Calcium in PDB 2duq: Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form

The structure of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form, PDB code: 2duq was solved by T.Satoh, N.P.Cowieson, R.Kato, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.200, 45.000, 117.000, 90.00, 131.90, 90.00
R / Rfree (%)	20.6 / 24.5

The structure of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form also contains other interesting chemical elements:

Chlorine

(Cl)

13 atoms

The binding sites of Calcium atom in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form (pdb code 2duq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form, PDB code: 2duq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:20.3 occ:1.00 O A:TYR164 2.3 21.0 1.0 OD2 A:ASP193 2.4 19.3 1.0 OD1 A:ASN166 2.4 20.2 1.0 O A:HOH339 2.4 16.7 1.0 OD2 A:ASP162 2.5 18.0 1.0 O A:HOH319 2.5 20.6 1.0 OD1 A:ASP162 2.6 18.4 1.0 CG A:ASP162 2.9 19.3 1.0 CG A:ASP193 3.5 20.2 1.0 C A:TYR164 3.5 21.2 1.0 CG A:ASN166 3.6 19.2 1.0 N A:ASN166 3.9 21.4 1.0 CB A:ASP193 4.2 17.7 1.0 CB A:ASN166 4.2 21.4 1.0 CA A:TYR164 4.3 21.0 1.0 N A:TYR164 4.3 20.7 1.0 CA A:ASP193 4.4 18.6 1.0 CB A:ASP162 4.4 19.1 1.0 CE1 A:HIS190 4.4 21.4 1.0 OD1 A:ASP193 4.5 21.4 1.0 CB A:TYR164 4.5 20.8 1.0 O A:HIS190 4.5 20.6 1.0 CE2 A:PHE174 4.5 23.3 1.0 N A:PRO165 4.5 21.9 1.0 CA A:PRO165 4.6 22.1 1.0 OH A:TYR188 4.6 22.1 1.0 ND2 A:ASN166 4.7 18.9 1.0 CA A:ASN166 4.7 20.8 1.0 ND1 A:HIS190 4.7 22.4 1.0 C A:PRO165 4.7 21.4 1.0 O A:ASP131 4.8 18.1 1.0 OD2 A:ASP131 4.8 21.2 1.0 CD2 A:TYR164 4.8 21.7 1.0 CZ A:PHE148 4.9 19.1 1.0 N A:ASP193 4.9 18.4 1.0 CE1 A:PHE148 5.0 21.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of VIP36 Exoplasmic/Lumenal Domain, CA2+/Man-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:23.3 occ:1.00 OD1 B:ASN166 2.3 23.9 1.0 O B:TYR164 2.3 23.8 1.0 OD2 B:ASP193 2.4 25.9 1.0 O B:HOH337 2.4 17.9 1.0 OD2 B:ASP162 2.6 26.2 1.0 O B:HOH335 2.6 27.7 1.0 OD1 B:ASP162 2.7 26.0 1.0 CG B:ASP162 3.0 24.3 1.0 CG B:ASN166 3.4 25.7 1.0 CG B:ASP193 3.5 27.7 1.0 C B:TYR164 3.5 24.7 1.0 N B:ASN166 3.9 27.5 1.0 CB B:ASN166 4.1 28.0 1.0 CB B:ASP193 4.1 27.4 1.0 CA B:TYR164 4.3 24.0 1.0 CA B:ASP193 4.4 27.9 1.0 N B:TYR164 4.4 23.2 1.0 CB B:TYR164 4.4 24.3 1.0 OD1 B:ASP193 4.5 25.0 1.0 O B:HIS190 4.5 27.0 1.0 CE2 B:PHE174 4.5 28.7 1.0 ND2 B:ASN166 4.5 27.8 1.0 CB B:ASP162 4.5 23.1 1.0 N B:PRO165 4.5 25.7 1.0 CE1 B:HIS190 4.6 26.8 1.0 CA B:PRO165 4.6 26.3 1.0 CA B:ASN166 4.6 28.5 1.0 OH B:TYR188 4.7 29.8 1.0 C B:PRO165 4.7 26.8 1.0 OD2 B:ASP131 4.7 23.5 1.0 CD2 B:TYR164 4.7 23.5 1.0 O B:ASP131 4.8 20.2 1.0 O B:HOH403 4.9 32.7 1.0 ND1 B:HIS190 5.0 27.9 1.0 N B:ASP193 5.0 28.6 1.0

T.Satoh, N.P.Cowieson, W.Hakamata, H.Ideo, K.Fukushima, M.Kurihara, R.Kato, K.Yamashita, S.Wakatsuki. Structural Basis For Recognition of High Mannose Type Glycoproteins By Mammalian Transport Lectin VIP36 J.Biol.Chem. V. 282 28246 2007.
ISSN: ISSN 0021-9258
PubMed: 17652092
DOI: 10.1074/JBC.M703064200