Calcium in PDB 3ljt: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound, PDB code: 3ljt was solved by H.-S.Shieh, J.M.Williams, N.Caspers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.12 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.398, 44.518, 76.251, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.8

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound (pdb code 3ljt). 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 Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound, PDB code: 3ljt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound


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 Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:7.6 occ:1.00 O A:HOH5009 2.3 6.5 1.0 O A:CYS471 2.3 7.5 1.0 OE1 A:GLU270 2.4 9.7 1.0 O A:HOH5031 2.4 8.8 1.0 OD1 A:ASP360 2.4 6.2 1.0 OD1 A:ASP474 2.5 14.1 1.0 OD2 A:ASP360 2.6 6.1 1.0 OD2 A:ASP474 2.7 16.7 1.0 CG A:ASP360 2.9 6.2 1.0 CG A:ASP474 3.0 12.7 1.0 CD A:GLU270 3.4 9.2 1.0 C A:CYS471 3.6 7.7 1.0 CG A:GLU270 3.9 8.6 1.0 CA A:LEU472 4.2 8.1 1.0 O A:HOH5103 4.3 14.8 1.0 N A:LEU472 4.3 7.0 1.0 OE2 A:GLU270 4.4 11.6 1.0 CB A:ASP360 4.4 5.6 1.0 CB A:ASP474 4.5 11.6 1.0 CB A:GLU270 4.6 6.7 1.0 O A:GLN268 4.6 10.7 1.0 O A:ASP474 4.6 11.8 1.0 CA A:CYS471 4.6 7.5 1.0 C A:LEU472 4.7 7.5 1.0 CA A:CA903 4.7 40.9 1.0 O A:HOH5241 4.8 30.5 1.0 CB A:CYS471 4.8 7.1 1.0 ND1 A:HIS358 4.9 19.2 1.0 N A:ASP474 4.9 10.9 1.0 O A:HOH5005 4.9 11.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound


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 Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:40.9 occ:1.00 O A:HOH5157 2.5 24.5 1.0 O A:HOH5103 2.6 14.8 1.0 OD2 A:ASP474 2.6 16.7 1.0 O A:HOH5068 2.7 20.6 1.0 OE2 A:GLU270 2.7 11.6 1.0 O A:LEU475 3.2 13.7 1.0 CD A:GLU270 3.4 9.2 1.0 OE1 A:GLU270 3.4 9.7 1.0 CG A:ASP474 3.7 12.7 1.0 C A:LEU475 3.9 14.3 1.0 CA A:PRO476 4.0 15.6 1.0 CB A:ASP474 4.2 11.6 1.0 O A:HOH5082 4.3 20.0 1.0 N A:PRO476 4.3 14.6 1.0 O A:HOH5031 4.5 8.8 1.0 N A:ARG477 4.7 17.8 1.0 CA A:CA902 4.7 7.6 1.0 C A:PRO476 4.7 16.1 1.0 CG A:GLU270 4.7 8.6 1.0 OD1 A:ASP474 4.8 14.1 1.0 O A:HOH5533 4.8 25.8 1.0 N A:LEU475 4.8 12.6 1.0 C A:ASP474 4.9 12.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound


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 Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:7.6 occ:1.00 OD1 A:ASP369 2.3 6.1 1.0 OE1 A:GLU398 2.3 5.2 1.0 O A:THR378 2.3 5.0 0.5 O A:CYS376 2.4 7.6 1.0 O A:HOH5014 2.4 10.7 1.0 O A:THR378 2.4 4.8 0.5 O A:LEU370 2.4 6.1 1.0 N A:LEU370 3.1 7.1 1.0 CD A:GLU398 3.3 8.0 1.0 C A:LEU370 3.3 6.6 1.0 C A:CYS376 3.4 6.4 1.0 CG A:ASP369 3.5 5.9 1.0 C A:THR378 3.5 5.8 0.5 C A:THR378 3.6 5.6 0.5 OE2 A:GLU398 3.6 10.2 1.0 C A:ASP369 3.6 6.7 1.0 CA A:LEU370 3.7 6.7 1.0 O A:HOH5089 3.9 15.7 1.0 CA A:ASP369 4.0 6.3 1.0 CB A:LEU370 4.0 7.5 1.0 N A:THR378 4.1 7.2 0.5 C A:ASP377 4.1 7.0 1.0 N A:THR378 4.1 7.0 0.5 CA A:CYS376 4.2 7.0 1.0 CA A:THR378 4.3 6.3 0.2 O A:ASP377 4.3 8.0 1.0 CB A:ASP369 4.3 6.5 1.0 OD2 A:ASP369 4.4 6.9 1.0 O A:ASP369 4.4 7.4 1.0 CA A:THR378 4.4 2.0 0.2 CA A:THR378 4.4 5.8 0.5 CB A:CYS376 4.4 7.6 1.0 N A:ASP377 4.4 7.3 1.0 CB A:THR378 4.5 2.0 0.2 CG2 A:THR378 4.5 5.5 0.5 N A:LEU379 4.6 5.6 1.0 N A:CYS371 4.6 6.9 1.0 CA A:ASP377 4.6 7.6 1.0 CB A:THR378 4.6 6.4 0.2 CG A:GLU398 4.7 6.7 1.0 CA A:LEU379 4.7 5.5 1.0 O A:HOH5109 4.8 17.2 1.0 CD2 A:LEU379 4.8 8.8 1.0

H.S.Shieh, A.G.Tomasselli, K.J.Mathis, M.E.Schnute, S.S.Woodard, N.Caspers, J.M.Williams, J.R.Kiefer, G.Munie, A.Wittwer, A.M.Malfait, M.D.Tortorella. Structure Analysis Reveals the Flexibility of the Adamts-5 Active Site. Protein Sci. V. 20 735 2011.
ISSN: ISSN 0961-8368
PubMed: 21370305
DOI: 10.1002/PRO.606