Calcium in PDB 4fdi: The Molecular Basis of Mucopolysaccharidosis IV A

All present enzymatic activity of The Molecular Basis of Mucopolysaccharidosis IV A:
3.1.6.4;

The structure of The Molecular Basis of Mucopolysaccharidosis IV A, PDB code: 4fdi was solved by Y.Rivera-Colon, S.C.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.372, 155.522, 62.555, 90.00, 113.76, 90.00
R / Rfree (%)	16.4 / 21.1

The binding sites of Calcium atom in the The Molecular Basis of Mucopolysaccharidosis IV A (pdb code 4fdi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Molecular Basis of Mucopolysaccharidosis IV A, PDB code: 4fdi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Molecular Basis of Mucopolysaccharidosis IV A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Molecular Basis of Mucopolysaccharidosis IV A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:21.1 occ:1.00 OD1 A:ASP40 2.3 11.1 1.0 OD1 A:ASP39 2.3 16.0 1.0 OG1 A:DDZ79 2.4 9.9 1.0 OD1 A:ASN289 2.5 11.2 1.0 OD2 A:ASP288 2.5 18.1 1.0 OD1 A:ASP288 2.8 19.8 1.0 CG A:ASP288 3.0 17.5 1.0 CG A:ASN289 3.4 11.8 1.0 CG A:ASP40 3.4 12.7 1.0 CB A:DDZ79 3.5 10.8 1.0 CG A:ASP39 3.5 13.9 1.0 ND2 A:ASN289 3.7 5.4 1.0 N A:ASP40 3.7 11.6 1.0 CA A:DDZ79 3.7 10.5 1.0 N A:DDZ79 3.9 15.3 1.0 OG2 A:DDZ79 3.9 15.1 1.0 OD2 A:ASP40 4.1 11.6 1.0 O6 A:CIT604 4.1 51.0 1.0 OD2 A:ASP39 4.3 15.6 1.0 CD2 A:HIS236 4.3 21.6 1.0 CA A:ASP39 4.3 10.0 1.0 CE A:LYS310 4.3 18.5 1.0 C A:ASP39 4.4 11.1 1.0 CA A:ASP40 4.4 14.0 1.0 NZ A:LYS310 4.4 23.6 1.0 CB A:ASP40 4.5 12.2 1.0 CB A:ASP288 4.5 9.6 1.0 CB A:ASP39 4.5 12.4 1.0 NH2 A:ARG83 4.6 12.7 1.0 C A:LEU78 4.6 14.9 1.0 NZ A:LYS140 4.7 27.6 1.0 CB A:ASN289 4.7 8.0 1.0 NE2 A:HIS236 4.9 22.3 1.0 N A:ASN289 4.9 8.2 1.0

Calcium binding site 2 out of 2 in the The Molecular Basis of Mucopolysaccharidosis IV A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Molecular Basis of Mucopolysaccharidosis IV A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:19.9 occ:1.00 OG1 B:DDZ79 2.3 11.9 1.0 OD1 B:ASP39 2.3 16.5 1.0 OD1 B:ASP40 2.4 10.2 1.0 OD1 B:ASN289 2.5 10.8 1.0 OD2 B:ASP288 2.5 19.7 1.0 OD1 B:ASP288 2.8 19.4 1.0 CG B:ASP288 3.0 17.4 1.0 CG B:ASN289 3.4 11.9 1.0 CG B:ASP40 3.5 13.4 1.0 CB B:DDZ79 3.5 11.4 1.0 CG B:ASP39 3.6 15.6 1.0 ND2 B:ASN289 3.6 7.8 1.0 N B:ASP40 3.7 11.1 1.0 CA B:DDZ79 3.8 12.2 1.0 O6 B:CIT604 3.9 52.9 1.0 N B:DDZ79 4.0 15.5 1.0 OG2 B:DDZ79 4.0 15.8 1.0 OD2 B:ASP40 4.1 12.3 1.0 CA B:ASP39 4.3 10.1 1.0 CE B:LYS310 4.3 21.0 1.0 NZ B:LYS310 4.3 24.3 1.0 OD2 B:ASP39 4.3 16.1 1.0 C B:ASP39 4.3 13.6 1.0 CD2 B:HIS236 4.3 21.4 1.0 CA B:ASP40 4.4 15.3 1.0 CB B:ASP288 4.5 9.7 1.0 NH2 B:ARG83 4.5 11.5 1.0 CB B:ASP40 4.5 13.0 1.0 CB B:ASP39 4.5 11.8 1.0 NZ B:LYS140 4.5 26.7 1.0 C B:LEU78 4.7 14.9 1.0 CB B:ASN289 4.8 9.1 1.0 N B:ASN289 4.9 8.4 1.0 C6 B:CIT604 4.9 56.3 1.0 NE2 B:HIS236 4.9 23.2 1.0

Y.Rivera-Colon, E.K.Schutsky, A.Z.Kita, S.C.Garman. The Structure of Human Galns Reveals the Molecular Basis For Mucopolysaccharidosis IV A. J.Mol.Biol. V. 423 736 2012.
ISSN: ISSN 0022-2836
PubMed: 22940367
DOI: 10.1016/J.JMB.2012.08.020