Calcium in PDB 5nrt: Cys-Gly Dipeptidase Glij in Complex with CA2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with CA2+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with CA2+, PDB code: 5nrt was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.650, 98.650, 106.450, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 19.7

The structure of Cys-Gly Dipeptidase Glij in Complex with CA2+ also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Cys-Gly Dipeptidase Glij in Complex with CA2+ (pdb code 5nrt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cys-Gly Dipeptidase Glij in Complex with CA2+, PDB code: 5nrt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cys-Gly Dipeptidase Glij in Complex with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:64.0 occ:1.00 OE2 A:GLU134 3.3 62.5 1.0 NE2 A:HIS161 3.6 66.2 1.0 OD1 A:ASP25 3.7 48.9 1.0 OD1 A:ASP294 3.7 49.9 1.0 OE1 A:GLU134 3.7 61.1 1.0 O A:HOH710 3.9 63.4 1.0 CD A:GLU134 3.9 61.7 1.0 NE2 A:HIS203 4.0 59.6 1.0 NE2 A:HIS224 4.2 38.8 1.0 NE2 A:HIS23 4.2 45.1 1.0 OD2 A:ASP294 4.3 51.2 1.0 CD2 A:HIS161 4.3 68.0 1.0 CG A:ASP294 4.4 49.4 1.0 CG A:ASP25 4.5 46.9 1.0 CA A:GLY297 4.6 48.3 1.0 OD2 A:ASP25 4.7 48.4 1.0 CE1 A:HIS161 4.7 68.5 1.0 CE1 A:HIS203 4.8 57.7 1.0 CD2 A:HIS23 4.8 43.4 1.0 CD2 A:HIS224 4.8 38.5 1.0 O A:GLY297 4.9 54.2 1.0 CD2 A:HIS203 5.0 59.7 1.0

Calcium binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cys-Gly Dipeptidase Glij in Complex with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:73.7 occ:1.00 O A:HOH721 4.3 67.2 1.0 O A:HOH701 4.5 74.8 1.0 C A:MET298 4.7 54.4 1.0 N A:LEU299 4.8 57.1 1.0 O A:ASP296 4.9 47.0 1.0 O A:MET298 4.9 52.2 1.0 N A:MET298 5.0 53.8 1.0

A.Marion, M.Groll, D.H.Scharf, K.Scherlach, M.Glaser, H.Sievers, M.Schuster, C.Hertweck, A.A.Brakhage, I.Antes, E.M.Huber. Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase Glij. Acs Chem. Biol. V. 12 1874 2017.
ISSN: ESSN 1554-8937
PubMed: 28525266
DOI: 10.1021/ACSCHEMBIO.6B00847