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Calcium in PDB 3hy9: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound, PDB code: 3hy9 was solved by H.-S.Shieh, J.M.Williams, N.Caspers, K.J.Mathis, M.D.Tortorella, A.Tomasselli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.02 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.692, 44.444, 76.458, 90.00, 90.19, 90.00
R / Rfree (%) 15.9 / 23.8

Other elements in 3hy9:

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) 2 atoms

Calcium Binding Sites:

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 3hy9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 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: 3hy9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3hy9

Go back to Calcium Binding Sites List in 3hy9
Calcium binding site 1 out of 6 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:12.8
occ:1.00
 O A:CYS471 2.3 14.2 1.0
OE1 A:GLU270 2.4 12.8 1.0
OD1 A:ASP474 2.4 16.5 1.0
O A:HOH5001 2.4 7.7 1.0
OD1 A:ASP360 2.4 12.3 1.0
OD2 A:ASP360 2.5 10.1 1.0
OD2 A:ASP353 2.6 19.3 1.0
OD1 A:ASP353 2.7 19.3 1.0
CG A:ASP360 2.8 13.1 1.0
CG A:ASP353 3.0 18.5 1.0
CG A:ASP474 3.4 16.1 1.0
CD A:GLU270 3.4 13.2 1.0
C A:CYS471 3.6 14.4 1.0
OD2 A:ASP474 3.6 18.3 1.0
CA A:CA903 3.8 13.7 1.0
CG A:GLU270 4.1 13.2 1.0
OE2 A:GLU270 4.3 13.7 1.0
O A:HOH5117 4.3 26.4 1.0
CA A:LEU472 4.3 13.7 1.0
CB A:ASP360 4.3 12.9 1.0
N A:LEU472 4.4 13.9 1.0
CB A:ASP353 4.5 18.9 1.0
CA A:CYS471 4.5 15.1 1.0
CB A:GLU270 4.6 13.7 1.0
O A:GLN268 4.6 16.9 1.0
O A:ASP474 4.7 16.9 1.0
O A:HOH5010 4.7 10.8 1.0
CB A:ASP474 4.7 16.6 1.0
CB A:CYS471 4.8 15.0 1.0
CD2 A:HIS358 4.8 17.8 1.0
C A:LEU472 4.9 14.0 1.0
N A:ASP474 4.9 16.1 1.0

Calcium binding site 2 out of 6 in 3hy9

Go back to Calcium Binding Sites List in 3hy9
Calcium binding site 2 out of 6 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:13.7
occ:1.00
 OD2 A:ASP474 2.2 18.3 1.0
O A:HOH5033 2.3 12.5 1.0
O A:ASP353 2.3 19.2 1.0
OE1 A:GLU270 2.4 12.8 1.0
O A:HOH5026 2.4 14.5 1.0
OE2 A:GLU270 2.5 13.7 1.0
OD1 A:ASP353 2.5 19.3 1.0
CD A:GLU270 2.8 13.2 1.0
CG A:ASP474 3.3 16.1 1.0
CG A:ASP353 3.4 18.5 1.0
C A:ASP353 3.4 19.8 1.0
OD1 A:ASP474 3.8 16.5 1.0
CA A:CA902 3.8 12.8 1.0
CA A:ASP353 4.0 19.6 1.0
CB A:ASP353 4.1 18.9 1.0
O A:HOH5015 4.2 23.0 1.0
OD2 A:ASP353 4.2 19.3 1.0
CG A:GLU270 4.3 13.2 1.0
O A:LEU475 4.4 18.6 1.0
O A:HIS355 4.4 22.5 1.0
O A:HIS358 4.5 16.2 1.0
N A:ASP354 4.6 20.5 1.0
CB A:ASP474 4.6 16.6 1.0
CD2 A:HIS358 4.7 17.8 1.0
O A:HOH5150 4.7 30.5 1.0
O A:HOH5173 4.8 50.9 1.0
O A:HOH5001 4.8 7.7 1.0
CB A:HIS358 4.8 17.3 1.0
CA A:ASP354 5.0 21.3 1.0

