Calcium in PDB 4gnb: Human SMP30/Gnl

All present enzymatic activity of Human SMP30/Gnl:
3.1.1.17;

The structure of Human SMP30/Gnl, PDB code: 4gnb 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)	19.53 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.500, 50.786, 86.563, 90.00, 100.24, 90.00
R / Rfree (%)	18.9 / 21.8

The binding sites of Calcium atom in the Human SMP30/Gnl (pdb code 4gnb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human SMP30/Gnl, PDB code: 4gnb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human SMP30/Gnl


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:11.0 occ:1.00 OD1 A:ASN154 2.3 11.1 1.0 OE2 A:GLU18 2.3 18.5 1.0 OD1 A:ASP204 2.3 9.6 1.0 O A:HOH410 2.3 14.8 1.0 O A:HOH421 2.3 11.6 1.0 O A:HOH440 2.4 16.6 1.0 CD A:GLU18 3.0 18.3 1.0 CG A:ASN154 3.3 11.8 1.0 CG A:ASP204 3.4 10.5 1.0 OE1 A:GLU18 3.4 13.2 1.0 ND2 A:ASN154 3.7 11.8 1.0 O A:HOH457 3.8 25.6 1.0 ND2 A:ASN103 4.0 7.9 1.0 OD2 A:ASP204 4.0 11.3 1.0 O A:THR246 4.2 9.5 1.0 CG A:GLU18 4.2 16.4 1.0 N A:GLY205 4.3 7.8 1.0 O A:HOH419 4.4 13.6 1.0 OD1 A:ASN103 4.4 11.9 1.0 CB A:ASP104 4.5 6.8 1.0 C A:ASP204 4.5 7.1 1.0 OD2 A:ASP104 4.5 13.7 1.0 CB A:ASP204 4.5 10.1 1.0 CG A:ASN103 4.5 8.2 1.0 CG A:ASP104 4.6 16.2 1.0 CB A:ASN154 4.6 8.2 1.0 CA A:ASP204 4.7 11.3 1.0 CA A:GLY205 4.7 6.6 1.0 O A:HOH522 4.8 25.6 1.0 CA A:ASN154 5.0 7.4 1.0

Calcium binding site 2 out of 3 in the Human SMP30/Gnl


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:10.8 occ:1.00 OD1 B:ASP204 2.2 11.5 1.0 OD1 B:ASN154 2.2 13.7 1.0 OE2 B:GLU18 2.3 23.7 1.0 O B:HOH492 2.3 16.9 1.0 O B:HOH468 2.4 16.4 1.0 O B:HOH491 2.4 14.2 1.0 CD B:GLU18 3.0 17.6 1.0 CG B:ASN154 3.2 14.2 1.0 CG B:ASP204 3.3 12.4 1.0 OE1 B:GLU18 3.4 16.2 1.0 ND2 B:ASN154 3.6 11.7 1.0 OD2 B:ASP204 3.8 11.0 1.0 ND2 B:ASN103 4.1 9.3 1.0 CG B:GLU18 4.1 11.7 1.0 O B:THR246 4.2 8.5 1.0 N B:GLY205 4.3 8.3 1.0 O B:HOH495 4.4 14.4 1.0 CB B:ASP104 4.5 8.7 0.0 CB B:ASP104 4.5 8.4 1.0 CB B:ASP204 4.5 11.9 1.0 CB B:ASN154 4.5 11.5 1.0 OD1 B:ASN103 4.5 17.0 1.0 C B:ASP204 4.6 11.1 1.0 OD2 B:ASP104 4.6 16.1 0.0 OD1 B:ASP104 4.6 16.5 1.0 CG B:ASP104 4.6 14.9 1.0 CG B:ASP104 4.6 14.6 0.0 CG B:ASN103 4.7 11.7 1.0 CA B:ASP204 4.8 10.7 1.0 CA B:GLY205 4.8 6.4 1.0 CA B:ASN154 5.0 11.3 1.0 O B:HOH463 5.0 28.2 1.0

Calcium binding site 3 out of 3 in the Human SMP30/Gnl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human SMP30/Gnl within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:18.4 occ:1.00 O A:HOH490 2.3 21.5 1.0 O B:HOH467 2.4 26.1 1.0 O B:HOH484 2.4 22.4 1.0 O A:HOH500 2.4 16.3 1.0 O A:HOH498 2.4 20.2 1.0 OE1 B:GLU128 2.4 17.1 1.0 OE2 B:GLU128 2.6 17.3 1.0 CD B:GLU128 2.9 24.1 1.0 O B:HOH441 3.8 17.9 1.0 CG B:GLU128 4.4 19.4 1.0 O A:HOH432 4.5 15.4 1.0 OD2 A:ASP169 4.5 11.4 1.0 O A:HOH610 4.5 27.1 1.0 NE2 A:HIS130 4.6 15.4 1.0 OD2 A:ASP151 4.7 13.3 1.0 O A:GLN149 4.8 12.1 1.0 CB A:SER172 4.8 12.1 1.0 O B:HOH578 4.8 37.4 1.0 CD2 A:HIS130 4.8 13.7 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