Calcium in PDB 7ni3: Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3

All present enzymatic activity of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3:
1.11.2.2;

The structure of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3, PDB code: 7ni3 was solved by T.Sjogren, T.Inghardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.61 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.66, 63.64, 111.03, 90, 97.15, 90
R / Rfree (%)	17.5 / 22.4

The structure of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3 also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Iron	(Fe)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3 (pdb code 7ni3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3, PDB code: 7ni3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:3.0 occ:0.96 OD1 C:ASP172 2.2 5.7 1.0 O A:ASP96 2.3 9.9 1.0 O C:PHE170 2.3 3.0 1.0 OG C:SER174 2.4 16.2 1.0 OD1 A:ASP96 2.4 3.0 1.0 OG1 C:THR168 2.5 3.0 1.0 O C:THR168 2.7 8.9 1.0 CG C:ASP172 3.3 8.1 1.0 CB C:SER174 3.3 3.0 1.0 C A:ASP96 3.4 8.6 1.0 C C:PHE170 3.5 5.3 1.0 CG A:ASP96 3.6 3.0 1.0 C C:THR168 3.6 9.2 1.0 OD2 C:ASP172 3.8 9.1 1.0 CB C:THR168 3.8 3.0 1.0 N C:SER174 4.0 4.6 1.0 N C:ASP172 4.0 4.7 1.0 CA A:ASP96 4.0 3.0 1.0 N C:PHE170 4.1 4.5 1.0 CA C:THR168 4.2 4.0 1.0 CB A:ASP96 4.2 4.2 1.0 CA C:SER174 4.2 3.8 1.0 CA C:PHE170 4.3 3.0 1.0 C C:SER169 4.3 9.5 1.0 N C:THR168 4.4 3.0 1.0 CB C:ASP172 4.5 5.6 1.0 N A:LEU97 4.5 3.7 1.0 O C:SER169 4.5 8.8 1.0 N C:SER169 4.5 8.7 1.0 N C:VAL171 4.6 3.0 1.0 OD2 A:ASP96 4.6 3.0 1.0 O C:HOH736 4.6 3.0 1.0 CA C:ASP172 4.7 4.3 1.0 CA C:VAL171 4.7 3.0 1.0 N C:ALA173 4.8 8.0 1.0 CB C:PHE170 4.8 4.2 1.0 C C:ASP172 4.8 12.3 1.0 CG2 C:THR168 4.8 4.8 1.0 CA A:LEU97 4.8 3.4 1.0 CA C:SER169 4.8 7.7 1.0 C C:VAL171 4.9 6.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2205 b:3.0 occ:0.81 O B:ASP96 2.2 9.7 1.0 OG D:SER174 2.3 14.9 1.0 OD1 B:ASP96 2.3 8.9 1.0 OD1 D:ASP172 2.4 10.9 1.0 O D:PHE170 2.5 8.8 1.0 OG1 D:THR168 2.5 6.3 1.0 O D:THR168 2.6 8.0 1.0 CB D:SER174 3.3 11.1 1.0 C B:ASP96 3.3 10.6 1.0 CG B:ASP96 3.5 10.3 1.0 CG D:ASP172 3.5 11.8 1.0 C D:THR168 3.5 7.7 1.0 C D:PHE170 3.7 9.0 1.0 CB D:THR168 3.8 7.6 1.0 CA B:ASP96 3.9 7.2 1.0 OD2 D:ASP172 4.0 9.0 1.0 N D:SER174 4.1 7.6 1.0 CA D:THR168 4.1 3.0 1.0 N D:PHE170 4.1 4.6 1.0 CB B:ASP96 4.2 8.1 1.0 N D:THR168 4.2 3.4 1.0 N D:ASP172 4.2 3.2 1.0 C D:SER169 4.3 8.0 1.0 CA D:SER174 4.3 7.6 1.0 CA D:PHE170 4.4 3.4 1.0 N B:LEU97 4.4 8.5 1.0 OD2 B:ASP96 4.4 7.9 1.0 N D:SER169 4.5 4.9 1.0 O D:SER169 4.5 8.4 1.0 O B:HOH312 4.7 12.6 1.0 CB D:ASP172 4.7 5.7 1.0 N D:VAL171 4.7 7.2 1.0 CA D:SER169 4.8 4.8 1.0 CA B:LEU97 4.8 8.3 1.0 CG2 D:THR168 4.8 3.8 1.0 CA D:ASP172 4.9 4.1 1.0 CA D:VAL171 4.9 6.3 1.0 N D:ALA173 4.9 8.0 1.0 CB D:PHE170 4.9 3.7 1.0

T.Inghardt, T.Antonsson, C.Ericsson, D.Hovdal, P.Johannesson, C.Johansson, U.Jurva, J.Kajanus, B.Kull, E.Michaelsson, A.Pettersen, T.Sjogren, H.Sorensen, K.Westerlund, E.L.Lindstedt. Discovery of AZD4831, A Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As A Potential Treatment For Heart Failure with Preserved Ejection Fraction. J.Med.Chem. V. 65 11485 2022.
ISSN: ISSN 0022-2623
PubMed: 36005476
DOI: 10.1021/ACS.JMEDCHEM.1C02141