Magnesium in PDB 5n0u: Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah

The structure of Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah, PDB code: 5n0u was solved by H.Song, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.92 / 1.68
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	86.086, 91.881, 164.436, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.7

The binding sites of Magnesium atom in the Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah (pdb code 5n0u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah, PDB code: 5n0u:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:49.3 occ:1.00 OG A:SER21 2.9 31.7 1.0 CD A:PRO217 3.5 35.8 1.0 CB A:SER21 3.5 29.6 1.0 CG A:PRO217 3.5 36.1 1.0 CB A:ALA47 3.7 29.8 1.0 CD1 A:ILE22 4.1 29.9 1.0 O A:SER21 4.1 26.7 1.0 C A:SER21 4.4 27.4 1.0 SD A:MET216 4.5 39.0 0.4 CG1 A:ILE22 4.5 29.0 1.0 CA A:SER21 4.6 28.1 1.0 N A:PRO217 4.8 34.9 1.0 CB A:ILE22 4.9 28.4 1.0 CB A:PRO217 5.0 35.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:49.1 occ:1.00 O A:SER166 2.6 33.6 1.0 OH A:TYR202 2.8 37.4 1.0 O A:ILE248 2.9 33.1 1.0 O A:PRO249 3.1 38.8 1.0 C A:PRO249 3.4 38.0 1.0 CE1 A:TYR202 3.4 38.6 1.0 CZ A:TYR202 3.5 38.5 1.0 O A:SER163 3.6 37.0 1.0 N A:PRO250 3.7 39.1 1.0 C A:ILE248 3.7 34.2 1.0 N A:LEU168 3.8 30.5 1.0 CB A:LEU168 3.8 31.5 1.0 CA A:PRO250 3.9 40.9 1.0 C A:SER166 3.9 33.4 1.0 O A:HOH1122 4.0 36.7 1.0 CG2 A:ILE248 4.0 36.4 1.0 C A:HIS167 4.1 30.5 1.0 CA A:PRO249 4.2 36.3 1.0 N A:PRO249 4.3 35.4 1.0 CB A:ILE248 4.4 35.3 1.0 CA A:HIS167 4.4 31.0 1.0 CA A:LEU168 4.4 30.6 1.0 N A:HIS167 4.6 31.5 1.0 CD A:PRO250 4.6 38.7 1.0 CA A:ILE164 4.6 39.8 1.0 O A:ILE164 4.7 39.2 1.0 CD1 A:TYR202 4.7 40.1 1.0 CA A:ILE248 4.7 34.2 1.0 C A:SER163 4.7 38.9 1.0 C A:ILE164 4.7 39.4 1.0 CE2 A:TYR202 4.8 38.7 1.0 O A:HIS167 4.8 30.3 1.0 N A:SER166 4.8 35.6 1.0 C A:PRO250 4.8 42.9 1.0 CB A:PRO250 5.0 40.9 1.0 CA A:SER166 5.0 34.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:60.7 occ:1.00 OG A:SER31 2.5 31.0 1.0 O A:ALA332 2.5 29.4 1.0 O A:HOH1116 2.7 31.4 1.0 C A:ALA332 3.4 29.5 1.0 C A:LEU333 3.5 31.5 1.0 CA A:LEU333 3.5 30.8 1.0 CD A:PRO335 3.6 34.2 1.0 CB A:SER31 3.6 28.8 1.0 N A:ASP334 3.7 32.2 1.0 CG A:PRO335 3.7 34.3 1.0 N A:LEU333 3.7 30.0 1.0 N A:PRO335 3.8 34.5 1.0 O A:LEU333 3.9 30.8 1.0 CE1 A:TYR32 3.9 30.4 1.0 O A:HOH1011 3.9 38.5 1.0 O A:HOH1096 4.0 34.6 1.0 CA A:GLN28 4.2 26.0 1.0 CB A:GLN28 4.2 26.4 1.0 CD1 A:TYR32 4.2 29.9 1.0 C A:ASP334 4.3 34.1 1.0 O A:GLN28 4.4 26.9 1.0 CA A:ASP334 4.4 33.7 1.0 CA A:PRO335 4.4 35.2 1.0 CB A:PRO335 4.6 34.8 1.0 CA A:ALA332 4.6 28.9 1.0 CZ A:TYR32 4.7 31.6 1.0 O A:LEU331 4.8 30.8 1.0 C A:GLN28 4.8 25.8 1.0 CA A:SER31 4.9 28.6 1.0 CB A:LEU333 4.9 31.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Opha-DELTAC6 Mutant R72A in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:56.4 occ:1.00 CE1 A:HIS109 3.2 33.2 1.0 CA A:GLY102 3.4 27.0 1.0 SD A:MET124 3.5 27.3 1.0 O A:GLY102 3.5 29.2 1.0 NE2 A:HIS109 3.6 32.1 1.0 C A:GLY102 3.7 28.6 1.0 CE1 A:HIS100 3.7 23.6 1.0 CE A:MET124 4.2 28.6 1.0 N A:GLY102 4.3 25.4 1.0 ND1 A:HIS109 4.4 33.8 1.0 ND1 A:HIS100 4.5 23.4 1.0 NE2 A:HIS100 4.6 23.2 1.0 N A:VAL103 4.8 28.4 1.0 CD2 A:HIS109 4.9 32.8 1.0

H.Song, N.S.Van Der Velden, S.L.Shiran, P.Bleiziffer, C.Zach, R.Sieber, A.S.Imani, F.Krausbeck, M.Aebi, M.F.Freeman, S.Riniker, M.Kunzler, J.H.Naismith. A Molecular Mechanism For the Enzymatic Methylation of Nitrogen Atoms Within Peptide Bonds. Sci Adv V. 4 T2720 2018.
ISSN: ESSN 2375-2548
PubMed: 30151425
DOI: 10.1126/SCIADV.AAT2720