Magnesium in PDB 4qko: The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms

The structure of The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms, PDB code: 4qko was solved by R.Grinter, I.Josts, A.W.Roszak, C.J.Cogdell, D.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.88 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.390, 114.420, 120.220, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.5

The structure of The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms also contains other interesting chemical elements:

Bromine

(Br)

35 atoms

The binding sites of Magnesium atom in the The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms (pdb code 4qko). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms, PDB code: 4qko:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:38.0 occ:1.00 O B:HOH876 2.1 39.9 1.0 ND1 B:HIS656 2.2 50.7 1.0 NE2 B:HIS681 2.7 48.3 1.0 CG B:HIS656 3.0 43.9 1.0 CB B:HIS656 3.1 34.5 1.0 CD2 B:HIS681 3.3 46.5 1.0 CE1 B:HIS656 3.3 52.2 1.0 O B:HOH923 3.5 38.7 1.0 CA B:HIS656 3.7 30.2 1.0 CE1 B:HIS681 3.9 47.1 1.0 CE1 B:HIS685 4.1 65.1 1.0 NE2 B:HIS685 4.1 67.6 1.0 CD2 B:HIS656 4.2 50.0 1.0 NE2 B:HIS656 4.3 49.9 1.0 N B:HIS657 4.3 23.6 1.0 C B:HIS656 4.5 26.4 1.0 CG B:HIS681 4.6 46.5 1.0 ND1 B:HIS681 4.8 39.5 1.0 O B:HIS657 4.9 28.9 1.0 ND1 B:HIS685 4.9 64.0 1.0 CD2 B:HIS685 4.9 62.8 1.0 N B:HIS656 4.9 25.1 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg707 b:34.3 occ:1.00 ND1 D:HIS656 2.0 22.0 1.0 NE2 D:HIS681 2.2 27.2 1.0 O D:HOH829 2.3 25.9 1.0 NE2 D:HIS685 2.4 30.9 0.5 CE1 D:HIS656 2.9 23.6 1.0 CG D:HIS656 3.1 21.5 1.0 CE1 D:HIS685 3.1 31.3 0.5 CD2 D:HIS681 3.1 25.2 1.0 CE1 D:HIS681 3.2 27.3 1.0 CD2 D:HIS685 3.3 30.2 0.5 CB D:HIS656 3.5 19.5 1.0 CA D:HIS656 3.8 17.6 1.0 NE2 D:HIS656 4.1 22.3 1.0 O D:HOH818 4.1 30.3 1.0 CD2 D:HIS656 4.2 21.6 1.0 ND1 D:HIS685 4.2 30.6 0.5 ND1 D:HIS681 4.3 26.4 1.0 CG D:HIS681 4.3 23.1 1.0 CG D:HIS685 4.3 29.4 0.5 N D:HIS657 4.4 16.0 1.0 C D:HIS656 4.6 16.4 1.0 O D:HIS657 4.9 17.4 1.0 BR D:BR708 5.0 40.5 0.5

Magnesium binding site 3 out of 4 in the The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg707 b:33.1 occ:1.00 ND1 F:HIS656 2.0 23.9 0.5 NE2 F:HIS681 2.3 39.0 0.5 ND1 F:HIS656 2.5 19.0 0.5 O F:HOH805 2.5 28.6 1.0 NE2 F:HIS681 2.5 36.1 0.5 NE2 F:HIS685 2.7 71.5 1.0 CG F:HIS656 2.8 18.3 0.5 CE1 F:HIS656 2.9 23.9 0.5 CB F:HIS656 3.0 18.1 0.5 CD2 F:HIS681 3.0 35.1 0.5 CG F:HIS656 3.1 21.9 0.5 CD2 F:HIS681 3.2 37.1 0.5 CD2 F:HIS685 3.4 69.9 1.0 CE1 F:HIS656 3.4 19.2 0.5 CE1 F:HIS681 3.4 37.0 0.5 CB F:HIS656 3.6 19.9 0.5 CE1 F:HIS681 3.8 36.0 0.5 CE1 F:HIS685 3.8 70.7 1.0 CD2 F:HIS656 3.9 18.2 0.5 NE2 F:HIS656 4.0 23.3 0.5 CA F:HIS656 4.0 20.1 0.5 CD2 F:HIS656 4.1 22.1 0.5 NE2 F:HIS656 4.1 18.2 0.5 CA F:HIS656 4.2 18.9 0.5 CG F:HIS681 4.3 34.8 0.5 N F:HIS657 4.4 17.7 1.0 CG F:HIS681 4.4 37.5 0.5 ND1 F:HIS681 4.5 37.8 0.5 CG F:HIS685 4.6 67.5 1.0 ND1 F:HIS681 4.6 34.7 0.5 C F:HIS656 4.7 18.5 0.5 O F:HIS657 4.7 21.1 1.0 ND1 F:HIS685 4.7 69.2 1.0 C F:HIS656 4.8 17.9 0.5

Magnesium binding site 4 out of 4 in the The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg707 b:28.1 occ:1.00 ND1 H:HIS656 1.9 36.2 1.0 NE2 H:HIS681 2.2 35.1 1.0 O H:HOH802 2.3 29.9 1.0 NE2 H:HIS685 2.7 73.2 1.0 CE1 H:HIS656 2.7 37.9 1.0 CG H:HIS656 3.0 36.0 1.0 CD2 H:HIS681 3.1 33.3 1.0 CE1 H:HIS681 3.2 33.5 1.0 CE1 H:HIS685 3.4 73.3 1.0 CB H:HIS656 3.5 28.8 1.0 CD2 H:HIS685 3.8 69.5 1.0 CA H:HIS656 3.8 24.5 1.0 NE2 H:HIS656 3.9 35.7 1.0 O H:HOH832 4.0 37.5 1.0 CD2 H:HIS656 4.0 37.3 1.0 N H:HIS657 4.2 22.1 1.0 ND1 H:HIS681 4.3 32.6 1.0 CG H:HIS681 4.3 31.2 1.0 C H:HIS656 4.5 24.0 1.0 ND1 H:HIS685 4.6 72.5 1.0 O H:HIS657 4.6 26.8 1.0 CG H:HIS685 4.8 65.3 1.0

R.Grinter, I.Josts, L.C.Mccaughey, A.W.Roszak, K.I.Walen, S.Kelly, O.Byron, D.Walker. Structural Insights Into Pyocin S2 To Be Published.