Calcium in PDB 4gn8: Mouse SMP30/Gnl-1,5-Ag Complex

Enzymatic activity of Mouse SMP30/Gnl-1,5-Ag Complex

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

Protein crystallography data

The structure of Mouse SMP30/Gnl-1,5-Ag Complex, PDB code: 4gn8 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) 49.90 / 1.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.587, 102.587, 149.706, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 19

Calcium Binding Sites:

The binding sites of Calcium atom in the Mouse SMP30/Gnl-1,5-Ag Complex (pdb code 4gn8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mouse SMP30/Gnl-1,5-Ag Complex, PDB code: 4gn8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4gn8

Go back to Calcium Binding Sites List in 4gn8
Calcium binding site 1 out of 2 in the Mouse 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 Mouse SMP30/Gnl-1,5-Ag Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:16.0
occ:0.55
OD2 A:ASP204 2.1 23.4 1.0
OE2 A:GLU18 2.1 23.7 1.0
OD1 A:ASN154 2.1 17.0 1.0
O A:HOH582 2.1 25.7 1.0
O2 A:ASO305 2.2 21.3 1.0
O A:HOH590 2.5 34.1 1.0
CG A:ASN154 3.0 16.4 1.0
CD A:GLU18 3.0 23.9 1.0
ND2 A:ASN154 3.1 17.3 1.0
CG A:ASP204 3.2 26.8 1.0
OE1 A:GLU18 3.3 24.5 1.0
C2 A:ASO305 3.5 29.3 1.0
OD1 A:ASP204 3.7 21.3 1.0
ND2 A:ASN103 3.7 16.9 1.0
C1 A:ASO305 4.1 34.5 1.0
CG A:GLU18 4.2 19.1 1.0
O A:THR246 4.2 16.0 1.0
O A:HOH514 4.3 28.5 1.0
N A:GLY205 4.4 15.2 1.0
CB A:ASN154 4.4 15.8 1.0
CB A:ASP204 4.4 15.8 1.0
OD1 A:ASP104 4.4 24.9 1.0
CG A:ASN103 4.4 18.6 1.0
CB A:ASP104 4.4 15.1 1.0
C A:ASP204 4.5 16.6 1.0
OD1 A:ASN103 4.5 16.6 1.0
C3 A:ASO305 4.5 33.2 1.0
CG A:ASP104 4.6 25.0 1.0
CA A:ASP204 4.6 14.0 1.0
O3 A:ASO305 4.8 34.8 1.0
CA A:GLY205 4.9 14.6 1.0
CA A:ASN154 4.9 15.2 1.0
O A:ASP204 5.0 15.2 1.0

Calcium binding site 2 out of 2 in 4gn8

Go back to Calcium Binding Sites List in 4gn8
Calcium binding site 2 out of 2 in the Mouse 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 Mouse SMP30/Gnl-1,5-Ag Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:24.8
occ:0.22
O2 B:ASO314 2.1 22.8 1.0
OE2 B:GLU18 2.2 32.6 1.0
OD1 B:ASN154 2.2 21.0 1.0
O B:HOH565 2.2 33.3 1.0
OD2 B:ASP204 2.3 26.4 1.0
CD B:GLU18 2.9 28.3 1.0
CG B:ASN154 3.0 23.2 1.0
ND2 B:ASN154 3.1 19.5 1.0
OE1 B:GLU18 3.2 27.9 1.0
CG B:ASP204 3.4 24.6 1.0
O B:HOH487 3.5 28.5 1.0
C2 B:ASO314 3.5 30.1 1.0
ND2 B:ASN103 3.5 19.0 1.0
OD1 B:ASP204 3.9 20.8 1.0
C1 B:ASO314 4.0 33.5 1.0
CG B:GLU18 4.1 22.9 1.0
CG B:ASN103 4.3 19.2 1.0
OD1 B:ASN103 4.3 18.4 1.0
O B:THR246 4.3 16.9 1.0
CB B:ASP104 4.4 18.6 1.0
C3 B:ASO314 4.5 30.1 1.0
N B:GLY205 4.5 15.0 1.0
CB B:ASN154 4.5 18.2 1.0
OD1 B:ASP104 4.5 25.9 1.0
C B:ASP204 4.6 17.7 1.0
CB B:ASP204 4.6 15.2 1.0
CG B:ASP104 4.6 25.9 1.0
O3 B:ASO314 4.7 32.2 1.0
CA B:ASP204 4.8 14.4 1.0
CA B:ASN154 5.0 19.1 1.0
CA B:GLY205 5.0 15.0 1.0

Reference:

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
Page generated: Sat Dec 12 04:48:29 2020

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