Calcium in PDB 5amm: Structure of Leishmania Major Peroxidase D211N Mutant

All present enzymatic activity of Structure of Leishmania Major Peroxidase D211N Mutant:
1.11.1.11; 1.11.1.5;

The structure of Structure of Leishmania Major Peroxidase D211N Mutant, PDB code: 5amm was solved by G.Chreifi, J.B.Fields, S.A.Hollingsworth, M.Heyden, A.P.Arce, H.I.Magana-Garcia, T.L.Poulos, D.J.Tobias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.249, 78.310, 160.977, 90.00, 90.00, 90.00
R / Rfree (%)	18.418 / 24.455

The structure of Structure of Leishmania Major Peroxidase D211N Mutant also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Iron	(Fe)	2 atoms

The binding sites of Calcium atom in the Structure of Leishmania Major Peroxidase D211N Mutant (pdb code 5amm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Leishmania Major Peroxidase D211N Mutant, PDB code: 5amm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Leishmania Major Peroxidase D211N Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Leishmania Major Peroxidase D211N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca308 b:89.5 occ:1.00 OG A:SER86 2.5 56.0 1.0 O A:SER81 2.8 57.3 1.0 OE2 A:GLU69 2.9 59.2 1.0 O A:GLU69 3.1 46.2 1.0 OG A:SER72 3.2 64.8 1.0 OE2 A:GLU92 3.2 63.5 1.0 CD A:GLU69 3.2 56.5 1.0 OE1 A:GLU69 3.3 53.1 1.0 C A:SER81 3.6 62.5 1.0 OE1 A:GLU92 3.6 61.3 1.0 O A:GLY80 3.6 65.3 1.0 CD A:GLU92 3.8 63.1 1.0 CB A:SER86 3.9 61.5 1.0 CA A:PRO82 3.9 52.3 1.0 C A:GLU69 4.0 49.4 1.0 CB A:SER72 4.1 60.2 1.0 N A:PRO82 4.1 57.5 1.0 CA A:GLU69 4.3 48.4 1.0 OG A:SER84 4.3 56.5 1.0 CG A:GLU69 4.4 54.5 1.0 N A:SER86 4.4 56.0 1.0 N A:ASN83 4.5 49.8 1.0 C A:PRO82 4.5 53.5 1.0 CA A:SER81 4.6 66.1 1.0 CA A:SER86 4.6 58.2 1.0 CB A:SER81 4.7 74.6 1.0 C A:GLY80 4.8 65.0 1.0 N A:MET87 4.8 55.2 1.0 CB A:GLU69 4.9 50.4 1.0 C A:SER86 5.0 58.0 1.0

Calcium binding site 2 out of 2 in the Structure of Leishmania Major Peroxidase D211N Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Leishmania Major Peroxidase D211N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca309 b:83.5 occ:1.00 OE2 B:GLU69 2.8 67.4 1.0 O B:GLU69 2.8 51.9 1.0 OE2 B:GLU92 2.9 62.3 1.0 OG B:SER86 2.9 66.6 1.0 OG B:SER72 3.0 72.5 1.0 O B:SER81 3.2 66.3 1.0 CD B:GLU69 3.3 64.9 1.0 OE1 B:GLU69 3.5 65.2 1.0 OE1 B:GLU92 3.6 66.1 1.0 CD B:GLU92 3.7 61.6 1.0 CB B:SER72 3.7 65.9 1.0 C B:GLU69 3.8 53.9 1.0 O B:GLY80 3.8 67.6 1.0 CA B:PRO82 3.8 59.6 1.0 C B:SER81 3.9 64.6 1.0 CA B:GLU69 4.1 54.8 1.0 N B:PRO82 4.1 58.4 1.0 CG B:GLU69 4.3 61.8 1.0 CB B:SER86 4.3 63.4 1.0 C B:PRO82 4.4 61.0 1.0 N B:ASN83 4.5 60.2 1.0 OG B:SER84 4.7 65.6 1.0 O B:HIS68 4.7 51.0 1.0 CB B:GLU69 4.7 58.2 1.0 N B:SER86 4.8 59.9 1.0 N B:SER72 4.9 58.3 1.0 CA B:SER72 4.9 64.1 1.0 N B:ALA70 4.9 54.5 1.0 C B:GLY80 4.9 67.1 1.0 CA B:SER86 5.0 61.9 1.0 N B:MET87 5.0 59.6 1.0

J.B.Fields, S.A.Hollingsworth, G.Chreifi, M.Heyden, A.P.Arce, H.I.Magana-Garcia, T.L.Poulos, D.J.Tobias. "Bind and Crawl" Association Mechanism of Leishmania Major Peroxidase and Cytochrome C Revealed By Brownian and Molecular Dynamics Simulations. Biochemistry V. 54 7272 2015.
ISSN: ISSN 0006-2960
PubMed: 26598276
DOI: 10.1021/ACS.BIOCHEM.5B00569