Calcium in PDB 4usc: Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa

The structure of Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa, PDB code: 4usc was solved by A.Bernardes, J.C.Santos, L.C.Textor, N.H.Cuadrado, E.Y.Kostetsky, M.G.Roig, J.R.C.Muniz, V.L.Shnyrov, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.11 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.180, 100.650, 132.310, 90.00, 90.00, 90.00
R / Rfree (%)	21.816 / 24.585

The structure of Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa (pdb code 4usc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa, PDB code: 4usc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa


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 Peroxidase From Palm Tree Chamaerops Excelsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1304 b:38.2 occ:1.00 O A:VAL229 2.2 38.3 1.0 OD2 A:ASP223 2.2 39.7 1.0 OG1 A:THR226 2.3 37.9 1.0 O A:SER170 2.4 43.5 1.0 OG A:SER170 2.4 40.1 1.0 O A:THR226 2.6 41.3 1.0 OD1 A:ASP231 2.6 41.1 1.0 C A:SER170 3.3 40.9 1.0 CG A:ASP231 3.4 44.2 1.0 CG A:ASP223 3.4 38.8 1.0 CB A:SER170 3.5 40.8 1.0 C A:VAL229 3.5 39.5 1.0 CB A:THR226 3.6 41.1 1.0 C A:THR226 3.6 40.4 1.0 CA A:SER170 3.7 41.5 1.0 OD2 A:ASP231 3.7 44.0 1.0 N A:ASP231 3.9 44.2 1.0 CB A:ASP223 4.0 39.4 1.0 CA A:THR226 4.1 40.0 1.0 CB A:ARG233 4.3 49.1 1.0 N A:THR226 4.3 39.9 1.0 N A:VAL229 4.3 41.5 1.0 CA A:VAL229 4.4 38.9 1.0 O A:ASP231 4.4 47.4 1.0 OD1 A:ASP223 4.4 36.5 1.0 N A:LEU230 4.4 39.1 1.0 N A:ILE171 4.5 39.7 1.0 CB A:ASP231 4.5 46.0 1.0 CB A:VAL229 4.6 39.5 1.0 CA A:LEU230 4.6 38.6 1.0 CA A:ASP231 4.7 45.8 1.0 N A:PRO227 4.7 38.6 1.0 C A:ASP231 4.7 48.2 1.0 N A:TYR234 4.7 40.0 1.0 CG2 A:THR226 4.8 41.0 1.0 C A:LEU230 4.8 43.1 1.0 CG2 A:ILE171 4.8 39.3 1.0 N A:ARG233 4.9 48.7 1.0 CG A:ARG233 5.0 53.6 1.0 C A:PRO227 5.0 41.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa


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 Peroxidase From Palm Tree Chamaerops Excelsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1305 b:42.2 occ:1.00 O A:VAL46 2.3 46.6 1.0 OD1 A:ASP43 2.3 43.2 1.0 OD1 A:ASP50 2.3 51.2 1.0 OG A:SER52 2.4 42.6 1.0 O A:HOH2009 2.5 44.6 1.0 O A:GLY48 2.5 46.7 1.0 O A:ASP43 2.6 50.1 1.0 C A:ASP43 3.4 49.1 1.0 CB A:SER52 3.5 45.5 1.0 C A:VAL46 3.5 48.3 1.0 CG A:ASP50 3.5 56.4 1.0 CG A:ASP43 3.5 46.5 1.0 CA A:ASP43 3.7 46.8 1.0 C A:GLY48 3.7 49.4 1.0 N A:SER52 3.8 46.9 1.0 N A:ASP50 4.1 52.6 1.0 OD2 A:ASP50 4.1 60.1 1.0 CA A:SER52 4.1 46.5 1.0 CB A:ASP43 4.2 44.7 1.0 N A:GLY48 4.2 52.0 1.0 C A:ARG47 4.3 54.1 1.0 CA A:VAL46 4.3 46.6 1.0 OE2 A:GLU64 4.3 50.9 1.0 N A:VAL53 4.4 48.7 1.0 N A:VAL46 4.4 44.2 1.0 N A:ARG47 4.4 52.0 1.0 CB A:ARG47 4.4 57.4 1.0 OD2 A:ASP43 4.5 46.9 1.0 CB A:VAL46 4.5 48.4 1.0 N A:CYS44 4.5 47.7 1.0 N A:GLY51 4.6 51.4 1.0 CA A:GLY48 4.6 51.8 1.0 CA A:ARG47 4.6 54.8 1.0 O A:ARG47 4.6 56.7 1.0 CB A:ASP50 4.6 56.1 1.0 N A:CYS49 4.7 51.4 1.0 O A:HIS42 4.7 38.0 1.0 OE1 A:GLU64 4.7 51.8 1.0 C A:SER52 4.7 48.9 1.0 CA A:ASP50 4.8 52.1 1.0 CA A:CYS49 4.8 53.2 1.0 C A:ASP50 4.8 51.4 1.0 C A:GLY51 4.9 50.9 1.0 C A:CYS49 5.0 54.6 1.0 N A:ASP43 5.0 43.1 1.0 CD A:GLU64 5.0 50.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa


