Cadmium in PDB 4h3o: Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution

The structure of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution, PDB code: 4h3o was solved by S.Kumar, S.Yamini, J.Kumar, P.Kaur, T.P.Singh, S.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.513, 57.234, 97.449, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.9

The structure of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution (pdb code 4h3o). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution, PDB code: 4h3o:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:81.5 occ:1.00 OE2 A:GLU46 2.5 32.1 1.0 CD A:GLU46 2.9 30.6 1.0 OE1 A:GLU46 3.1 31.4 1.0 O A:HOH326 3.3 26.6 1.0 CG A:GLU46 3.9 29.3 1.0 ND2 A:ASN30 4.7 18.4 1.0 O A:HOH386 4.9 20.1 1.0 ND2 A:ASN44 4.9 24.6 1.0

Cadmium binding site 2 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:56.5 occ:1.00 OE2 A:GLU8 2.4 24.1 1.0 O B:HOH304 2.5 31.3 1.0 OD2 A:ASP5 2.8 23.6 1.0 O B:HOH385 3.0 39.6 1.0 OE1 A:GLU8 3.1 23.6 1.0 CD A:GLU8 3.1 23.6 1.0 OD1 B:ASP91 3.3 28.0 1.0 CG A:ASP5 3.4 23.0 1.0 CB A:ASP5 3.9 21.8 1.0 OD1 A:ASP5 4.2 24.8 1.0 CG B:ASP91 4.3 25.5 1.0 O A:HOH358 4.5 49.8 1.0 CG A:GLU8 4.5 23.6 1.0 OD2 B:ASP91 4.6 27.8 1.0 O A:HOH354 4.6 34.0 1.0 O A:HOH384 4.6 34.1 1.0 N A:ASP5 4.7 21.2 1.0 N B:ASP91 4.9 21.9 1.0 CA A:ASP5 4.9 21.7 1.0 CD1 A:ILE3 5.0 22.0 1.0

Cadmium binding site 3 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:32.0 occ:1.00 OE1 B:GLU46 2.2 30.0 1.0 OE2 B:GLU46 2.3 28.6 1.0 CD B:GLU46 2.6 29.1 1.0 O B:HOH380 2.6 35.7 1.0 CG B:GLU46 4.0 29.1 1.0 OD2 B:ASP28 4.2 24.3 1.0 O B:HOH397 4.4 34.3 1.0 O B:HOH359 4.6 34.7 1.0 O B:HOH382 4.6 27.1 1.0 O B:HOH308 4.6 27.8 1.0 CB B:GLU46 4.7 29.1 1.0

Cadmium binding site 4 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:19.4 occ:1.00 O B:HOH393 2.2 15.1 1.0 NE2 B:HIS22 2.2 17.1 1.0 OE1 B:GLU19 2.3 17.8 1.0 OE2 B:GLU19 2.4 18.1 1.0 CD B:GLU19 2.7 17.9 1.0 CD2 B:HIS22 3.1 16.7 1.0 CE1 B:HIS22 3.3 16.9 1.0 O B:HOH360 4.2 29.1 1.0 CG B:GLU19 4.2 17.1 1.0 CG B:HIS22 4.3 17.2 1.0 ND1 B:HIS22 4.4 16.4 1.0 O B:PRO20 4.8 17.5 1.0 C B:PRO20 4.9 17.4 1.0 CA B:PRO20 4.9 17.2 1.0 CB B:GLU19 5.0 17.2 1.0

Cadmium binding site 5 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd203 b:19.8 occ:1.00 ND2 B:ASN7 2.3 12.4 1.0 OG B:SER59 2.4 17.9 1.0 O B:HOH358 2.5 19.9 1.0 OD1 B:ASN7 2.6 13.1 1.0 CG B:ASN7 2.8 13.8 1.0 CB B:SER59 3.5 17.7 1.0 N B:SER59 4.0 17.9 1.0 CB B:ASN7 4.2 14.6 1.0 CA B:SER59 4.4 17.7 1.0

Cadmium binding site 6 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd204 b:16.4 occ:1.00 O B:ASN7 2.1 14.6 1.0 O B:HOH305 2.2 14.5 1.0 C B:ASN7 3.3 14.8 1.0 O B:HOH363 4.0 25.7 1.0 CA B:GLU8 4.0 15.4 1.0 N B:GLU8 4.1 15.0 1.0 CB B:ASN7 4.3 14.6 1.0 CA B:ASN7 4.4 14.7 1.0 C B:GLU8 4.8 15.4 1.0 N B:GLY9 5.0 15.7 1.0

Cadmium binding site 7 out of 7 in the Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd205 b:66.6 occ:1.00 O B:HOH391 2.2 17.6 1.0 O B:HOH394 2.9 43.0 1.0 OD1 B:ASP35 2.9 19.4 1.0 OD2 B:ASP35 3.0 20.4 1.0 ND1 B:HIS36 3.1 20.9 1.0 CG B:ASP35 3.3 19.5 1.0 CE1 B:HIS36 3.6 20.1 1.0 O B:HOH386 4.0 51.2 1.0 CG B:HIS36 4.4 20.9 1.0 CB B:ASP35 4.7 18.9 1.0 O B:HOH375 4.9 39.3 1.0 NE2 B:HIS36 4.9 20.6 1.0 O B:ASP35 4.9 19.8 1.0 C B:ASP35 4.9 19.6 1.0 CB B:HIS36 5.0 21.1 1.0

S.Kumar, S.Yamini, J.Kumar, P.Kaur, T.P.Singh, S.Dey. Crystal Structure of A New Form of Lectin From Allium Sativum at 2.17 A Resolution To Be Published.