Calcium in PDB 4u9e: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3, PDB code: 4u9e was solved by F.A.Tezcan, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.66 / 2.80
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.313, 92.213, 98.599, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28.5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 (pdb code 4u9e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3, PDB code: 4u9e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3


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 Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:0.3 occ:0.50 OE2 A:GLU8 2.7 69.9 1.0 OE1 A:GLU8 2.8 69.9 1.0 OD1 A:ASP5 3.0 72.6 1.0 CD A:GLU8 3.1 68.9 1.0 CA A:CA206 3.6 0.6 0.5 CA A:CA204 3.9 90.1 1.0 O A:HOH301 4.0 53.0 1.0 CG A:ASP5 4.2 71.7 1.0 O A:HOH311 4.3 68.1 1.0 CG A:GLU8 4.7 66.4 1.0 CD A:GLU4 4.7 77.9 1.0 CG A:GLU4 4.8 75.9 1.0 OE2 A:GLU4 4.8 79.6 1.0 CA A:ASP5 4.8 67.3 1.0 N A:ASP5 5.0 67.5 1.0 CB A:ASP5 5.0 69.4 1.0 O A:GLU4 5.0 67.6 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3


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 Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:60.9 occ:0.50 O A:LYS19 2.6 57.6 1.0 O A:HOH319 2.7 85.1 0.5 OD1 A:ASP21 2.9 61.8 1.0 OD2 A:ASP21 3.3 61.9 1.0 CG A:ASP21 3.5 62.1 1.0 C A:LYS19 3.8 56.1 1.0 CB A:LYS19 4.4 54.7 1.0 CA A:LYS19 4.5 54.8 1.0 N A:ALA20 4.8 57.4 1.0 C A:ALA20 4.8 59.6 1.0 N A:ASP21 4.9 60.7 1.0 CA A:ALA20 4.9 58.4 1.0 CB A:ASP21 4.9 61.7 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3


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 Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:90.1 occ:1.00 OE1 A:GLU8 2.4 69.9 1.0 O1A A:HEM201 2.9 64.4 1.0 OE1 A:GLU4 2.9 77.7 1.0 O A:HOH321 2.9 55.4 1.0 CD A:GLU4 3.5 77.9 1.0 CD A:GLU8 3.6 68.9 1.0 CG A:GLU4 3.8 75.9 1.0 CA A:CA202 3.9 0.3 0.5 CGA A:HEM201 4.1 65.0 1.0 CG A:GLU8 4.4 66.4 1.0 OE2 A:GLU4 4.4 79.6 1.0 OE2 A:GLU8 4.5 69.9 1.0 O2A A:HEM201 4.6 66.3 1.0 O A:HOH307 4.9 55.8 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3


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 Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:95.3 occ:0.50 NE1 A:TRP66 4.1 43.6 1.0 CA A:GLY70 4.4 39.2 1.0 CE2 A:TRP66 4.6 43.7 1.0 CZ2 A:TRP66 4.8 43.8 1.0 O A:HOH329 4.8 44.4 1.0 O A:HOH338 4.8 54.8 1.0 CD1 A:TRP66 4.8 43.9 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3


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 the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, A104/57G AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:0.6 occ:0.50 OE2 A:GLU8 2.2 69.9 1.0 O A:HOH311 2.7 68.1 1.0 CD A:GLU8 3.2 68.9 1.0 CA A:CA202 3.6 0.3 0.5 CG A:GLU8 4.0 66.4 1.0 OE1 A:GLU8 4.0 69.9 1.0 O A:HOH331 4.1 59.5 1.0 CB A:GLU8 4.3 64.1 1.0 O A:HOH368 4.6 79.0 1.0 O A:HOH335 4.7 50.9 1.0 OD1 A:ASP5 4.8 72.6 1.0

W.J.Song, A.F.Tezcan. A Designed Supramolecular Protein Assembly with in Vivo Enzymatic Activity Science V. 346 1525 2014.
ISSN: ISSN 0036-8075
PubMed: 25525249
DOI: 10.1126/SCIENCE.1259680