Magnesium in PDB 5lhm: Crystal Structure of Safc From Myxococcus Xanthus Apo-Form

The structure of Crystal Structure of Safc From Myxococcus Xanthus Apo-Form, PDB code: 5lhm was solved by S.Gerhardt, J.Netzer, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.18 / 1.31
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.558, 64.558, 118.163, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 19.6

The structure of Crystal Structure of Safc From Myxococcus Xanthus Apo-Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Safc From Myxococcus Xanthus Apo-Form (pdb code 5lhm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Safc From Myxococcus Xanthus Apo-Form, PDB code: 5lhm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Safc From Myxococcus Xanthus Apo-Form


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 Safc From Myxococcus Xanthus Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:23.2 occ:1.00 OE1 A:GLU65 2.4 16.1 1.0 O A:HOH1165 2.8 35.9 1.0 N A:VAL68 2.9 10.6 1.0 O A:VAL66 3.1 12.4 1.0 CD A:GLU65 3.3 18.0 1.0 CG A:GLU65 3.4 13.8 1.0 CA A:GLY67 3.6 11.0 1.0 CE2 A:PHE140 3.7 12.4 1.0 CB A:ASP142 3.7 16.4 1.0 CA A:VAL68 3.7 9.3 1.0 C A:GLY67 3.7 12.5 1.0 C A:VAL66 3.7 11.4 1.0 CD2 A:PHE140 3.8 12.1 1.0 N A:GLY67 4.0 10.9 1.0 O A:HOH1120 4.0 14.9 1.0 O A:ASP142 4.1 22.0 1.0 N A:ASP142 4.3 13.9 1.0 CE2 A:PHE69 4.3 19.6 1.0 CD2 A:PHE69 4.4 18.4 1.0 CA A:ASP142 4.4 15.0 1.0 OE2 A:GLU65 4.5 17.2 1.0 C A:VAL68 4.5 11.0 1.0 O A:HOH1123 4.6 44.9 1.0 OD2 A:ASP142 4.6 30.6 1.0 N A:VAL66 4.7 10.0 1.0 CG A:ASP142 4.7 26.1 1.0 O A:VAL68 4.7 9.8 1.0 C A:ASP142 4.8 18.2 1.0 O A:PHE140 4.8 12.5 1.0 CB A:SER73 4.8 13.3 1.0 CB A:GLU65 4.9 11.1 1.0 CA A:VAL66 4.9 10.0 1.0 O A:GLY67 4.9 11.1 1.0 CZ A:PHE140 4.9 12.7 1.0 CG2 A:VAL68 5.0 12.6 1.0 CB A:VAL68 5.0 12.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Safc From Myxococcus Xanthus Apo-Form


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 Safc From Myxococcus Xanthus Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:32.7 occ:1.00 O A:ALA211 2.1 25.8 1.0 OE1 A:GLN47 2.1 26.5 1.0 O A:GLY213 2.4 13.5 1.0 OD1 A:ASP168 2.5 22.2 1.0 O A:ILE210 3.0 20.1 1.0 C A:ALA211 3.0 23.0 1.0 CD A:GLN47 3.2 29.8 1.0 C A:GLY213 3.2 11.9 1.0 CB A:ALA211 3.5 18.9 1.0 O A:HOH1232 3.6 32.8 1.0 N A:GLY213 3.7 12.6 1.0 CG A:ASP168 3.7 17.9 1.0 NE2 A:GLN47 3.8 22.5 1.0 CA A:ALA211 3.8 17.3 1.0 N A:ASN169 3.9 11.1 1.0 C A:ASP212 4.0 12.7 1.0 CB A:LEU214 4.0 10.6 1.0 CD1 A:LEU214 4.0 15.5 1.0 N A:LEU214 4.0 9.7 1.0 N A:ASP212 4.0 17.6 1.0 C A:ILE210 4.0 19.6 1.0 CA A:GLY213 4.1 11.8 1.0 CA A:LEU214 4.2 9.8 1.0 CA A:ASP212 4.4 14.8 1.0 N A:ALA211 4.4 16.6 1.0 OD2 A:ASP168 4.4 25.2 1.0 CG A:GLN47 4.5 18.7 1.0 O A:ASP212 4.5 13.5 1.0 CG A:LEU214 4.5 14.5 1.0 CA A:ASN169 4.6 12.3 1.0 CB A:ASP212 4.7 16.6 1.0 CA A:ASP168 4.7 11.6 1.0 CB A:ASP168 4.8 15.0 1.0 CG2 A:ILE210 4.8 16.9 1.0 C A:ASP168 4.8 12.2 1.0

J.Siegrist, J.Netzer, S.Mordhorst, L.Karst, S.Gerhardt, O.Einsle, M.Richter, J.N.Andexer. Functional and Structural Characterisation of A Bacterial O-Methyltransferase and Factors Determining Regioselectivity. Febs Lett. V. 591 312 2017.
ISSN: ISSN 1873-3468
PubMed: 27990630
DOI: 10.1002/1873-3468.12530