Zinc in PDB 3enr: Zinc-Calcium Concanavalin A at pH 6.15

The structure of Zinc-Calcium Concanavalin A at pH 6.15, PDB code: 3enr was solved by J.Bouckaert, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.130, 96.460, 87.420, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.3

The structure of Zinc-Calcium Concanavalin A at pH 6.15 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Zinc-Calcium Concanavalin A at pH 6.15 (pdb code 3enr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc-Calcium Concanavalin A at pH 6.15, PDB code: 3enr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zinc-Calcium Concanavalin A at pH 6.15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Calcium Concanavalin A at pH 6.15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:62.0 occ:1.00 OD2 A:ASP10 2.4 37.5 1.0 NE2 A:HIS24 2.5 36.0 1.0 OE1 A:GLU8 2.5 48.7 1.0 OD1 A:ASP19 2.5 66.4 1.0 CD A:GLU8 3.2 48.0 1.0 OE2 A:GLU8 3.3 42.2 1.0 OG A:SER34 3.3 49.6 1.0 CG A:ASP19 3.3 57.9 1.0 CD2 A:HIS24 3.4 44.5 1.0 CE1 A:HIS24 3.6 44.0 1.0 CG A:ASP10 3.6 47.1 1.0 OD2 A:ASP19 3.8 41.6 1.0 O A:VAL32 4.0 45.7 1.0 CB A:ASP10 4.0 41.4 1.0 CA A:CA1003 4.3 76.2 1.0 CB A:ASP19 4.5 60.1 1.0 CG A:GLU8 4.6 53.6 1.0 CG A:HIS24 4.6 39.9 1.0 CA A:ASP19 4.6 61.7 1.0 OD1 A:ASP10 4.6 50.7 1.0 ND1 A:HIS24 4.7 33.1 1.0 CB A:SER34 4.7 46.4 1.0 CD A:PRO20 5.0 65.3 1.0 N A:SER34 5.0 41.5 1.0

Zinc binding site 2 out of 4 in the Zinc-Calcium Concanavalin A at pH 6.15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Calcium Concanavalin A at pH 6.15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:63.6 occ:1.00 OD2 A:ASP82 2.2 77.0 1.0 OD2 A:ASP80 2.2 44.0 1.0 CG A:ASP82 2.5 68.6 1.0 CB A:ASP82 2.6 49.6 1.0 OD1 A:ASP80 2.8 41.6 1.0 CG A:ASP80 2.8 37.3 1.0 NZ A:LYS59 3.4 48.6 1.0 OD1 A:ASP82 3.5 78.3 1.0 CA A:ASP82 4.0 49.8 1.0 CE A:LYS59 4.3 44.4 1.0 CB A:ASP80 4.3 36.8 1.0 OD1 A:ASN83 4.3 61.0 1.0 N A:ASP82 4.3 47.8 1.0 C A:ASP82 4.7 50.1 1.0 CD A:LYS59 4.9 42.7 1.0

Zinc binding site 3 out of 4 in the Zinc-Calcium Concanavalin A at pH 6.15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Calcium Concanavalin A at pH 6.15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:47.4 occ:1.00 OD2 B:ASP10 2.0 25.9 1.0 NE2 B:HIS24 2.2 32.9 1.0 OD1 B:ASP19 2.4 66.8 1.0 OE1 B:GLU8 2.5 52.2 1.0 CG B:ASP19 3.1 58.6 1.0 CG B:ASP10 3.1 33.8 1.0 CE1 B:HIS24 3.1 36.6 1.0 CD2 B:HIS24 3.2 36.2 1.0 CD B:GLU8 3.4 49.2 1.0 OD2 B:ASP19 3.4 52.0 1.0 OE2 B:GLU8 3.6 44.8 1.0 CB B:ASP10 3.6 44.5 1.0 OG B:SER34 3.8 35.1 1.0 O B:HOH1048 3.8 44.3 1.0 O B:HOH1040 4.0 31.1 1.0 OD1 B:ASP10 4.1 43.0 1.0 CB B:ASP19 4.3 59.1 1.0 ND1 B:HIS24 4.3 32.5 1.0 CG B:HIS24 4.3 36.4 1.0 O B:VAL32 4.4 48.0 1.0 CA B:ASP19 4.5 60.3 1.0 CA B:CA1004 4.7 54.2 1.0 CG B:GLU8 4.7 49.1 1.0 CD B:PRO20 4.9 59.8 1.0

Zinc binding site 4 out of 4 in the Zinc-Calcium Concanavalin A at pH 6.15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Calcium Concanavalin A at pH 6.15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:49.8 occ:1.00 OD2 B:ASP80 2.2 33.7 1.0 OD2 B:ASP82 2.6 81.0 1.0 CB B:ASP82 2.6 54.3 1.0 CG B:ASP82 2.9 74.1 1.0 CG B:ASP80 3.1 32.6 1.0 OD1 B:ASP80 3.2 35.8 1.0 OD1 B:ASN83 3.9 70.1 1.0 OD1 B:ASP82 4.0 87.0 1.0 CA B:ASP82 4.0 50.8 1.0 NZ B:LYS59 4.1 45.9 1.0 CB B:ASP80 4.5 29.4 1.0 C B:ASP82 4.5 53.2 1.0 N B:ASP82 4.5 43.4 1.0 O B:ASP82 4.8 54.1 1.0 CE B:LYS59 4.8 43.9 1.0 CG B:ASN83 5.0 65.9 1.0 N B:ASN83 5.0 51.9 1.0

J.Bouckaert, R.Loris, L.Wyns. Zinc/Calcium- and Cadmium/Cadmium-Substituted Concanavalin A: Interplay of Metal Binding, pH and Molecular Packing. Acta Crystallogr.,Sect.D V. 56 1569 2000.
ISSN: ISSN 0907-4449
PubMed: 11092923
DOI: 10.1107/S0907444900013342