Calcium in PDB 6dyi: Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3

The structure of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3, PDB code: 6dyi was solved by F.A.Tezcan, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.25 / 1.96
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.580, 45.940, 126.509, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.5

The structure of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 (pdb code 6dyi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3, PDB code: 6dyi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:47.0 occ:0.50 O B:HOH357 2.4 48.3 0.5 O B:LYS19 2.7 46.7 1.0 O B:HOH350 2.9 51.7 1.0 OD1 B:ASP21 3.2 68.6 1.0 OD2 B:ASP21 3.6 69.9 1.0 CG B:ASP21 3.7 69.0 1.0 C B:LYS19 3.9 54.0 1.0 CB B:LYS19 4.4 39.3 1.0 CA B:LYS19 4.5 49.6 1.0 N B:ALA20 4.9 30.0 1.0

Calcium binding site 2 out of 6 in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:49.8 occ:1.00 OD2 B:ASP5 2.5 51.7 1.0 O B:HOH317 2.5 49.4 1.0 OD2 B:ASP2 2.6 65.4 1.0 OD1 B:ASP5 3.0 52.4 1.0 CG B:ASP5 3.0 54.4 1.0 CG B:ASP2 3.4 48.2 1.0 OD1 B:ASP2 3.5 43.0 1.0 OE2 B:GLU4 4.0 38.9 0.4 CA B:CA207 4.0 50.3 0.5 CG B:GLU4 4.2 40.6 0.4 CB B:ASP5 4.4 43.6 1.0 CD B:GLU4 4.5 39.3 0.4 CG B:GLU4 4.8 42.7 0.6 CB B:ASP2 4.8 42.7 1.0 N B:ASP5 4.9 32.7 1.0

Calcium binding site 3 out of 6 in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca206 b:57.0 occ:1.00 O1A B:HEC202 2.8 60.7 1.0 O2A B:HEC202 3.0 37.1 1.0 O B:HOH325 3.2 43.7 1.0 OE1 B:GLU4 3.2 41.8 0.6 CGA B:HEC202 3.3 35.5 1.0 OE1 B:GLU4 3.3 31.7 0.4 O2D B:HEC202 4.4 31.4 1.0 CD B:GLU4 4.4 41.8 0.6 CD B:GLU4 4.5 39.3 0.4 O B:HOH362 4.7 35.1 1.0 CBA B:HEC202 4.8 27.8 1.0 CB B:GLU4 4.8 31.7 0.6 CB B:GLU4 4.8 32.0 0.4

Calcium binding site 4 out of 6 in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca207 b:50.3 occ:0.50 OD1 B:ASP5 2.5 52.4 1.0 O B:HOH312 2.6 49.7 1.0 OE2 B:GLU8 2.6 53.6 1.0 OE2 B:GLU4 2.7 38.9 0.4 CD B:GLU8 3.3 62.3 1.0 OE1 B:GLU8 3.5 65.7 1.0 CG B:ASP5 3.7 54.4 1.0 CD B:GLU4 3.8 39.3 0.4 CA B:CA205 4.0 49.8 1.0 CG B:GLU4 4.2 40.6 0.4 CA B:ASP5 4.5 31.3 1.0 OD2 B:ASP5 4.5 51.7 1.0 CG B:GLU8 4.6 38.4 1.0 CB B:ASP5 4.7 43.6 1.0 N B:ASP5 4.8 32.7 1.0 OE1 B:GLU4 4.8 31.7 0.4 O B:GLU4 4.9 35.9 0.6 O B:HOH327 4.9 32.5 1.0 O B:GLU4 4.9 35.8 0.4 C B:GLU4 5.0 35.4 0.6 C B:GLU4 5.0 35.3 0.4

Calcium binding site 5 out of 6 in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca208 b:40.3 occ:0.25 O B:HOH326 2.5 41.4 0.5 OE2 B:GLU81 3.0 68.8 1.0 CD B:GLU81 3.6 81.9 1.0 OE1 B:GLU81 3.9 79.4 1.0 CB B:GLU81 4.3 40.7 1.0 CG B:GLU81 4.6 46.7 1.0 O B:GLU81 4.7 47.1 1.0

Calcium binding site 6 out of 6 in the Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca209 b:78.3 occ:1.00 O B:ALA1 2.5 55.5 1.0 O B:HOH348 2.7 46.4 1.0 OD2 B:ASP39 2.8 51.9 1.0 N B:ALA1 2.8 65.7 1.0 OD1 B:ASP39 3.2 50.9 1.0 CG B:ASP39 3.3 38.7 1.0 C B:ALA1 3.4 45.8 1.0 CA B:ALA1 3.6 54.6 1.0 CB B:ALA1 4.4 42.2 1.0 N B:ASP2 4.5 37.4 1.0 CB B:ASP39 4.8 34.6 1.0

J.Rittle, M.J.Field, M.T.Green, F.A.Tezcan. An Efficient, Step-Economical Strategy For the Design of Functional Metalloproteins. Nat.Chem. V. 11 434 2019.
ISSN: ESSN 1755-4349
PubMed: 30778140
DOI: 10.1038/S41557-019-0218-9