Calcium in PDB 2zag: Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus

The structure of Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus, PDB code: 2zag was solved by N.Maita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.402, 266.397, 73.982, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.2

The structure of Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus (pdb code 2zag). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus, PDB code: 2zag:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus


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 the Semet-Substituted Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:32.5 occ:1.00 O A:TYR793 2.6 28.7 1.0 OE1 A:GLU554 2.6 26.9 1.0 OE2 A:GLU554 2.7 27.1 1.0 O A:ALA759 2.8 29.1 1.0 OE2 A:GLU796 2.9 45.3 1.0 CD A:GLU554 3.0 23.9 1.0 OE1 A:GLU796 3.2 41.7 1.0 CD A:GLU796 3.3 43.3 1.0 C A:ALA759 3.6 28.3 1.0 N A:ALA759 3.8 26.7 1.0 C A:TYR793 3.8 30.7 1.0 OG A:SER758 4.1 30.1 1.0 CA A:ALA759 4.2 27.3 1.0 N A:PHE760 4.4 27.3 1.0 CG A:GLU554 4.6 24.2 1.0 CD A:LYS705 4.6 16.4 1.0 CB A:ALA759 4.6 27.0 1.0 CA A:PHE760 4.6 27.3 1.0 CA A:LEU794 4.7 33.4 1.0 N A:LEU794 4.7 30.6 1.0 CG A:GLU796 4.7 42.8 1.0 C A:SER758 4.7 28.6 1.0 CA A:TYR793 4.7 32.4 1.0 CA A:SER758 4.9 30.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus


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 the Semet-Substituted Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:34.2 occ:1.00 O B:TYR793 2.5 36.9 1.0 OE1 B:GLU554 2.7 36.1 1.0 OE2 B:GLU554 2.8 37.1 1.0 OE2 B:GLU796 2.9 50.1 1.0 O B:ALA759 2.9 33.0 1.0 OE1 B:GLU796 3.1 48.0 1.0 CD B:GLU554 3.1 34.8 1.0 CD B:GLU796 3.2 47.8 1.0 C B:TYR793 3.7 37.9 1.0 C B:ALA759 3.8 33.6 1.0 N B:ALA759 4.2 35.0 1.0 CG B:GLU796 4.5 46.8 1.0 OG B:SER758 4.5 34.4 1.0 CA B:ALA759 4.5 34.1 1.0 N B:PHE760 4.6 32.8 1.0 CA B:TYR793 4.6 40.1 1.0 CG B:GLU554 4.6 33.5 1.0 CA B:LEU794 4.6 36.6 1.0 N B:LEU794 4.7 36.3 1.0 CA B:PHE760 4.7 32.2 1.0 CD B:LYS705 4.7 37.1 1.0 CB B:TYR793 5.0 41.7 1.0 CD2 B:LEU794 5.0 27.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3 b:57.3 occ:1.00 O C:TYR793 2.7 62.7 1.0 OE1 C:GLU796 2.7 74.0 1.0 OE2 C:GLU554 2.7 45.6 1.0 O C:ALA759 2.8 46.0 1.0 OE1 C:GLU554 2.9 49.2 1.0 CD C:GLU554 3.1 47.2 1.0 CD C:GLU796 3.3 72.3 1.0 OE2 C:GLU796 3.6 72.7 1.0 C C:ALA759 3.6 44.5 1.0 C C:TYR793 3.8 63.6 1.0 N C:ALA759 4.0 45.0 1.0 OG C:SER758 4.3 51.6 1.0 CA C:ALA759 4.4 43.8 1.0 N C:PHE760 4.4 43.9 1.0 CG C:GLU796 4.4 71.0 1.0 CA C:TYR793 4.5 63.5 1.0 CG C:GLU554 4.5 46.0 1.0 CA C:PHE760 4.6 43.0 1.0 N C:LEU794 4.8 64.2 1.0 C C:SER758 4.8 47.4 1.0 CB C:TYR793 4.8 63.6 1.0 CD C:LYS705 4.8 52.6 1.0 CA C:LEU794 4.9 65.2 1.0 CB C:ALA759 4.9 40.9 1.0 CD1 C:PHE760 5.0 40.7 1.0 CA C:SER758 5.0 49.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Semet-Substituted Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4 b:30.4 occ:1.00 O D:TYR793 2.6 41.9 1.0 OE2 D:GLU554 2.7 29.1 1.0 O D:ALA759 2.7 28.6 1.0 OE2 D:GLU796 3.0 56.8 1.0 OE1 D:GLU554 3.1 29.1 1.0 OE1 D:GLU796 3.1 53.9 1.0 CD D:GLU554 3.2 27.7 1.0 CD D:GLU796 3.3 54.4 1.0 C D:TYR793 3.6 42.2 1.0 C D:ALA759 3.7 29.5 1.0 N D:ALA759 4.2 30.5 1.0 CA D:TYR793 4.3 42.5 1.0 CA D:ALA759 4.5 29.8 1.0 N D:LEU794 4.5 41.6 1.0 CA D:LEU794 4.6 42.6 1.0 N D:PHE760 4.6 27.7 1.0 CG D:GLU554 4.6 25.7 1.0 CB D:TYR793 4.6 42.9 1.0 CG D:GLU796 4.7 54.7 1.0 CA D:PHE760 4.7 27.6 1.0 OG D:SER758 4.8 30.2 1.0 CD D:LYS705 4.8 26.4 1.0 CB D:ALA759 4.8 29.6 1.0

M.Igura, N.Maita, J.Kamishikiryo, M.Yamada, T.Obita, K.Maenaka, D.Kohda. Structure-Guided Identification of A New Catalytic Motif of Oligosaccharyltransferase Embo J. V. 27 234 2008.
ISSN: ISSN 0261-4189
PubMed: 18046457
DOI: 10.1038/SJ.EMBOJ.7601940