Magnesium in PDB 3sy0: S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex

The structure of S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex, PDB code: 3sy0 was solved by H.P.Nguyen, N.O.Seto, C.R.Mackenzie, L.Brade, P.Kosma, H.Brade, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 1.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.600, 80.900, 130.600, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.2

The structure of S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex (pdb code 3sy0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex, PDB code: 3sy0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg216 b:26.2 occ:1.00 ND1 A:HIS188 2.0 22.0 1.0 OD2 A:ASP150 2.0 22.2 1.0 CE1 A:HIS188 2.7 20.3 1.0 CG A:ASP150 3.1 20.4 1.0 CG A:HIS188 3.1 18.9 1.0 O A:ARG187 3.5 20.5 1.0 O A:HOH294 3.5 27.1 1.0 CB A:ASP150 3.6 18.3 1.0 CB A:HIS188 3.7 16.8 1.0 CA A:HIS188 3.8 16.5 1.0 NE2 A:HIS188 3.9 18.9 1.0 CD2 A:HIS188 4.1 19.0 1.0 OD1 A:ASP150 4.2 20.3 1.0 C A:ARG187 4.4 20.1 1.0 N A:HIS188 4.6 16.6 1.0 O A:HOH345 4.8 29.7 1.0 N A:ASN189 4.9 15.4 1.0 C A:HIS188 4.9 17.4 1.0 O A:HOH395 5.0 31.1 1.0

Magnesium binding site 2 out of 2 in the S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S25-2- A(2-8)-A(2-4)Kdo Trisaccharide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg217 b:27.0 occ:1.00 NE2 B:HIS162 1.7 24.5 1.0 OD1 A:ASN137 1.9 24.6 1.0 CE1 B:HIS162 2.4 28.9 1.0 O B:HOH687 2.5 34.0 1.0 CG A:ASN137 2.8 26.8 1.0 CD2 B:HIS162 3.0 28.7 1.0 ND2 A:ASN137 3.0 36.1 1.0 ND1 B:HIS162 3.6 31.4 1.0 O A:HOH394 3.9 24.0 1.0 CG B:HIS162 3.9 24.7 1.0 CB A:ASN137 4.2 21.3 1.0 OG A:SER173 4.3 18.3 1.0 OD1 A:ASP169 4.5 32.1 1.0 N A:ASN137 4.7 19.1 1.0 CA A:ASN137 4.7 18.1 1.0 OG1 A:THR171 4.7 19.2 1.0 CB A:ASN136 5.0 20.7 1.0

H.P.Nguyen, N.O.Seto, C.R.Mackenzie, L.Brade, P.Kosma, H.Brade, S.V.Evans. Germline Antibody Recognition of Distinct Carbohydrate Epitopes Nat.Struct.Biol. V. 10 1019 2003.
ISSN: ISSN 1072-8368
PubMed: 14625588
DOI: 10.1038/NSB1014