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

Protein crystallography data

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

Other elements in 3sy0:

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

Zinc (Zn) 1 atom

Magnesium Binding Sites:

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 3sy0

Go back to Magnesium Binding Sites List in 3sy0
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 3sy0

Go back to Magnesium Binding Sites List in 3sy0
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

Reference:

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
Page generated: Thu Aug 15 11:11:10 2024

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