Magnesium in PDB 3t77: S25-2- A(2-4)Kdo Disaccharide Complex

The structure of S25-2- A(2-4)Kdo Disaccharide Complex, PDB code: 3t77 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)	19.82 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.900, 81.800, 130.300, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.6

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

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the S25-2- A(2-4)Kdo Disaccharide Complex (pdb code 3t77). 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(2-4)Kdo Disaccharide Complex, PDB code: 3t77:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the S25-2- A(2-4)Kdo Disaccharide 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(2-4)Kdo Disaccharide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg216 b:39.1 occ:1.00 ND2 A:ASN137 2.1 38.9 1.0 CE1 B:HIS162 2.1 33.1 1.0 NE2 B:HIS162 2.2 36.6 1.0 O A:HOH431 2.4 45.5 1.0 OD1 A:ASN137 2.4 40.5 1.0 CG A:ASN137 2.6 31.0 1.0 O A:HOH270 3.4 34.3 1.0 ND1 B:HIS162 3.5 40.1 1.0 CD2 B:HIS162 3.6 34.7 1.0 CB A:ASN137 4.1 31.8 1.0 CG B:HIS162 4.2 32.9 1.0 OD1 A:ASP169 4.2 42.0 1.0 OG A:SER173 4.4 28.3 1.0 OG1 A:THR171 4.5 32.0 1.0 CA A:ASN137 4.7 29.7 1.0 OD1 A:ASP166 4.7 39.0 1.0 N A:ASN137 4.8 25.5 1.0

Magnesium binding site 2 out of 2 in the S25-2- A(2-4)Kdo Disaccharide 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(2-4)Kdo Disaccharide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg217 b:38.4 occ:1.00 N A:ASP1 1.9 50.0 1.0 OD2 A:ASP1 2.0 51.5 1.0 O A:ASP1 2.1 40.0 1.0 O A:HOH370 2.2 50.5 1.0 CA A:ASP1 2.7 45.2 1.0 C A:ASP1 2.7 41.4 1.0 CG A:ASP1 3.0 50.3 1.0 CB A:ASP1 3.4 44.2 1.0 O A:HOH285 3.9 39.8 1.0 N A:ILE2 4.0 37.6 1.0 OD1 A:ASP1 4.1 55.5 1.0 CA A:ILE2 4.9 31.7 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