Atomistry » Calcium » PDB 4gdj-4gna » 4gn7
Atomistry »
  Calcium »
    PDB 4gdj-4gna »
      4gn7 »

Calcium in PDB 4gn7: Mouse SMP30/Gnl

Enzymatic activity of Mouse SMP30/Gnl

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

Protein crystallography data

The structure of Mouse SMP30/Gnl, PDB code: 4gn7 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) 51.34 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.678, 102.678, 147.817, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Mouse SMP30/Gnl (pdb code 4gn7). 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, PDB code: 4gn7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4gn7

Go back to Calcium Binding Sites List in 4gn7
Calcium binding site 1 out of 2 in the Mouse SMP30/Gnl


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:32.6
occ:1.00
O A:HOH576 2.1 26.8 1.0
OD2 A:ASP204 2.2 30.4 1.0
OE2 A:GLU18 2.2 36.0 1.0
O A:HOH577 2.3 31.0 1.0
O A:HOH578 2.4 34.3 1.0
OD1 A:ASN154 2.4 29.4 1.0
CD A:GLU18 3.0 32.2 1.0
OE1 A:GLU18 3.2 34.2 1.0
CG A:ASP204 3.2 30.6 1.0
CG A:ASN154 3.2 30.7 1.0
ND2 A:ASN154 3.4 23.5 1.0
OD1 A:ASP204 3.7 29.9 1.0
ND2 A:ASN103 3.8 21.3 1.0
O A:THR246 4.1 23.7 1.0
O A:HOH485 4.2 29.9 1.0
CG A:GLU18 4.2 27.4 1.0
N A:GLY205 4.4 23.9 1.0
OD1 A:ASP104 4.4 30.8 1.0
OD1 A:ASN103 4.5 24.0 1.0
CG A:ASN103 4.5 26.1 1.0
CB A:ASP204 4.5 20.1 1.0
CB A:ASP104 4.5 26.4 1.0
CG A:ASP104 4.6 30.4 1.0
C A:ASP204 4.6 23.4 1.0
CB A:ASN154 4.7 24.7 1.0
CA A:ASP204 4.8 21.4 1.0
CA A:GLY205 4.9 22.3 1.0
C A:THR246 5.0 21.1 1.0

Calcium binding site 2 out of 2 in 4gn7

Go back to Calcium Binding Sites List in 4gn7
Calcium binding site 2 out of 2 in the Mouse SMP30/Gnl


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:47.4
occ:1.00
OD1 B:ASN154 2.2 36.8 1.0
OD2 B:ASP204 2.2 29.8 1.0
O B:HOH528 2.3 35.4 1.0
OE2 B:GLU18 2.3 37.6 1.0
O B:HOH553 2.4 44.1 1.0
CD B:GLU18 3.0 35.4 1.0
CG B:ASN154 3.1 40.4 1.0
OE1 B:GLU18 3.2 36.8 1.0
CG B:ASP204 3.3 32.6 1.0
ND2 B:ASN154 3.4 35.9 1.0
ND2 B:ASN103 3.7 34.0 1.0
O B:HOH512 3.8 41.0 1.0
OD1 B:ASP204 3.8 30.5 1.0
O B:THR246 4.1 24.9 1.0
CG B:GLU18 4.3 28.2 1.0
OD1 B:ASN103 4.4 32.6 1.0
CB B:ASP104 4.4 32.4 1.0
N B:GLY205 4.4 24.3 1.0
CG B:ASN103 4.4 35.1 1.0
OD1 B:ASP104 4.5 39.8 1.0
CB B:ASN154 4.5 26.0 1.0
CB B:ASP204 4.6 24.6 1.0
C B:ASP204 4.6 28.5 1.0
CG B:ASP104 4.6 35.4 1.0
CA B:ASP204 4.8 25.1 1.0
O B:HOH559 4.8 43.8 1.0
CA B:GLY205 4.9 26.4 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 04:48:25 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy