Calcium in PDB 6dyd: Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyd 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)	37.28 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.569, 87.770, 37.460, 90.00, 95.56, 90.00
R / Rfree (%)	19.6 / 24.7

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Copper	(Cu)	1 atom

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

Calcium binding site 1 out of 5 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:38.7 occ:1.00 O A:ALA1 2.2 28.4 1.0 O A:HOH358 2.6 42.0 1.0 OD2 A:ASP39 2.6 28.2 1.0 O A:HOH344 2.7 35.5 1.0 OD1 A:ASP39 2.7 26.7 1.0 O A:HOH354 2.7 41.2 1.0 O A:HOH355 2.7 35.2 1.0 O A:HOH308 2.9 31.5 1.0 CG A:ASP39 3.0 25.4 1.0 C A:ALA1 3.4 31.4 1.0 CB A:ALA1 4.2 31.7 1.0 CA A:ALA1 4.2 32.8 1.0 N A:ASP2 4.4 28.9 1.0 CB A:ASP39 4.5 19.2 1.0 CA A:ASP2 4.5 23.9 1.0 O A:ASP39 4.6 16.0 1.0 OD1 A:ASN6 4.7 24.6 1.0 C A:ASP39 5.0 17.1 1.0

Calcium binding site 2 out of 5 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:48.5 occ:1.00 O2D A:HEC203 2.2 34.7 1.0 O A:HOH364 3.0 29.1 1.0 CGD A:HEC203 3.4 32.3 1.0 O A:HOH332 3.4 42.0 1.0 O1D A:HEC203 3.9 30.9 1.0 OXT A:ARG106 4.3 22.8 1.0 CG A:PRO46 4.4 21.2 1.0 CAD A:HEC203 4.4 22.9 1.0 CBD A:HEC203 4.5 22.7 1.0 OE1 A:GLU4 4.6 42.8 1.0 O A:HOH349 4.7 30.9 1.0 O A:HOH373 4.7 40.7 1.0 CB A:PRO46 4.8 22.1 1.0

Calcium binding site 3 out of 5 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:27.0 occ:1.00 OD1 C:ASP2 2.4 23.0 1.0 OE2 C:GLU4 2.4 35.9 1.0 O C:HOH346 2.5 30.8 1.0 O C:HOH313 2.5 27.6 1.0 CD C:GLU4 2.8 40.3 1.0 CG C:ASP2 3.3 35.0 1.0 CG C:GLU4 3.4 39.2 1.0 OD2 C:ASP2 3.5 31.2 1.0 OE1 C:GLU4 3.5 51.4 1.0 O C:HOH324 4.6 36.0 1.0 CB C:ASP2 4.6 31.0 1.0 OD1 C:ASP5 4.7 30.7 1.0 CB C:GLU4 4.9 32.3 1.0

Calcium binding site 4 out of 5 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:38.4 occ:1.00 O C:HOH341 2.4 33.7 1.0 OE2 C:GLU8 2.5 36.4 1.0 CD C:GLU8 3.6 44.3 1.0 OE1 C:GLU8 4.0 43.5 1.0 OD1 C:ASP5 4.5 30.7 1.0 CG C:GLU8 4.8 41.0 1.0

Calcium binding site 5 out of 5 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:44.3 occ:1.00 O C:ALA1 2.2 37.4 1.0 O C:HOH321 2.6 38.3 1.0 OD2 C:ASP39 2.6 30.7 1.0 O C:HOH351 2.8 43.7 1.0 O C:HOH329 2.8 33.3 1.0 OD1 C:ASP39 2.9 30.1 1.0 O C:HOH305 3.1 35.8 1.0 CG C:ASP39 3.1 32.2 1.0 C C:ALA1 3.4 35.4 1.0 CA C:ALA1 4.0 39.5 1.0 N C:ASP2 4.4 30.2 1.0 O C:ASP39 4.5 23.8 1.0 CB C:ASP39 4.6 24.9 1.0 CB C:ALA1 4.6 39.4 1.0 CA C:ASP2 4.6 29.6 1.0 OD1 C:ASN6 4.8 28.1 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