Calcium in PDB 6std: Scytalone Dehydratase Plus Inhibitor 3

All present enzymatic activity of Scytalone Dehydratase Plus Inhibitor 3:
4.2.1.94;

The structure of Scytalone Dehydratase Plus Inhibitor 3, PDB code: 6std was solved by Z.Wawrzak, T.Sandalova, J.J.Steffens, G.S.Basarab, T.Lundqvist, Y.Lindqvist, D.B.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.680, 91.410, 161.020, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.4

The structure of Scytalone Dehydratase Plus Inhibitor 3 also contains other interesting chemical elements:

Bromine	(Br)	3 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Calcium atom in the Scytalone Dehydratase Plus Inhibitor 3 (pdb code 6std). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Scytalone Dehydratase Plus Inhibitor 3, PDB code: 6std:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Scytalone Dehydratase Plus Inhibitor 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Scytalone Dehydratase Plus Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:15.0 occ:0.50 OD1 A:ASP164 2.6 25.2 1.0 OE2 A:GLU163 2.6 35.0 1.0 O A:HOH711 2.6 25.2 1.0 OE1 A:GLU163 2.7 39.3 1.0 CD A:GLU163 3.0 33.1 1.0 CG A:ASP164 3.8 26.8 1.0 CA A:CA502 3.9 22.9 1.0 OE1 A:GLU167 4.1 51.4 1.0 O A:HOH720 4.1 38.0 1.0 CA A:ASP164 4.3 22.9 1.0 CG A:GLU163 4.5 30.6 1.0 N A:ASP164 4.5 23.1 1.0 CB A:ASP164 4.6 23.6 1.0 OD2 A:ASP164 4.7 26.2 1.0 CD A:GLU167 4.8 50.0 1.0 C A:GLU163 4.8 23.8 1.0 O A:GLU163 4.9 22.5 1.0

Calcium binding site 2 out of 5 in the Scytalone Dehydratase Plus Inhibitor 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Scytalone Dehydratase Plus Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:22.9 occ:1.00 OD2 A:ASP164 2.5 26.2 1.0 O A:HOH720 2.6 38.0 1.0 OD1 A:ASP164 2.7 25.2 1.0 CG A:ASP164 2.9 26.8 1.0 CA A:CA501 3.9 15.0 0.5 OE1 A:GLU163 4.2 39.3 1.0 CB A:ASP164 4.4 23.6 1.0 O A:HOH615 4.8 26.8 1.0

Calcium binding site 3 out of 5 in the Scytalone Dehydratase Plus Inhibitor 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Scytalone Dehydratase Plus Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:29.4 occ:1.00 O B:ARG51 2.3 24.2 1.0 OD1 B:ASP55 2.5 27.8 1.0 O B:HOH727 2.7 48.7 1.0 O B:HOH728 2.9 35.0 1.0 C B:ARG51 3.3 25.0 1.0 CG B:ASP55 3.7 24.5 1.0 CA B:ASP55 4.1 24.0 1.0 N B:SER52 4.2 25.8 1.0 CA B:SER52 4.2 26.7 1.0 O B:HOH685 4.2 44.5 1.0 CA B:ARG51 4.2 24.1 1.0 CB B:ASP55 4.3 23.6 1.0 CB B:ARG51 4.5 23.1 1.0 N B:ASP55 4.5 23.1 1.0 OD2 B:ASP55 4.6 27.3 1.0 C B:SER52 4.8 26.9 1.0 O B:SER52 4.8 27.1 1.0

Calcium binding site 4 out of 5 in the Scytalone Dehydratase Plus Inhibitor 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Scytalone Dehydratase Plus Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:18.8 occ:1.00 OD1 C:ASP55 2.3 22.2 1.0 O C:ARG51 2.4 19.3 1.0 O C:HOH669 2.6 40.2 1.0 O C:HOH694 2.7 35.7 1.0 C C:ARG51 3.5 20.2 1.0 CG C:ASP55 3.5 24.0 1.0 CA C:ASP55 4.0 19.9 1.0 CB C:ASP55 4.1 20.8 1.0 N C:SER52 4.3 20.9 1.0 CA C:SER52 4.3 22.3 1.0 O C:HOH689 4.3 32.0 1.0 CA C:ARG51 4.4 19.4 1.0 N C:ASP55 4.4 20.0 1.0 OD2 C:ASP55 4.5 26.1 1.0 CB C:ARG51 4.6 17.4 1.0 O C:HOH737 4.7 29.4 1.0 C C:SER52 5.0 22.5 1.0 O C:SER52 5.0 23.1 1.0

Calcium binding site 5 out of 5 in the Scytalone Dehydratase Plus Inhibitor 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Scytalone Dehydratase Plus Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:25.5 occ:1.00 OD1 C:ASP171 2.5 22.7 1.0 O C:HOH753 2.5 37.3 1.0 O C:HOH632 2.5 28.8 1.0 O C:HOH665 2.6 35.0 1.0 O C:HOH757 2.6 28.8 1.0 CG C:ASP171 3.5 29.6 1.0 O C:HOH671 4.1 26.9 1.0 CB C:ASP171 4.3 26.6 1.0 OD2 C:ASP171 4.4 26.8 1.0 CA C:ASP171 4.6 30.8 1.0 O C:THR168 4.6 26.4 1.0 O C:HOH740 4.6 31.3 1.0 O C:HOH687 4.7 27.1 1.0

Z.Wawrzak, T.Sandalova, J.J.Steffens, G.S.Basarab, T.Lundqvist, Y.Lindqvist, D.B.Jordan. High-Resolution Structures of Scytalone Dehydratase-Inhibitor Complexes Crystallized at Physiological pH. Proteins V. 35 425 1999.
ISSN: ISSN 0887-3585
PubMed: 10382670
DOI: 10.1002/(SICI)1097-0134(19990601)35:4<425::AID-PROT6>3.3.CO;2-T