Calcium in PDB 1dnw: Human Myeloperoxidase-Cyanide-Thiocyanate Complex

All present enzymatic activity of Human Myeloperoxidase-Cyanide-Thiocyanate Complex:
1.11.1.7;

The structure of Human Myeloperoxidase-Cyanide-Thiocyanate Complex, PDB code: 1dnw was solved by M.Blair-Johnson, T.J.Fiedler, R.E.Fenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.260, 63.770, 92.600, 90.00, 97.51, 90.00
R / Rfree (%)	19.7 / 22.4

The structure of Human Myeloperoxidase-Cyanide-Thiocyanate Complex also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex (pdb code 1dnw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex, PDB code: 1dnw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Myeloperoxidase-Cyanide-Thiocyanate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:7.7 occ:1.00 O A:ASP96 2.3 9.8 1.0 O C:PHE170 2.4 8.9 1.0 OG1 C:THR168 2.4 11.9 1.0 OD1 C:ASP172 2.4 8.5 1.0 OD2 A:ASP96 2.5 9.9 1.0 O C:THR168 2.5 7.7 1.0 OG C:SER174 2.5 8.3 1.0 C C:THR168 3.3 8.3 1.0 C A:ASP96 3.4 8.3 1.0 CB C:SER174 3.4 6.0 1.0 CG C:ASP172 3.5 7.9 1.0 CG A:ASP96 3.6 8.6 1.0 C C:PHE170 3.6 9.3 1.0 CB C:THR168 3.7 8.2 1.0 OD2 C:ASP172 3.9 8.9 1.0 CA C:THR168 4.0 8.3 1.0 N C:PHE170 4.0 8.8 1.0 CA A:ASP96 4.1 8.4 1.0 N C:THR168 4.2 7.8 1.0 C C:SER169 4.2 10.1 1.0 N C:ASP172 4.2 9.4 1.0 N C:SER174 4.2 6.2 1.0 N C:SER169 4.3 9.7 1.0 CB A:ASP96 4.3 8.9 1.0 CA C:PHE170 4.3 9.3 1.0 CA C:SER174 4.4 5.9 1.0 O C:SER169 4.4 10.0 1.0 N A:LEU97 4.5 8.0 1.0 OD1 A:ASP96 4.5 8.0 1.0 O C:HOH671 4.5 10.1 1.0 CA C:SER169 4.6 10.4 1.0 N C:VAL171 4.6 9.4 1.0 CB C:ASP172 4.7 8.4 1.0 CG2 C:THR168 4.7 8.7 1.0 CA A:LEU97 4.8 9.0 1.0 CA C:VAL171 4.8 9.2 1.0 CA C:ASP172 4.9 8.7 1.0 N C:ALA173 4.9 8.9 1.0 CB C:PHE170 5.0 8.6 1.0

Calcium binding site 2 out of 2 in the Human Myeloperoxidase-Cyanide-Thiocyanate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Myeloperoxidase-Cyanide-Thiocyanate Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2 b:8.9 occ:1.00 O B:ASP96 2.3 10.3 1.0 O D:THR168 2.3 10.2 1.0 OG1 D:THR168 2.4 12.4 1.0 OG D:SER174 2.4 11.5 1.0 O D:PHE170 2.5 11.2 1.0 OD2 B:ASP96 2.5 9.7 1.0 OD1 D:ASP172 2.5 11.2 1.0 C D:THR168 3.3 10.0 1.0 CB D:SER174 3.4 10.6 1.0 C B:ASP96 3.4 10.4 1.0 CG D:ASP172 3.6 12.7 1.0 CB D:THR168 3.6 9.3 1.0 CG B:ASP96 3.6 9.4 1.0 C D:PHE170 3.7 10.0 1.0 CA D:THR168 3.9 10.1 1.0 OD2 D:ASP172 4.0 12.9 1.0 N D:SER174 4.1 11.6 1.0 CA B:ASP96 4.1 10.3 1.0 N D:PHE170 4.1 9.7 1.0 N D:THR168 4.1 9.5 1.0 N D:ASP172 4.2 11.8 1.0 C D:SER169 4.2 11.3 1.0 N D:SER169 4.3 11.3 1.0 CA D:SER174 4.3 10.4 1.0 CA D:PHE170 4.4 9.9 1.0 CB B:ASP96 4.4 9.9 1.0 O D:SER169 4.4 12.3 1.0 O D:HOH686 4.5 7.7 1.0 OD1 B:ASP96 4.5 8.2 1.0 N B:LEU97 4.5 10.0 1.0 CA D:SER169 4.7 10.8 1.0 CG2 D:THR168 4.7 8.7 1.0 N D:VAL171 4.7 10.0 1.0 CB D:ASP172 4.8 10.7 1.0 CA B:LEU97 4.8 9.8 1.0 CA D:VAL171 4.9 11.4 1.0 CA D:ASP172 4.9 11.7 1.0 N D:ALA173 4.9 11.6 1.0 CB D:PHE170 4.9 9.7 1.0

M.Blair-Johnson, T.Fiedler, R.Fenna. Human Myeloperoxidase: Structure of A Cyanide Complex and Its Interaction with Bromide and Thiocyanate Substrates at 1.9 A Resolution. Biochemistry V. 40 13990 2001.
ISSN: ISSN 0006-2960
PubMed: 11705390
DOI: 10.1021/BI0111808