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 Peroxidase From Palm Tree Chamaerops Excelsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1309 b:44.6 occ:1.00 O B:VAL46 2.3 61.0 1.0 OD1 B:ASP43 2.4 51.3 1.0 OD1 B:ASP50 2.4 52.2 1.0 OG B:SER52 2.4 48.9 1.0 O B:GLY48 2.5 46.5 1.0 O B:HOH2008 2.6 44.7 1.0 O B:ASP43 2.6 48.9 1.0 C B:ASP43 3.4 48.6 1.0 CB B:SER52 3.5 50.7 1.0 C B:VAL46 3.5 57.8 1.0 CG B:ASP50 3.5 55.2 1.0 CG B:ASP43 3.6 47.9 1.0 CA B:ASP43 3.7 47.4 1.0 C B:GLY48 3.7 51.5 1.0 N B:SER52 3.8 49.8 1.0 N B:ASP50 4.1 54.8 1.0 OD2 B:ASP50 4.1 55.2 1.0 CA B:SER52 4.1 50.1 1.0 N B:GLY48 4.2 57.1 1.0 CB B:ASP43 4.3 46.3 1.0 OE2 B:GLU64 4.3 58.5 1.0 C B:ARG47 4.3 59.5 1.0 N B:VAL53 4.3 50.2 1.0 CA B:VAL46 4.4 55.3 1.0 CB B:ARG47 4.4 64.9 1.0 CB B:VAL46 4.4 53.5 1.0 N B:ARG47 4.4 59.9 1.0 N B:VAL46 4.5 52.9 1.0 OD2 B:ASP43 4.5 46.0 1.0 N B:CYS44 4.6 50.1 1.0 CA B:ARG47 4.6 61.3 1.0 CA B:GLY48 4.6 56.1 1.0 N B:GLY51 4.6 54.2 1.0 O B:ARG47 4.6 64.7 1.0 CB B:ASP50 4.7 55.5 1.0 N B:CYS49 4.7 53.0 1.0 C B:SER52 4.7 50.2 1.0 O B:HIS42 4.7 41.2 1.0 CA B:ASP50 4.8 53.6 1.0 OE1 B:GLU64 4.8 59.8 1.0 CA B:CYS49 4.8 55.2 1.0 C B:ASP50 4.8 53.9 1.0 C B:GLY51 4.9 49.5 1.0 CD B:GLU64 5.0 56.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Peroxidase From Palm Tree Chamaerops Excelsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1310 b:37.0 occ:1.00 O B:VAL229 2.2 48.0 1.0 OG1 B:THR226 2.3 34.2 1.0 OD2 B:ASP223 2.3 42.6 1.0 O B:SER170 2.4 40.2 1.0 O B:THR226 2.5 34.3 1.0 OG B:SER170 2.5 38.0 1.0 OD1 B:ASP231 2.7 46.3 1.0 C B:SER170 3.4 37.5 1.0 C B:VAL229 3.4 43.8 1.0 CG B:ASP223 3.5 37.7 1.0 CB B:THR226 3.5 38.8 1.0 C B:THR226 3.5 35.6 1.0 CG B:ASP231 3.5 48.1 1.0 CB B:SER170 3.5 40.4 1.0 CA B:SER170 3.7 40.1 1.0 OD2 B:ASP231 3.8 49.2 1.0 CB B:ASP223 4.0 37.7 1.0 CA B:THR226 4.0 36.5 1.0 N B:ASP231 4.0 43.5 1.0 N B:VAL229 4.2 39.9 1.0 CA B:VAL229 4.3 40.6 1.0 CB B:ARG233 4.3 49.6 1.0 N B:THR226 4.3 38.6 1.0 N B:LEU230 4.4 42.2 1.0 OD1 B:ASP223 4.5 34.8 1.0 N B:ILE171 4.5 36.9 1.0 CB B:VAL229 4.5 40.1 1.0 O B:ASP231 4.5 47.5 1.0 N B:PRO227 4.6 34.9 1.0 CA B:LEU230 4.6 40.7 1.0 CB B:ASP231 4.7 48.3 1.0 N B:TYR234 4.8 40.7 1.0 CG2 B:THR226 4.8 39.0 1.0 CA B:ASP231 4.8 45.9 1.0 CG2 B:ILE171 4.8 40.0 1.0 C B:ASP231 4.8 45.9 1.0 C B:LEU230 4.9 42.5 1.0 CG B:ARG233 4.9 53.4 1.0 N B:ARG233 4.9 51.6 1.0 C B:PRO227 5.0 35.9 1.0

A.Bernardes, L.C.Textor, J.C.Santos, N.H.Cuadrado, E.Y.Kostetsky, M.G.Roig, V.N.Bavro, J.R.C.Muniz, V.L.Shnyrov, I.Polikarpov. Crystal Structure Analysis of Peroxidase From the Palm Tree Chamaerops Excelsa. Biochimie V. 111 58 2015.
ISSN: ISSN 0300-9084
PubMed: 25660651
DOI: 10.1016/J.BIOCHI.2015.01.014