Calcium in PDB 2zai: Crystal Structure of the Soluble Domain of STT3 From P. Furiosus

The structure of Crystal Structure of the Soluble Domain of STT3 From P. Furiosus, PDB code: 2zai 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.935, 265.297, 74.138, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.3

The structure of Crystal Structure of the 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 Soluble Domain of STT3 From P. Furiosus (pdb code 2zai). 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 Soluble Domain of STT3 From P. Furiosus, PDB code: 2zai:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the 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 Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:26.1 occ:1.00 O A:TYR793 2.5 27.0 1.0 OE1 A:GLU554 2.6 22.4 1.0 OE1 A:GLU796 2.6 34.4 1.0 O A:ALA759 2.7 26.2 1.0 OE2 A:GLU554 2.8 19.7 1.0 CD A:GLU554 3.0 19.9 1.0 CD A:GLU796 3.5 37.5 1.0 OE2 A:GLU796 3.6 34.5 1.0 C A:ALA759 3.7 26.2 1.0 C A:TYR793 3.7 29.2 1.0 N A:ALA759 4.2 26.9 1.0 CG A:GLU554 4.4 18.4 1.0 OG A:SER758 4.5 28.7 1.0 CA A:ALA759 4.6 25.5 1.0 N A:PHE760 4.6 26.0 1.0 CA A:PHE760 4.6 25.4 1.0 CA A:TYR793 4.6 30.0 1.0 N A:LEU794 4.6 30.1 1.0 CA A:LEU794 4.6 32.2 1.0 CG A:GLU796 4.9 38.9 1.0 CD2 A:LEU794 4.9 34.0 1.0 CD A:LYS705 5.0 20.6 1.0 CD1 A:TYR793 5.0 29.9 1.0 CB A:TYR793 5.0 28.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the 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 Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:37.8 occ:1.00 O B:TYR793 2.6 33.2 1.0 O B:ALA759 2.6 25.0 1.0 OE1 B:GLU796 2.7 46.3 1.0 OE2 B:GLU554 2.7 31.7 1.0 OE1 B:GLU554 2.8 33.6 1.0 CD B:GLU554 3.1 31.4 1.0 OE2 B:GLU796 3.3 43.4 1.0 CD B:GLU796 3.3 44.2 1.0 C B:ALA759 3.6 28.3 1.0 C B:TYR793 3.8 34.9 1.0 O B:HOH971 4.1 33.4 1.0 N B:ALA759 4.2 30.1 1.0 N B:PHE760 4.4 27.9 1.0 CA B:PHE760 4.4 28.8 1.0 OG B:SER758 4.5 29.1 1.0 CA B:ALA759 4.5 30.0 1.0 CG B:GLU554 4.5 30.6 1.0 CA B:TYR793 4.6 36.4 1.0 CA B:LEU794 4.7 37.1 1.0 N B:LEU794 4.7 34.5 1.0 CG B:GLU796 4.8 43.0 1.0 CD B:LYS705 4.8 38.7 1.0 CB B:TYR793 4.9 35.2 1.0 C B:SER758 5.0 32.3 1.0 CD2 B:LEU794 5.0 32.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the 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 Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3 b:53.5 occ:1.00 O C:TYR793 2.6 55.4 1.0 OE1 C:GLU554 2.7 46.1 1.0 OE2 C:GLU796 2.7 59.6 1.0 O C:ALA759 2.8 41.5 1.0 OE2 C:GLU554 2.9 46.0 1.0 CD C:GLU554 3.1 44.4 1.0 CD C:GLU796 3.4 60.6 1.0 OE1 C:GLU796 3.4 59.4 1.0 C C:TYR793 3.8 56.8 1.0 C C:ALA759 3.9 41.2 1.0 N C:ALA759 4.4 42.7 1.0 OG C:SER758 4.5 51.9 1.0 CA C:LEU794 4.6 57.0 1.0 CG C:GLU554 4.6 42.6 1.0 N C:LEU794 4.6 57.4 1.0 CG C:GLU796 4.7 60.4 1.0 CA C:TYR793 4.7 57.1 1.0 CA C:PHE760 4.7 40.2 1.0 N C:PHE760 4.8 40.8 1.0 CD C:LYS705 4.8 51.8 1.0 CA C:ALA759 4.8 41.9 1.0 CD2 C:LEU794 4.9 54.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the 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 Soluble Domain of STT3 From P. Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4 b:38.1 occ:1.00 O D:TYR793 2.5 29.3 1.0 OE1 D:GLU796 2.7 36.2 1.0 OE2 D:GLU554 2.7 27.8 1.0 O D:ALA759 2.7 31.1 1.0 OE1 D:GLU554 2.8 28.8 1.0 CD D:GLU554 3.1 28.2 1.0 CD D:GLU796 3.5 38.3 1.0 C D:TYR793 3.7 32.0 1.0 OE2 D:GLU796 3.7 39.5 1.0 C D:ALA759 3.8 29.8 1.0 N D:ALA759 4.3 30.7 1.0 CA D:TYR793 4.4 34.0 1.0 CD D:LYS705 4.5 30.1 1.0 CG D:GLU554 4.5 26.0 1.0 CB D:TYR793 4.6 34.2 1.0 CA D:ALA759 4.6 29.4 1.0 N D:PHE760 4.7 29.0 1.0 N D:LEU794 4.7 30.9 1.0 CA D:PHE760 4.7 28.1 1.0 OG D:SER758 4.7 33.0 1.0 CA D:LEU794 4.8 33.0 1.0 CG D:GLU796 5.0 39.3 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