Calcium in PDB 4ex9: Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate

The structure of Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate, PDB code: 4ex9 was solved by T.Oja, L.Niiranen, T.Sandalova, K.D.Klika, J.Niemi, P.Mantsala, G.Schneider, M.Metsa-Ketela, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.15
Space group	I 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	168.790, 168.790, 168.790, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24.8

The structure of Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate (pdb code 4ex9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate, PDB code: 4ex9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate


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 Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:65.4 occ:1.00 OD1 A:ASP138 2.3 68.2 1.0 O A:HOH501 2.8 65.3 1.0 CG A:ASP138 3.4 68.2 1.0 OD1 A:ASN259 3.6 0.7 1.0 OD2 A:ASP138 4.1 68.5 1.0 O10 A:5RP402 4.2 66.4 1.0 CA A:ASP138 4.3 65.3 1.0 CB A:ASP138 4.4 66.8 1.0 CG A:ASN259 4.4 0.2 1.0 ND2 A:ASN259 4.5 0.6 1.0 N A:ILE139 4.5 63.4 1.0 O A:ILE139 4.7 61.1 1.0 C A:ASP138 4.7 64.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate


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 Prealnumycin C-Glycosynthase Alna in Complex with Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:87.4 occ:0.33 OD1 A:ASP135 2.4 73.4 1.0 CG A:ASP135 3.6 72.4 1.0 OD2 A:ASP135 4.1 72.3 1.0 O A:GLU134 4.6 71.1 1.0 CB A:ASP135 4.8 71.0 1.0 CG A:GLU134 4.9 72.5 1.0

T.Oja, L.Niiranen, T.Sandalova, K.D.Klika, J.Niemi, P.Mantsala, G.Schneider, M.Metsa-Ketela. Structural Basis For C-Ribosylation in the Alnumycin A Biosynthetic Pathway. Proc.Natl.Acad.Sci.Usa V. 110 1291 2013.
ISSN: ISSN 0027-8424
PubMed: 23297194
DOI: 10.1073/PNAS.1207407110