Calcium in PDB 4n6f: Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P

The structure of Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P, PDB code: 4n6f was solved by X.Zhang, Y.Zhang, C.Kinsland, E.Sasaki, H.G.Sun, M.J.Lu, T.Liu, A.Ou, J.Li, Y.Chen, H.Liu, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 2.25
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	168.940, 168.940, 42.367, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.2

The binding sites of Calcium atom in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P (pdb code 4n6f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P, PDB code: 4n6f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P


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 Amycolatopsis Orientalis Bexx Complexed with G6P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:40.5 occ:1.00 OD1 A:ASP58 2.3 49.2 1.0 O A:HOH445 2.4 41.0 1.0 O A:HOH401 2.5 37.5 1.0 OD2 A:ASP56 2.6 38.7 1.0 OD1 A:ASP56 2.6 36.0 1.0 CG A:ASP56 2.9 38.2 1.0 CG A:ASP58 3.4 49.9 1.0 OD2 A:ASP58 3.8 51.0 1.0 CB A:ASP56 4.4 40.3 1.0 N A:ASN59 4.6 41.6 1.0 C A:ASP58 4.6 45.7 1.0 CB A:ASP58 4.7 48.0 1.0 CB A:ASN59 4.8 39.0 1.0 O A:ASP58 4.9 48.2 1.0 N A:ASP58 4.9 45.7 1.0 CA A:ASP58 4.9 46.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P


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 Amycolatopsis Orientalis Bexx Complexed with G6P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:41.8 occ:1.00 OE2 A:GLU72 2.3 46.9 1.0 OD1 A:ASP68 2.3 36.4 1.0 O A:HOH423 2.3 37.0 1.0 OD1 A:ASP71 2.5 43.8 1.0 O A:ASP68 2.5 32.6 1.0 O A:HOH425 2.7 51.6 1.0 O A:HOH424 2.8 52.5 1.0 CD A:GLU72 3.4 46.1 1.0 CG A:ASP71 3.4 43.2 1.0 C A:ASP68 3.4 34.1 1.0 CG A:ASP68 3.5 35.1 1.0 OD2 A:ASP71 3.5 47.9 1.0 CA A:ASP68 3.7 34.6 1.0 CG A:GLU72 3.7 46.0 1.0 CB A:ASP68 4.2 35.1 1.0 OE1 A:GLU72 4.5 46.3 1.0 OD2 A:ASP68 4.5 36.0 1.0 N A:LEU69 4.7 33.5 1.0 O A:MET67 4.8 34.4 1.0 CB A:GLU72 4.8 45.2 1.0 CB A:ASP71 4.8 41.2 1.0 N A:ASP68 5.0 34.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P


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 Amycolatopsis Orientalis Bexx Complexed with G6P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:44.0 occ:1.00 O A:HOH448 2.3 37.1 1.0 O A:HOH437 2.6 36.3 1.0 O A:GLY188 2.7 30.1 1.0 O A:HOH447 2.9 36.8 1.0 C A:GLY188 3.4 27.0 1.0 CA A:GLY188 4.1 26.2 1.0 CG2 A:ILE189 4.2 25.9 1.0 N A:ILE189 4.2 26.1 1.0 CA A:ILE189 4.4 25.2 1.0 OE2 A:GLU154 4.5 25.6 1.0 O A:HOH467 4.6 39.4 1.0 CB A:ILE189 5.0 25.0 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P


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 Amycolatopsis Orientalis Bexx Complexed with G6P within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:49.7 occ:0.50 O B:GLN32 2.2 46.8 1.0 OD2 B:ASP34 2.5 46.6 1.0 C B:GLN32 3.3 48.1 1.0 CG B:ASP34 3.7 45.1 1.0 CA B:CA303 3.8 63.0 0.5 CA B:GLN32 4.0 49.4 1.0 CB B:GLN32 4.2 53.0 1.0 OD1 B:ASP34 4.4 43.1 1.0 N B:TYR33 4.4 45.7 1.0 C B:TYR33 4.6 43.6 1.0 CA B:TYR33 4.6 44.3 1.0 N B:ASP34 4.7 42.3 1.0 CB B:ASP34 4.7 43.6 1.0 O B:TYR33 4.9 41.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:46.8 occ:1.00 O B:ILE184 2.2 39.4 1.0 O B:HOH422 2.3 41.1 1.0 O B:HOH421 2.4 51.4 1.0 O B:ILE187 2.5 44.3 1.0 O B:HOH423 2.5 32.8 1.0 O B:HOH424 2.5 49.5 1.0 C B:ILE184 3.5 42.6 1.0 C B:ILE187 3.7 43.0 1.0 CG2 B:ILE184 4.1 38.9 1.0 CA B:ILE184 4.3 42.5 1.0 N B:GLU185 4.4 46.2 1.0 CA B:GLY188 4.5 41.9 1.0 N B:GLY188 4.5 41.4 1.0 N B:ILE187 4.5 47.1 1.0 C B:GLU185 4.5 50.5 1.0 O B:ILE189 4.5 36.1 1.0 O B:GLU185 4.6 51.9 1.0 O B:GLY188 4.6 46.6 1.0 CA B:GLU185 4.6 51.1 1.0 C B:GLY188 4.6 42.5 1.0 CA B:ILE187 4.6 45.1 1.0 CB B:ILE184 4.8 40.5 1.0 O B:HOH440 4.9 33.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Amycolatopsis Orientalis Bexx Complexed with G6P within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:63.0 occ:0.50 OD1 B:ASP34 2.1 43.1 1.0 OD2 B:ASP34 2.8 46.6 1.0 CG B:ASP34 2.8 45.1 1.0 CA B:CA301 3.8 49.7 0.5 NH1 B:ARG61 4.3 45.8 1.0 CB B:ASP34 4.3 43.6 1.0 O B:TYR33 4.6 41.0 1.0 O B:GLN32 4.7 46.8 1.0 NH2 B:ARG61 4.9 47.9 1.0 CA B:ASP34 4.9 43.5 1.0

E.Sasaki, X.Zhang, H.G.Sun, M.Y.Lu, T.L.Liu, A.Ou, J.Y.Li, Y.H.Chen, S.E.Ealick, H.W.Liu. Co-Opting Sulphur-Carrier Proteins From Primary Metabolic Pathways For 2-Thiosugar Biosynthesis. Nature V. 509 427 2014.
ISSN: ISSN 0028-0836
PubMed: 24814342
DOI: 10.1038/NATURE13256