Calcium binding site 3 out of 6 in 3hy9

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Calcium binding site 3 out of 6 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:18.2
occ:1.00
 O A:HOH5029 2.2 21.9 1.0
O A:CYS376 2.3 23.9 1.0
O A:LEU370 2.3 24.3 1.0
OE1 A:GLU398 2.4 14.9 1.0
O A:THR378 2.4 18.0 1.0
OD1 A:ASP369 2.4 25.6 1.0
N A:LEU370 3.3 24.1 1.0
C A:LEU370 3.4 24.2 1.0
CD A:GLU398 3.4 15.1 1.0
C A:CYS376 3.4 24.6 1.0
C A:THR378 3.5 17.9 1.0
CG A:ASP369 3.6 26.5 1.0
OE2 A:GLU398 3.7 17.1 1.0
C A:ASP369 3.8 24.5 1.0
CA A:LEU370 3.8 23.9 1.0
N A:THR378 4.0 20.1 1.0
C A:ASP377 4.1 21.2 1.0
CA A:ASP369 4.1 24.5 1.0
CA A:CYS376 4.1 25.7 1.0
CA A:THR378 4.2 19.3 1.0
O A:ASP377 4.4 20.4 1.0
CB A:LEU370 4.4 23.9 1.0
N A:ASP377 4.4 23.2 1.0
CB A:CYS376 4.4 25.9 1.0
OD2 A:ASP369 4.5 28.5 1.0
CB A:ASP369 4.5 24.8 1.0
O A:ASP369 4.5 24.5 1.0
CB A:THR378 4.5 19.5 1.0
CA A:ASP377 4.6 22.2 1.0
N A:CYS371 4.6 24.2 1.0
N A:LEU379 4.6 16.7 1.0
O A:HOH5210 4.6 45.8 1.0
CD2 A:LEU379 4.7 17.6 1.0
CG A:GLU398 4.7 15.3 1.0
CA A:LEU379 4.8 15.9 1.0
O A:HOH5049 4.9 28.5 1.0

Calcium binding site 4 out of 6 in 3hy9

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Calcium binding site 4 out of 6 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 4 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
B:Ca902

b:14.0
occ:1.00
 O B:CYS471 2.4 12.5 1.0
O B:HOH6012 2.4 10.5 1.0
OD1 B:ASP360 2.5 8.1 1.0
OE1 B:GLU270 2.5 12.2 1.0
OD2 B:ASP360 2.6 8.7 1.0
OD1 B:ASP474 2.6 16.2 1.0
OD1 B:ASP353 2.6 16.5 1.0
OD2 B:ASP353 2.7 17.3 1.0
CG B:ASP360 2.8 10.3 1.0
CG B:ASP353 3.0 18.7 1.0
OD2 B:ASP474 3.3 18.4 1.0
CG B:ASP474 3.3 16.1 1.0
CD B:GLU270 3.5 15.3 1.0
C B:CYS471 3.6 12.3 1.0
CA B:CA903 3.8 15.5 1.0
CG B:GLU270 4.2 14.6 1.0
OE2 B:GLU270 4.3 15.7 1.0
CB B:ASP360 4.4 10.5 1.0
CA B:LEU472 4.4 11.7 1.0
N B:LEU472 4.5 11.5 1.0
CB B:ASP353 4.5 19.8 1.0
CA B:CYS471 4.6 11.6 1.0
O B:GLN268 4.6 12.3 1.0
O B:HOH6014 4.6 14.8 1.0
O B:ASP474 4.6 17.1 1.0
O B:HOH6025 4.7 9.3 1.0
CB B:GLU270 4.8 13.2 1.0
CB B:CYS471 4.8 11.9 1.0
CB B:ASP474 4.8 16.4 1.0
CD2 B:HIS358 4.8 16.9 1.0
O B:HOH6083 4.9 21.2 1.0
C B:LEU472 4.9 11.8 1.0

