0 CG A:ASP183 3.5 78.2 1.0 C A:ASP185 3.5 82.3 1.0 OD1 A:ASP183 3.9 86.3 1.0 CB A:ASP185 4.0 92.7 1.0 CG A:ARG289 4.2 93.0 1.0 CA A:ASP185 4.3 88.1 1.0 CB A:ASP288 4.3 74.6 1.0 OD1 A:ASP287 4.3 82.0 1.0 N A:ARG289 4.4 89.2 1.0 O A:HOH502 4.5 55.9 1.0 N A:GLY186 4.5 78.8 1.0 CD A:ARG289 4.7 90.2 1.0 N A:ASP185 4.7 88.8 1.0 CA A:GLY186 4.7 78.4 1.0 N A:ASP288 4.7 72.1 1.0 CB A:ARG289 4.7 91.7 1.0 CB A:ASP183 4.8 75.5 1.0 C A:GLY186 4.9 77.0 1.0 CA A:ASP288 4.9 77.0 1.0

Magnesium binding site 2 out of 6 in the Structure of PNKP1/Rnl/HEN1 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 PNKP1/Rnl/HEN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:48.9 occ:1.00 O B:HOH608 1.9 60.6 1.0 O B:HOH606 2.3 56.0 1.0 O2A B:ATP501 2.6 67.8 1.0 OE2 B:GLU120 3.2 56.9 1.0 O B:GLY64 3.4 60.3 1.0 PA B:ATP501 3.8 68.6 1.0 O3A B:ATP501 3.8 0.0 1.0 O B:TYR62 3.9 51.1 1.0 N B:GLY64 4.0 39.6 1.0 O4' B:ATP501 4.1 43.8 1.0 C B:GLY64 4.2 59.8 1.0 C1' B:ATP501 4.3 44.8 1.0 C4' B:ATP501 4.3 45.6 1.0 O5' B:ATP501 4.3 46.6 1.0 CD B:GLU120 4.3 56.3 1.0 OE2 B:GLU294 4.3 60.9 1.0 O2' B:ATP501 4.6 39.4 1.0 CA B:MET63 4.6 41.9 1.0 NZ B:LYS61 4.7 43.8 1.0 CA B:GLY64 4.8 60.9 1.0 C B:MET63 4.8 39.8 1.0 O1B B:ATP501 4.8 0.4 1.0 OE1 B:GLU120 4.8 61.2 1.0 C5' B:ATP501 5.0 47.1 1.0

Magnesium binding site 3 out of 6 in the Structure of PNKP1/Rnl/HEN1 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 PNKP1/Rnl/HEN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:41.7 occ:1.00 OE1 C:GLN64 3.6 97.3 1.0 OH C:TYR122 3.6 53.6 1.0 O C:TYR181 3.7 77.5 1.0 O B:HOH621 3.8 64.9 1.0 NE2 C:GLN68 3.9 66.8 1.0 OE2 B:GLU135 4.2 87.7 1.0 CZ C:TYR122 4.3 52.0 1.0 CD2 C:LEU58 4.3 49.0 1.0 OE1 B:GLU135 4.5 95.3 1.0 C C:TYR181 4.6 80.1 1.0 CD C:GLN68 4.6 63.8 1.0 CD C:GLN64 4.7 95.7 1.0 CA C:TYR181 4.7 81.6 1.0 CE1 C:TYR122 4.7 50.1 1.0 CD B:GLU135 4.8 85.6 1.0 CG C:GLN68 4.9 59.0 1.0

Magnesium binding site 4 out of 6 in the Structure of PNKP1/Rnl/HEN1 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 PNKP1/Rnl/HEN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:56.1 occ:1.00 OD2 D:ASP183 1.8 83.8 1.0 O D:ASP185 2.3 89.3 1.0 OD2 D:ASP288 2.5 66.5 1.0 CG D:ASP183 2.9 85.6 1.0 O D:HOH507 3.0 65.4 1.0 OD1 D:ASP183 3.5 84.8 1.0 C D:ASP185 3.5 88.0 1.0 CG D:ASP288 3.6 65.8 1.0 OD2 D:ASP287 3.8 87.3 1.0 N D:ARG289 4.1 72.7 1.0 CB D:ASP288 4.1 60.5 1.0 CB D:ASP183 4.2 88.8 1.0 CB D:ARG289 4.2 80.5 1.0 CA D:ASP185 4.3 89.1 1.0 CB D:ASP185 4.4 92.4 1.0 OG1 D:THR187 4.4 72.8 1.0 N D:ASP185 4.5 89.0 1.0 N D:GLY186 4.5 84.0 1.0 N D:ASP288 4.6 58.5 1.0 NZ D:LYS268 4.6 75.5 1.0 OD1 D:ASP288 4.7 65.8 1.0 CA D:GLY186 4.7 79.0 1.0 CA D:ASP288 4.7 56.6 1.0 CA D:ARG289 4.8 73.9 1.0 O D:HOH502 4.9 58.6 1.0 CG D:ASP287 4.9 85.6 1.0 C D:ASP288 4.9 64.1 1.0

Magnesium binding site 5 out of 6 in the Structure of PNKP1/Rnl/HEN1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of PNKP1/Rnl/HEN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:68.8 occ:1.00 O2A E:ATP501 2.3 0.8 1.0 O E:HOH607 2.7 47.1 1.0 OE2 E:GLU294 3.3 85.6 1.0 O E:TYR62 3.6 76.5 1.0 OE2 E:GLU120 3.6 66.5 1.0 PA E:ATP501 3.6 0.5 1.0 SD E:MET63 3.8 0.6 1.0 OE1 E:GLU294 4.0 86.9 1.0 O3A E:ATP501 4.0 0.4 1.0 CD E:GLU294 4.1 87.5 1.0 O4' E:ATP501 4.1 67.8 1.0 NZ E:LYS61 4.1 48.0 1.0 N E:GLY64 4.2 71.8 1.0 CA E:MET63 4.3 70.5 1.0 O5' E:ATP501 4.3 78.7 1.0 O E:GLY64 4.4 93.1 1.0 C1' E:ATP501 4.4 63.5 1.0 C E:TYR62 4.6 74.4 1.0 C4' E:ATP501 4.7 70.6 1.0 C E:MET63 4.7 74.9 1.0 OH E:TYR319 4.8 91.6 1.0 O1A E:ATP501 4.9 1.0 1.0 CD E:GLU120 4.9 66.7 1.0 C E:GLY64 4.9 85.0 1.0 N E:MET63 5.0 67.2 1.0

Magnesium binding site 6 out of 6 in the Structure of PNKP1/Rnl/HEN1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of PNKP1/Rnl/HEN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:54.2 occ:1.00 OE1 F:GLN64 3.1 0.6 1.0 OH F:TYR122 3.6 74.4 1.0 O F:TYR181 3.7 95.0 1.0 NE2 F:GLN68 4.0 75.3 1.0 OE1 E:GLU135 4.0 92.3 1.0 CD F:GLN64 4.2 0.6 1.0 OE2 E:GLU135 4.3 90.0 1.0 CZ F:TYR122 4.4 71.1 1.0 C F:TYR181 4.5 98.7 1.0 CD E:GLU135 4.5 88.3 1.0 CD2 F:LEU58 4.6 78.2 1.0 CE1 F:TYR122 4.6 68.5 1.0 CD F:GLN68 4.7 76.6 1.0 NE2 F:GLN64 4.8 0.9 1.0 CA F:TYR181 4.9 89.1 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