Sodium in PDB 1nxd: Crystal Structure of Mnmn Concanavalin A

The structure of Crystal Structure of Mnmn Concanavalin A, PDB code: 1nxd was solved by F.J.Lopez-Jaramillo, L.A.Gonzalez-Ramirez, A.Albert, F.Santoyo-Gonzalez, A.Vargas-Berenguel, F.Otalora, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.00 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	101.300, 118.000, 249.500, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.1

The structure of Crystal Structure of Mnmn Concanavalin A also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of Mnmn Concanavalin A (pdb code 1nxd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Mnmn Concanavalin A, PDB code: 1nxd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Mnmn Concanavalin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ 1:Na1012 b:30.4 occ:1.00 O 1:HOH1147 2.2 23.9 1.0 O 1:LEU107 2.3 10.2 1.0 O 1:ASN131 2.4 23.5 1.0 O 1:HOH1151 2.4 23.2 1.0 O 2:HOH1131 2.4 22.4 1.0 O 2:HOH1116 2.6 32.4 1.0 C 1:LEU107 3.3 10.0 1.0 C 1:ASN131 3.5 21.3 1.0 OE1 2:GLU122 3.6 40.1 1.0 O 1:HOH1190 3.7 32.0 1.0 CA 1:LEU107 3.8 10.0 1.0 CB 1:LEU107 3.9 11.3 1.0 CA 1:ASN131 4.2 20.1 1.0 OD1 1:ASN153 4.2 16.4 1.0 O 1:HOH1171 4.4 38.4 1.0 N 1:SER108 4.5 9.9 1.0 CD 2:GLU122 4.5 37.4 1.0 N 1:GLN132 4.5 22.5 1.0 O 1:HOH1159 4.6 35.8 1.0 O 1:GLY152 4.7 17.4 1.0 CB 1:ASN131 4.7 20.9 1.0 CB 1:SER108 4.8 12.6 1.0 OE2 2:GLU122 4.8 40.2 1.0 CA 1:GLN132 4.8 23.5 1.0 CA 1:SER108 4.8 10.2 1.0 CG 1:LEU107 4.9 14.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Mnmn Concanavalin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ 2:Na1009 b:38.2 occ:1.00 O 2:HOH1135 1.8 29.6 1.0 O 2:HOH1167 2.2 40.1 1.0 O 2:ASN131 2.4 24.2 1.0 O 2:LEU107 2.7 13.2 1.0 O 2:HOH1096 2.8 27.5 1.0 C 2:ASN131 3.5 23.5 1.0 C 2:LEU107 3.7 12.6 1.0 OD1 2:ASN153 3.9 24.1 1.0 CA 2:LEU107 4.1 12.3 1.0 CB 2:LEU107 4.2 12.0 1.0 CA 2:ASN131 4.3 22.0 1.0 N 2:GLN132 4.4 24.8 1.0 O 2:GLY152 4.5 21.4 1.0 CA 2:GLN132 4.5 26.2 1.0 N 2:SER108 4.9 11.9 1.0 CB 2:ASN131 4.9 22.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Mnmn Concanavalin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ 3:Na1011 b:35.7 occ:1.00 O 3:HOH1106 1.9 26.2 1.0 O 3:HOH1101 2.2 24.6 1.0 O 3:LEU107 2.4 12.7 1.0 O 3:HOH1105 2.4 25.2 1.0 O 3:HOH1085 2.6 27.1 1.0 O 3:ASN131 2.7 24.7 1.0 C 3:LEU107 3.3 12.2 1.0 CB 3:LEU107 3.7 13.5 1.0 C 3:ASN131 3.8 22.5 1.0 CA 3:LEU107 3.8 12.4 1.0 OD1 3:ASN153 4.2 20.4 1.0 O 3:HOH1150 4.2 48.5 1.0 CA 3:ASN131 4.3 20.3 1.0 N 3:SER108 4.5 12.0 1.0 CG 3:LEU107 4.6 15.6 1.0 CB 3:SER108 4.8 14.3 1.0 CB 3:ASN131 4.8 18.9 1.0 N 3:GLN132 4.9 22.6 1.0 O 3:GLY152 4.9 18.2 1.0 CA 3:SER108 4.9 12.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Mnmn Concanavalin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ 4:Na1010 b:34.2 occ:1.00 O 4:HOH1141 2.0 30.4 1.0 O 4:ASN131 2.3 23.8 1.0 O 4:HOH1199 2.5 36.2 1.0 O 4:HOH1078 2.5 21.2 1.0 O 4:LEU107 2.5 12.3 1.0 O 4:HOH1109 2.6 22.5 1.0 C 4:ASN131 3.3 21.1 1.0 C 4:LEU107 3.6 12.0 1.0 CA 4:ASN131 3.9 19.1 1.0 CA 4:LEU107 4.3 12.4 1.0 CB 4:LEU107 4.3 13.9 1.0 CB 4:ASN131 4.4 19.1 1.0 N 4:GLN132 4.4 21.0 1.0 OD1 4:ASN153 4.6 17.0 1.0 O 4:HOH1059 4.6 27.2 1.0 O 4:HOH1114 4.6 33.0 1.0 N 4:SER108 4.7 11.1 1.0 CB 4:SER108 4.8 13.9 1.0 OD1 4:ASN131 4.8 21.8 1.0 CA 4:GLN132 4.9 22.8 1.0 O 4:GLY152 4.9 16.9 1.0 CA 4:SER108 5.0 10.6 1.0

F.J.Lopez-Jaramillo, L.A.Gonzalez-Ramirez, A.Albert, F.Santoyo-Gonzalez, A.Vargas-Berenguel, F.Otalora. Structure of Concanavalin A at pH 8: Bound Solvent and Crystal Contacts. Acta Crystallogr.,Sect.D V. 60 1048 2004.
ISSN: ISSN 0907-4449
PubMed: 15159564
DOI: 10.1107/S0907444904007000