Magnesium in PDB 5log: Crystal Structure of Safc From Myxococcus Xanthus Bound to Sam

The structure of Crystal Structure of Safc From Myxococcus Xanthus Bound to Sam, PDB code: 5log 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)	71.86 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.840, 51.017, 72.677, 90.00, 98.58, 90.00
R / Rfree (%)	17.6 / 21.2

The structure of Crystal Structure of Safc From Myxococcus Xanthus Bound to Sam 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 Bound to Sam (pdb code 5log). 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 Bound to Sam, PDB code: 5log:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Safc From Myxococcus Xanthus Bound to Sam


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 Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:25.5 occ:1.00 O A:HOH1101 2.0 12.5 1.0 OD2 A:ASP168 2.0 25.5 1.0 OD1 A:ASP142 2.0 24.4 1.0 OD1 A:ASN169 2.1 20.9 1.0 O1 A:LDP1004 2.3 23.9 0.5 O2 A:LDP1004 2.4 18.9 0.5 CG A:ASP142 3.0 26.3 1.0 CG A:ASN169 3.1 30.2 1.0 CG A:ASP168 3.1 25.3 1.0 C3 A:LDP1004 3.1 25.6 0.5 C4 A:LDP1004 3.2 23.5 0.5 OD2 A:ASP142 3.3 25.8 1.0 ND2 A:ASN169 3.4 20.1 1.0 CB A:ASP168 3.6 16.8 1.0 NZ A:LYS145 4.1 20.2 1.0 OD1 A:ASP168 4.1 24.5 1.0 O A:MET41 4.2 31.5 1.0 O A:HOH1126 4.2 28.4 1.0 CB A:ASP142 4.3 18.9 1.0 CB A:ASN169 4.4 19.0 1.0 C2 A:LDP1004 4.4 28.6 0.5 C5 A:LDP1004 4.5 27.9 0.5 N A:ASN169 4.6 16.5 1.0 CG2 A:ILE43 4.7 25.4 1.0 O A:ASP142 4.7 21.5 1.0 C A:ASP168 4.8 18.2 1.0 CA A:ASP168 4.8 14.7 1.0 CA A:ASP142 4.8 17.3 1.0 CE A:LYS145 4.9 23.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Safc From Myxococcus Xanthus Bound to Sam


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 Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:16.4 occ:1.00 O B:HOH436 2.0 20.3 1.0 OD1 B:ASP142 2.1 22.2 1.0 OD1 B:ASN169 2.3 17.2 1.0 O B:HOH441 2.3 17.4 1.0 OD2 B:ASP168 2.3 18.6 1.0 O B:THR40 3.1 36.6 1.0 CG B:ASP142 3.2 22.1 1.0 CG B:ASN169 3.2 26.3 1.0 CG B:ASP168 3.4 15.8 1.0 O B:HOH498 3.5 26.0 1.0 OD2 B:ASP142 3.6 23.4 1.0 ND2 B:ASN169 3.6 17.0 1.0 CB B:ASP168 3.9 13.2 1.0 NZ B:LYS145 4.0 16.1 1.0 C B:THR40 4.2 36.3 1.0 CA B:MET41 4.3 30.1 1.0 O B:HOH402 4.3 16.4 1.0 OD1 B:ASP168 4.4 22.4 1.0 CB B:ASP142 4.5 14.4 1.0 O B:ASP142 4.5 13.9 1.0 CB B:ASN169 4.6 14.2 1.0 N B:MET41 4.7 30.7 1.0 CA B:ASP142 4.8 13.3 1.0 CD1 B:ILE43 4.8 35.2 1.0 CE B:LYS145 4.9 14.0 1.0 N B:ASN169 4.9 12.8 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