Calcium in PDB 9l5o: Crystal Structure of the Mutant Y549A of Collagenase Vhac

All present enzymatic activity of Crystal Structure of the Mutant Y549A of Collagenase Vhac:
3.4.24.3;

The structure of Crystal Structure of the Mutant Y549A of Collagenase Vhac, PDB code: 9l5o was solved by W.X.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.78 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.366, 49.478, 90.225, 90, 103.79, 90
R / Rfree (%)	17.8 / 22.1

The structure of Crystal Structure of the Mutant Y549A of Collagenase Vhac also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Mutant Y549A of Collagenase Vhac (pdb code 9l5o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Mutant Y549A of Collagenase Vhac, PDB code: 9l5o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Mutant Y549A of Collagenase Vhac


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 the Mutant Y549A of Collagenase Vhac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:18.6 occ:1.00 O A:GLY485 2.3 19.0 1.0 O A:GLY491 2.3 19.3 1.0 O A:LEU489 2.3 21.9 1.0 O A:HOH1005 2.3 16.8 1.0 O A:HOH856 2.3 18.9 1.0 OE2 A:GLU446 2.4 22.3 1.0 C A:GLY485 3.3 16.0 1.0 CD A:GLU446 3.4 20.1 1.0 C A:GLY491 3.5 21.6 1.0 C A:LEU489 3.6 23.2 1.0 N A:GLY491 3.7 22.8 1.0 OE1 A:GLU446 3.7 20.8 1.0 CA A:GLY485 3.8 18.4 1.0 C A:TYR490 3.8 23.2 1.0 O A:HOH988 3.9 19.2 1.0 O A:TYR490 4.1 21.1 1.0 CA A:GLY491 4.2 22.1 1.0 OD2 A:ASP410 4.2 18.8 1.0 O A:HOH893 4.3 15.2 1.0 CA A:TYR490 4.4 19.4 1.0 CB A:LEU489 4.4 18.3 1.0 N A:TYR490 4.4 22.5 1.0 CG A:PRO449 4.5 21.8 1.0 N A:ARG486 4.5 17.4 1.0 CA A:LEU489 4.5 17.6 1.0 N A:GLY492 4.5 24.7 1.0 O A:HOH901 4.7 21.2 1.0 CG A:GLU446 4.7 18.5 1.0 CG2 A:VAL407 4.7 17.3 1.0 CA A:GLY492 4.8 21.5 1.0 CA A:ARG486 4.8 17.3 1.0 N A:LEU489 4.9 17.2 1.0 O A:GLY492 5.0 22.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Mutant Y549A of Collagenase Vhac


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 the Mutant Y549A of Collagenase Vhac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:27.4 occ:1.00 OD1 A:ASP421 2.2 25.9 1.0 O A:ASN376 2.3 26.2 1.0 O A:HOH895 2.4 27.6 1.0 OE1 A:GLU462 2.4 24.4 1.0 O A:HOH1017 2.4 31.2 1.0 O A:HOH1011 2.5 28.7 1.0 OE2 A:GLU462 2.5 24.8 1.0 CD A:GLU462 2.8 22.8 1.0 CG A:ASP421 3.5 32.2 1.0 C A:ASN376 3.5 24.2 1.0 OD2 A:ASP421 4.2 36.2 1.0 CG A:GLU462 4.2 23.6 1.0 OD1 A:ASN376 4.3 45.5 1.0 CB A:ASN376 4.3 32.0 1.0 O A:ASP421 4.3 25.5 1.0 OE1 A:GLN381 4.3 27.9 1.0 C1 A:GOL708 4.4 42.2 1.0 N A:MET377 4.4 20.9 1.0 CG A:ASN376 4.4 34.0 1.0 CA A:ASN376 4.4 27.8 1.0 CA A:MET377 4.4 23.2 1.0 CB A:ASP421 4.5 24.4 1.0 CA A:ASP421 4.5 24.5 1.0 O A:HOH837 4.5 22.0 1.0 CB A:GLU462 4.7 22.1 1.0 NE2 A:GLN381 4.8 22.6 1.0 C A:ASP421 4.9 25.0 1.0 O1 A:GOL708 5.0 42.1 1.0 CG A:MET377 5.0 23.7 1.0 N A:ASN376 5.0 25.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Mutant Y549A of Collagenase Vhac


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 the Mutant Y549A of Collagenase Vhac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca711 b:28.9 occ:1.00 O A:THR523 2.4 26.1 1.0 O A:SER528 2.4 33.7 1.0 O A:HOH910 2.4 28.8 1.0 OD1 A:ASP526 2.4 29.6 1.0 OD2 A:ASP526 2.5 34.5 1.0 OG A:SER528 2.5 32.9 1.0 OG1 A:THR523 2.5 26.0 1.0 O A:HOH1132 2.5 33.9 1.0 CG A:ASP526 2.8 34.1 1.0 C A:THR523 3.3 30.0 1.0 C A:SER528 3.4 32.8 1.0 CA A:THR523 3.5 31.3 1.0 CB A:THR523 3.5 32.8 1.0 CB A:SER528 3.7 33.5 1.0 CA A:SER528 3.9 33.5 1.0 N A:SER528 4.0 35.8 1.0 CB A:ASP526 4.3 34.7 1.0 CG2 A:THR523 4.4 28.9 1.0 OD2 A:ASP546 4.4 29.3 1.0 NE1 A:TRP551 4.4 27.9 1.0 OD1 A:ASP546 4.5 26.2 1.0 N A:ILE524 4.5 27.1 1.0 O A:HOH1186 4.5 39.6 1.0 O A:HOH1028 4.5 40.7 1.0 N A:THR529 4.6 31.7 1.0 CZ2 A:TRP551 4.8 29.6 1.0 CG A:ASP546 4.8 27.0 1.0 N A:THR523 4.9 28.3 1.0

W.X.Zhao, W.X.Zhao. N/A N/A.