Calcium in PDB 7vlz: Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7

The structure of Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7, PDB code: 7vlz was solved by H.Y.Cao, Y.Wang, M.Peng, Y.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.84 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.641, 50.573, 90.968, 90, 104.98, 90
R / Rfree (%)	16.6 / 18.7

The structure of Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 (pdb code 7vlz). 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 the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7, PDB code: 7vlz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7


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 Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:13.7 occ:1.00 O A:LEU489 2.3 13.9 1.0 O A:GLY491 2.3 16.2 1.0 O A:GLY485 2.3 13.6 1.0 O A:HOH1075 2.3 14.3 1.0 O A:HOH1155 2.3 14.5 1.0 OE2 A:GLU446 2.4 12.4 1.0 C A:GLY485 3.4 11.8 1.0 CD A:GLU446 3.4 15.9 1.0 C A:GLY491 3.5 16.0 1.0 C A:LEU489 3.5 13.5 1.0 N A:GLY491 3.7 15.7 1.0 OE1 A:GLU446 3.8 15.0 1.0 CA A:GLY485 3.8 12.9 1.0 C A:TYR490 3.9 16.6 1.0 O A:HOH839 4.0 15.1 1.0 O A:TYR490 4.2 15.5 1.0 CA A:GLY491 4.2 15.5 1.0 OD2 A:ASP410 4.2 12.4 1.0 O A:HOH946 4.3 14.2 1.0 CA A:TYR490 4.4 15.8 1.0 N A:TYR490 4.4 14.5 1.0 CB A:LEU489 4.4 13.6 1.0 CA A:LEU489 4.5 11.3 1.0 CG A:PRO449 4.5 14.8 1.0 N A:ARG486 4.5 10.8 1.0 N A:GLY492 4.5 14.6 1.0 O A:HOH1135 4.6 15.3 1.0 CG A:GLU446 4.7 14.4 1.0 CG2 A:VAL407 4.8 14.3 1.0 CA A:GLY492 4.8 18.3 1.0 CA A:ARG486 4.9 12.4 1.0 N A:LEU489 4.9 12.9 1.0 O A:GLY492 4.9 15.9 1.0 C A:GLY492 4.9 14.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7


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 Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:14.4 occ:1.00 OD1 A:ASP421 2.3 16.2 1.0 O A:HOH1216 2.3 17.2 1.0 O A:ASN376 2.3 14.4 1.0 O A:HOH1384 2.4 19.6 1.0 OE1 A:GLU462 2.5 14.7 1.0 O A:HOH997 2.5 15.9 1.0 OE2 A:GLU462 2.5 13.7 1.0 CD A:GLU462 2.8 12.3 1.0 CG A:ASP421 3.5 18.1 1.0 C A:ASN376 3.5 14.8 1.0 O A:HOH1051 4.2 26.7 1.0 O A:HOH1141 4.2 21.0 1.0 CB A:ASN376 4.2 17.7 1.0 CG A:GLU462 4.2 13.1 1.0 OD2 A:ASP421 4.3 18.9 1.0 O A:ASP421 4.3 14.8 1.0 O A:HOH1341 4.3 28.2 1.0 CG A:ASN376 4.4 18.2 1.0 O A:HOH1654 4.4 32.2 1.0 N A:MET377 4.4 14.8 1.0 CA A:ASN376 4.5 13.5 1.0 O A:HOH828 4.5 13.2 1.0 OE1 A:GLN381 4.5 15.6 1.0 CB A:ASP421 4.5 15.5 1.0 CA A:MET377 4.5 13.6 1.0 CA A:ASP421 4.5 12.5 1.0 ND2 A:ASN376 4.6 25.2 1.0 O A:HOH1564 4.6 32.9 1.0 CB A:GLU462 4.7 14.1 1.0 OD1 A:ASN376 4.9 21.4 1.0 O A:HOH1537 4.9 35.5 1.0 NE2 A:GLN381 4.9 13.6 1.0 C A:ASP421 5.0 14.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7


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 Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:21.8 occ:1.00 O A:HOH1609 2.3 33.8 1.0 O A:HOH907 2.4 21.1 1.0 O A:HOH1643 2.4 35.0 1.0 O A:HOH1333 2.4 21.5 1.0 O A:THR529 2.4 15.4 1.0 O A:HOH1246 2.4 26.3 1.0 O A:HOH1289 2.5 21.2 1.0 C A:THR529 3.6 12.9 1.0 N A:THR529 4.0 15.0 1.0 O A:HOH1119 4.1 18.0 1.0 O A:HOH1442 4.3 34.8 1.0 CA A:THR529 4.4 13.7 1.0 OE1 A:GLU534 4.4 14.8 1.0 O A:HOH1583 4.5 32.4 1.0 OG1 A:THR529 4.5 16.5 1.0 O A:HOH1604 4.5 35.4 1.0 O A:HOH1413 4.6 17.1 1.0 N A:PHE530 4.6 11.8 1.0 OE2 A:GLU534 4.8 23.3 1.0 O A:HOH1337 4.8 31.0 1.0 CA A:PHE530 4.8 13.2 1.0 O A:HOH1641 4.9 35.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7


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 the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:14.4 occ:1.00 OD1 A:ASP526 2.3 16.1 1.0 O A:HOH884 2.4 12.4 1.0 O A:SER528 2.4 13.7 1.0 OG1 A:THR523 2.4 12.2 1.0 O A:THR523 2.5 13.9 1.0 O A:HOH1316 2.6 18.6 1.0 OD2 A:ASP526 2.6 17.4 1.0 OG A:SER528 2.6 15.3 1.0 CG A:ASP526 2.8 15.9 1.0 C A:THR523 3.4 11.7 1.0 C A:SER528 3.4 14.6 1.0 CB A:THR523 3.5 12.1 1.0 CA A:THR523 3.6 13.0 1.0 CB A:SER528 3.6 16.0 1.0 CA A:SER528 3.9 16.1 1.0 N A:SER528 4.0 17.9 1.0 CB A:ASP526 4.3 17.4 1.0 NE1 A:TRP551 4.3 10.9 1.0 OD2 A:ASP546 4.4 14.8 1.0 O A:HOH998 4.4 25.3 1.0 OD1 A:ASP546 4.4 16.4 1.0 CG2 A:THR523 4.5 12.1 1.0 N A:THR529 4.6 15.0 1.0 O A:HOH1413 4.6 17.1 1.0 N A:ILE524 4.6 11.0 1.0 CZ2 A:TRP551 4.7 10.3 1.0 CG A:ASP546 4.7 13.9 1.0 CE2 A:TRP551 4.9 11.1 1.0 O A:HOH1069 4.9 21.8 1.0 N A:THR523 5.0 12.2 1.0

Y.Wang, H.Y.Cao, M.Peng. Crystal Structure of the Collagenase Unit of A Vibrio Collagenase From Vibrio Harveyi VHJR7 To Be Published.