Calcium in PDB 6dyb: Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3

The structure of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyb 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)	38.23 / 2.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.008, 73.008, 143.994, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 30.9

The structure of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 (pdb code 6dyb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:49.7 occ:1.00 OE1 A:GLU4 2.2 41.2 1.0 OE2 A:GLU8 2.4 47.2 1.0 O1A A:HEC201 2.5 35.8 1.0 CD A:GLU4 3.5 46.6 1.0 CD A:GLU8 3.6 51.0 1.0 CGA A:HEC201 3.6 41.7 1.0 O2A A:HEC201 4.0 50.4 1.0 CG A:GLU8 4.1 49.5 1.0 CG A:GLU4 4.3 44.5 1.0 O A:HOH304 4.4 49.8 0.5 OE2 A:GLU4 4.4 56.3 1.0 OE1 A:GLU8 4.6 56.1 1.0 CBA A:HEC201 4.8 42.7 1.0

Calcium binding site 2 out of 6 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:52.8 occ:1.00 OD1 A:ASP5 2.1 47.8 1.0 O A:HOH303 2.2 44.1 1.0 OE1 A:GLU8 2.3 56.1 1.0 O A:HOH304 2.5 49.8 0.5 CG A:ASP5 3.3 54.0 1.0 CD A:GLU8 3.3 51.0 1.0 OE2 A:GLU8 3.7 47.2 1.0 OD2 A:ASP5 4.1 52.8 1.0 CB A:ASP5 4.2 58.0 1.0 CA A:ASP5 4.4 50.3 1.0 CG A:GLU8 4.6 49.5 1.0 CB A:GLU8 4.8 37.8 1.0

Calcium binding site 3 out of 6 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:82.1 occ:1.00 OE2 A:GLU4 2.6 56.3 1.0 CD A:GLU4 3.6 46.6 1.0 CG A:GLU4 3.9 44.5 1.0 CB A:GLU4 4.0 45.0 1.0 O1D A:HEC201 4.5 53.2 1.0 OE1 A:GLU4 4.7 41.2 1.0 OD2 A:ASP2 4.7 55.3 1.0 OD1 A:ASP2 4.7 60.5 1.0

Calcium binding site 4 out of 6 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:94.8 occ:1.00 O A:HOH305 3.8 54.4 1.0 OD1 A:ASP12 4.0 59.8 1.0 OD2 A:ASP12 4.9 52.9 1.0 CG A:ASP12 4.9 55.8 1.0

Calcium binding site 5 out of 6 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:99.4 occ:0.50 O1A C:HEC201 2.3 93.5 1.0 OE2 C:GLU4 2.7 98.4 1.0 CGA C:HEC201 3.2 96.2 1.0 O2A C:HEC201 3.4 92.4 1.0 CD C:GLU4 4.0 99.7 1.0 CB C:GLU4 4.4 0.9 1.0 O1D C:HEC201 4.5 0.9 1.0 CBA C:HEC201 4.6 91.7 1.0 OE1 C:GLU8 4.7 92.3 1.0 CG C:GLU4 4.8 99.9 1.0 OE1 C:GLU4 4.8 99.9 1.0

Calcium binding site 6 out of 6 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:99.5 occ:1.00 OE1 C:GLU4 2.9 99.9 1.0 CD C:GLU4 3.9 99.7 1.0 OE2 C:GLU4 4.1 98.4 1.0 O2D C:HEC201 4.1 0.5 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