Calcium in PDB 5yt7: Crystal Structure of Circularly Permutated Azurin 3

The structure of Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7 was solved by H.H.Chen, H.P.Liu, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.02 / 1.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.888, 87.968, 66.096, 90.00, 110.22, 90.00
R / Rfree (%)	16.2 / 21.7

The structure of Crystal Structure of Circularly Permutated Azurin 3 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Copper	(Cu)	4 atoms
Sodium	(Na)	3 atoms

The binding sites of Calcium atom in the Crystal Structure of Circularly Permutated Azurin 3 (pdb code 5yt7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:57.9 occ:1.00 O3 A:NO3203 2.4 29.2 1.0 OD2 A:ASP112 2.7 23.5 1.0 OD1 A:ASP112 3.1 25.0 1.0 N A:NO3203 3.3 32.1 1.0 CG A:ASP112 3.3 21.2 1.0 O1 A:NO3203 3.4 39.1 1.0 O A:SER113 3.5 23.2 1.0 N A:LYS104 4.1 20.9 1.0 O A:HOH401 4.1 35.5 1.0 O A:HOH379 4.2 35.7 1.0 CA A:THR103 4.2 19.4 1.0 O A:HIS102 4.4 19.5 1.0 CE A:LYS104 4.4 48.7 1.0 O2 A:NO3203 4.4 34.7 1.0 C A:THR103 4.5 19.9 1.0 C A:SER113 4.5 19.8 1.0 CB A:ASP112 4.8 23.6 1.0 CB A:LYS104 4.9 26.7 1.0 CB A:THR103 5.0 18.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:37.4 occ:1.00 O B:ILE16 2.3 50.5 1.0 O B:GLY18 2.4 45.5 1.0 OD1 B:ASP42 2.5 32.1 1.0 OG B:SER44 2.5 36.6 1.0 OD2 B:ASP42 2.5 32.5 1.0 O B:HOH409 2.6 35.9 1.0 CG B:ASP42 2.9 31.9 1.0 CB B:SER44 3.3 33.3 1.0 C B:ILE16 3.6 47.4 1.0 C B:GLY18 3.6 48.9 1.0 N B:ILE16 4.0 37.1 1.0 N B:GLY18 4.1 50.9 1.0 N B:SER44 4.2 24.2 1.0 CA B:ILE16 4.3 44.0 1.0 CB B:ASP42 4.4 27.5 1.0 CA B:SER44 4.4 27.9 1.0 C B:PRO17 4.4 49.5 1.0 CA B:GLY18 4.5 47.8 1.0 N B:GLY19 4.5 50.9 1.0 N B:PRO17 4.6 50.4 1.0 CA B:PRO17 4.6 48.4 1.0 CA B:GLY19 4.6 52.3 1.0 CB B:ILE16 4.7 42.8 1.0 O B:PRO17 5.0 56.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:71.1 occ:1.00 O2 B:NO3205 2.3 32.8 1.0 O1 B:NO3205 2.8 35.8 1.0 N B:NO3205 2.9 30.0 1.0 O3 B:NO3205 4.3 28.6 1.0 OE1 B:GLU125 4.3 48.4 1.0 OE2 B:GLU125 4.4 40.3 1.0 CD B:GLU125 4.7 41.4 1.0 O B:GLY124 5.0 32.4 1.0

H.H.Chen, B.Su, T.T.Zhang, A.Huang, H.P.Liu, Y.Yu, J.Wang. Engineering the Metal-Binding Loop of A Blue Copper Protein By Circular Permutation Rsc Adv 56093 2017.
ISSN: ESSN 2046-2069
DOI: 10.1039/C7RA11512A