Calcium in PDB 4gnc: Human SMP30/Gnl-1,5-Ag Complex

All present enzymatic activity of Human SMP30/Gnl-1,5-Ag Complex:
3.1.1.17;

The structure of Human SMP30/Gnl-1,5-Ag Complex, PDB code: 4gnc was solved by S.Aizawa, M.Senda, A.Harada, N.Maruyama, T.Ishida, T.Aigaki, A.Ishigami, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.407, 50.202, 86.569, 90.00, 99.65, 90.00
R / Rfree (%)	19.5 / 23

The binding sites of Calcium atom in the Human SMP30/Gnl-1,5-Ag Complex (pdb code 4gnc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human SMP30/Gnl-1,5-Ag Complex, PDB code: 4gnc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human SMP30/Gnl-1,5-Ag Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human SMP30/Gnl-1,5-Ag Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:21.8 occ:1.00 OD1 A:ASN154 2.1 25.1 1.0 O A:HOH476 2.3 30.6 1.0 OE2 A:GLU18 2.3 27.6 1.0 OD1 A:ASP204 2.3 21.2 1.0 OD1 A:ASP104 2.4 21.4 0.8 O2 A:ASO303 2.4 30.7 0.7 O3 A:ASO303 2.5 33.5 0.7 OD2 A:ASP104 2.5 22.4 0.6 CG A:ASP104 2.8 21.1 0.3 C2 A:ASO303 2.9 27.0 0.7 CG A:ASN154 3.1 26.0 1.0 CD A:GLU18 3.2 26.1 1.0 C3 A:ASO303 3.2 31.3 0.7 CG A:ASP204 3.4 24.8 1.0 ND2 A:ASN154 3.6 28.2 1.0 OE1 A:GLU18 3.9 33.3 1.0 OD2 A:ASP204 4.0 24.5 1.0 CG A:GLU18 4.1 26.0 1.0 ND2 A:ASN103 4.1 23.2 1.0 O A:HOH469 4.3 25.3 1.0 O A:THR246 4.3 19.1 1.0 CB A:ASP104 4.3 17.7 1.0 C4 A:ASO303 4.4 32.8 0.7 C1 A:ASO303 4.4 31.4 0.7 CB A:ASN154 4.4 24.7 1.0 N A:GLY205 4.4 17.4 1.0 C A:ASP204 4.6 15.7 1.0 CB A:ASP204 4.7 21.3 1.0 CG A:ASN103 4.7 24.2 1.0 OD1 A:ASN103 4.7 26.8 1.0 CA A:ASN154 4.8 21.5 1.0 CA A:ASP204 4.9 16.8 1.0 CA A:GLY205 4.9 20.6 1.0

Calcium binding site 2 out of 2 in the Human SMP30/Gnl-1,5-Ag Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human SMP30/Gnl-1,5-Ag Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:19.0 occ:1.00 OD1 B:ASN154 2.1 25.4 1.0 O B:HOH474 2.3 27.3 1.0 OD1 B:ASP204 2.3 18.8 1.0 OE2 B:GLU18 2.3 29.2 1.0 O3 B:ASO302 2.4 24.6 1.0 O2 B:ASO302 2.4 28.0 1.0 OD1 B:ASP104 2.4 19.6 0.5 OD2 B:ASP104 2.6 18.7 0.5 CG B:ASP104 2.9 19.1 0.0 CD B:GLU18 3.1 25.1 1.0 C2 B:ASO302 3.1 28.0 1.0 CG B:ASN154 3.2 22.0 1.0 C3 B:ASO302 3.3 23.7 1.0 CG B:ASP204 3.3 21.3 1.0 OE1 B:GLU18 3.7 27.4 1.0 OD2 B:ASP204 3.7 21.6 1.0 ND2 B:ASN154 3.8 21.7 1.0 CG B:GLU18 4.0 21.9 1.0 ND2 B:ASN103 4.0 15.7 1.0 O B:THR246 4.2 18.5 1.0 CB B:ASN154 4.3 20.9 1.0 CB B:ASP104 4.4 17.4 0.5 CB B:ASP104 4.4 17.4 0.5 OD2 B:ASP104 4.4 22.7 0.5 N B:GLY205 4.5 15.4 1.0 CG B:ASP104 4.5 20.9 0.5 C1 B:ASO302 4.6 28.5 1.0 C4 B:ASO302 4.6 28.0 1.0 O B:HOH465 4.6 32.8 1.0 O B:HOH414 4.6 24.4 1.0 CB B:ASP204 4.6 19.0 1.0 C B:ASP204 4.6 19.7 1.0 CG B:ASN103 4.7 19.9 1.0 CA B:ASN154 4.8 16.0 1.0 OD1 B:ASN103 4.8 26.0 1.0 CA B:GLY205 4.9 14.9 1.0 CA B:ASP204 4.9 16.2 1.0

S.Aizawa, M.Senda, A.Harada, N.Maruyama, T.Ishida, T.Aigaki, A.Ishigami, T.Senda. Structural Basis of the Gamma-Lactone-Ring Formation in Ascorbic Acid Biosynthesis By the Senescence Marker Protein-30/Gluconolactonase Plos One V. 8 53706 2013.
ISSN: ESSN 1932-6203
PubMed: 23349732
DOI: 10.1371/JOURNAL.PONE.0053706