Magnesium in PDB 8jeb: Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN)

The structure of Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN), PDB code: 8jeb was solved by H.Unno, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.4, 82.495, 44.201, 90, 90, 90
R / Rfree (%)	15.6 / 17.5

The binding sites of Magnesium atom in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN) (pdb code 8jeb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN), PDB code: 8jeb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN)


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 CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:23.4 occ:1.00 O B:HOH2251 2.1 32.7 1.0 O B:HOH2117 2.2 20.7 1.0 O B:HOH2212 2.2 32.0 1.0 OG B:SER6 2.2 17.5 1.0 O B:HOH2111 2.3 25.2 1.0 O B:HOH2193 2.5 24.2 1.0 CB B:SER6 3.3 16.9 1.0 N B:SER6 3.8 14.6 1.0 CA B:SER6 4.1 15.4 1.0 OE1 B:GLU66 4.2 15.4 1.0 O B:HOH2217 4.3 30.4 1.0 O B:ACY2002 4.5 25.2 1.0 OXT B:ACY2002 4.5 23.4 1.0 O B:TRP4 4.6 15.8 1.0 CG B:GLU66 4.8 13.8 1.0 CD B:GLU66 4.9 14.7 1.0 C B:VAL5 4.9 14.0 1.0 C B:ACY2002 4.9 21.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN)


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 CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2004 b:19.5 occ:1.00 O B:HOH2209 2.0 23.6 1.0 OD1 B:ASP94 2.0 17.1 1.0 O B:HOH2157 2.1 24.1 1.0 O B:HOH2191 2.1 17.9 1.0 O B:HOH2133 2.1 26.1 1.0 CG B:ASP94 3.1 19.1 1.0 OD2 B:ASP94 3.5 24.4 1.0 N B:ASP94 4.1 12.4 1.0 OXT B:ACY2001 4.1 28.4 1.0 O B:ASP94 4.2 15.7 1.0 CB B:ASP94 4.3 14.7 1.0 O B:ALA92 4.6 13.1 1.0 CA B:ASP94 4.6 12.5 1.0 O B:HOH2218 4.7 26.7 1.0 O B:ACY2001 4.8 20.3 1.0 C B:ASP94 4.8 12.9 1.0 O B:HOH2162 4.9 16.7 1.0 C B:ACY2001 4.9 22.6 1.0 CA B:ILE93 4.9 11.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2005 b:24.7 occ:1.00 O B:HOH2171 1.9 36.2 1.0 OD1 B:ASN10 2.0 17.0 1.0 O B:HOH2245 2.1 31.6 1.0 O B:HOH2103 2.1 30.6 1.0 O B:HOH2148 2.2 29.8 1.0 O B:HOH2129 2.2 26.2 1.0 CG B:ASN10 3.2 15.6 1.0 ND2 B:ASN10 3.8 16.7 1.0 OE2 B:GLU49 4.1 26.6 1.0 N B:ASN10 4.1 14.7 1.0 OE1 B:GLU49 4.1 25.5 1.0 O B:HOH2159 4.2 30.8 1.0 O B:HOH2254 4.3 34.3 1.0 OG1 B:THR11 4.3 21.3 1.0 CB B:ASN10 4.3 15.3 1.0 CD B:GLU49 4.6 26.5 1.0 CA B:ASN10 4.6 14.8 1.0 C B:ASN10 4.8 14.6 1.0 N B:THR11 4.9 14.1 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:18.9 occ:1.00 O A:HOH335 2.0 29.5 1.0 O A:HOH328 2.0 27.5 1.0 OD1 A:ASN10 2.1 20.7 1.0 O A:HOH321 2.1 26.5 1.0 CG A:ASN10 3.2 19.9 1.0 ND2 A:ASN10 3.7 22.4 1.0 OE2 A:GLU49 4.1 27.7 1.0 OG1 A:THR11 4.2 20.9 1.0 OE1 A:GLU49 4.2 23.8 1.0 CB A:ASN10 4.5 16.5 1.0 N A:ASN10 4.5 15.0 1.0 C A:ASN10 4.5 15.0 1.0 CD A:GLU49 4.6 27.0 1.0 N A:THR11 4.7 15.3 1.0 CA A:ASN10 4.7 15.6 1.0 O A:HOH387 4.7 33.8 1.0 O A:ASN10 4.9 16.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of CGL1 From Crassostrea Gigas, Mannotetraose-Bound Form (CGL1/Man(Alpha)1-2MAN(Alpha)1-2MAN(Alpha)1-6MAN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:26.3 occ:1.00 O A:HOH324 2.2 22.0 1.0 OG A:SER6 2.3 19.5 1.0 O A:HOH305 2.4 35.5 1.0 O A:HOH401 2.6 22.3 1.0 CB A:SER6 3.4 17.6 1.0 N A:SER6 3.9 16.6 1.0 CA A:SER6 4.2 15.7 1.0 OE1 A:GLU66 4.3 17.0 1.0 O A:HOH407 4.4 38.4 1.0 OXT A:ACY201 4.4 28.3 1.0 O A:TRP4 4.6 16.8 1.0 O A:ACY201 4.6 25.4 1.0 CG A:GLU66 4.9 14.0 1.0 C A:VAL5 4.9 15.0 1.0 CD A:GLU66 4.9 15.0 1.0 C A:ACY201 5.0 26.9 1.0

T.Hatakeyama, K.Masuda, M.Kudo, K.Tanaka, A.Takeuchi, H.Unno. Mannose Oligosaccharide Recognition of CGL1, A Mannose-Specific Lectin Containing DM9 Motifs From Crassostrea Gigas, Revealed By X-Ray Crystallographic Analysis. J.Biochem. 2023.
ISSN: ISSN 0021-924X
PubMed: 37793172
DOI: 10.1093/JB/MVAD073