Calcium binding site 5 out of 6 in 3hy9

Go back to Calcium Binding Sites List in 3hy9
Calcium binding site 5 out of 6 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 5 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
B:Ca903

b:15.5
occ:1.00
 O B:HOH6180 2.3 21.6 1.0
O B:ASP353 2.3 21.0 1.0
OD2 B:ASP474 2.3 18.4 1.0
O B:HOH6097 2.4 15.7 1.0
OE2 B:GLU270 2.5 15.7 1.0
OD1 B:ASP353 2.5 16.5 1.0
OE1 B:GLU270 2.7 12.2 1.0
CD B:GLU270 3.0 15.3 1.0
C B:ASP353 3.4 21.4 1.0
CG B:ASP353 3.5 18.7 1.0
CG B:ASP474 3.5 16.1 1.0
CA B:CA902 3.8 14.0 1.0
CA B:ASP353 4.1 20.3 1.0
CB B:ASP353 4.2 19.8 1.0
OD1 B:ASP474 4.2 16.2 1.0
OD2 B:ASP353 4.4 17.3 1.0
CG B:GLU270 4.4 14.6 1.0
NH2 B:ARG477 4.5 30.1 1.0
N B:ASP354 4.5 22.0 1.0
CB B:ASP474 4.6 16.4 1.0
O B:HIS355 4.6 23.6 1.0
O B:HIS358 4.7 16.2 1.0
CD2 B:HIS358 4.8 16.9 1.0
O B:HOH6012 4.8 10.5 1.0
CA B:ASP354 4.8 23.5 1.0

Calcium binding site 6 out of 6 in 3hy9

Go back to Calcium Binding Sites List in 3hy9
Calcium binding site 6 out of 6 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 6 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
B:Ca904

b:11.7
occ:1.00
 O B:CYS376 2.2 13.9 1.0
OD1 B:ASP369 2.2 11.7 1.0
O B:THR378 2.3 12.4 1.0
O B:LEU370 2.4 12.4 1.0
OE2 B:GLU398 2.4 10.5 1.0
O B:HOH6003 2.4 11.6 1.0
N B:LEU370 3.1 12.2 1.0
C B:LEU370 3.3 12.6 1.0
C B:CYS376 3.3 14.5 1.0
CD B:GLU398 3.4 12.2 1.0
CG B:ASP369 3.5 13.4 1.0
C B:THR378 3.5 12.7 1.0
OE1 B:GLU398 3.6 10.6 1.0
CA B:LEU370 3.7 12.6 1.0
C B:ASP369 3.7 12.4 1.0
N B:THR378 4.0 14.2 1.0
O B:HOH6068 4.0 19.5 1.0
C B:ASP377 4.0 14.1 1.0
CA B:ASP369 4.0 12.5 1.0
CA B:CYS376 4.1 14.8 1.0
CB B:LEU370 4.2 12.7 1.0
CA B:THR378 4.3 13.9 1.0
CB B:CYS376 4.3 15.1 1.0
O B:ASP377 4.3 13.7 1.0
N B:ASP377 4.3 14.3 1.0
OD2 B:ASP369 4.4 14.6 1.0
CB B:ASP369 4.4 12.8 1.0
O B:ASP369 4.5 11.6 1.0
CA B:ASP377 4.5 14.4 1.0
N B:LEU379 4.6 11.4 1.0
N B:CYS371 4.6 12.0 1.0
O B:HOH6107 4.7 22.4 1.0
CB B:THR378 4.7 15.1 1.0
CG B:GLU398 4.7 13.1 1.0
CA B:LEU379 4.8 11.5 1.0
CD2 B:LEU379 4.9 11.7 1.0

Reference:

M.D.Tortorella, A.G.Tomasselli, K.J.Mathis, M.E.Schnute, S.S.Woodard, G.Munie, J.M.Williams, N.Caspers, A.J.Wittwer, A.M.Malfait, H.S.Shieh. Structural and Inhibition Analysis Reveals the Mechanism of Selectivity of A Series of Aggrecanase Inhibitors J.Biol.Chem. V. 284 24185 2009.
ISSN: ISSN 0021-9258
PubMed: 19586907
DOI: 10.1074/JBC.M109.029116
Page generated: Sat Jul 13 11:17:30 2024

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