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Calcium in PDB 3hyg: 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: 3hyg 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) 26.41 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.818, 44.491, 76.655, 90.00, 90.26, 90.00
R / Rfree (%) 18.1 / 21

Other elements in 3hyg:

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 3hyg). 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: 3hyg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3hyg

Go back to Calcium Binding Sites List in 3hyg
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:7.9
occ:1.00
 O A:CYS471 2.3 9.5 1.0
OE1 A:GLU270 2.4 8.7 1.0
OD1 A:ASP474 2.4 13.7 1.0
O A:HOH5001 2.4 9.4 1.0
OD1 A:ASP360 2.5 8.8 1.0
OD2 A:ASP360 2.5 7.2 1.0
OD1 A:ASP353 2.6 8.5 1.0
OD2 A:ASP353 2.6 12.3 1.0
CG A:ASP360 2.9 7.6 1.0
CG A:ASP353 3.0 9.5 1.0
CD A:GLU270 3.4 8.3 1.0
CG A:ASP474 3.4 12.4 1.0
C A:CYS471 3.6 9.0 1.0
CA A:CA903 3.7 9.2 1.0
OD2 A:ASP474 3.8 13.8 1.0
CG A:GLU270 4.1 7.8 1.0
OE2 A:GLU270 4.3 9.2 1.0
O A:HOH5062 4.3 20.8 1.0
CB A:ASP360 4.4 8.5 1.0
CA A:LEU472 4.4 9.0 1.0
N A:LEU472 4.4 9.1 1.0
CB A:ASP353 4.5 10.7 1.0
CA A:CYS471 4.5 9.8 1.0
CB A:GLU270 4.6 8.1 1.0
O A:GLN268 4.6 10.3 1.0
O A:ASP474 4.7 10.0 1.0
CB A:CYS471 4.7 9.7 1.0
CB A:ASP474 4.8 10.6 1.0
O A:HOH5013 4.8 10.3 1.0
CD2 A:HIS358 4.8 12.1 1.0
N A:ASP474 4.9 9.9 1.0
C A:LEU472 4.9 9.3 1.0

Calcium binding site 2 out of 6 in 3hyg

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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:9.2
occ:1.00
 O A:HOH5018 2.3 11.9 1.0
OD2 A:ASP474 2.3 13.8 1.0
O A:ASP353 2.3 11.6 1.0
O A:HOH5014 2.4 11.7 1.0
OE1 A:GLU270 2.4 8.7 1.0
OD1 A:ASP353 2.4 8.5 1.0
OE2 A:GLU270 2.5 9.2 1.0
CD A:GLU270 2.8 8.3 1.0
CG A:ASP474 3.3 12.4 1.0
CG A:ASP353 3.4 9.5 1.0
C A:ASP353 3.4 12.1 1.0
OD1 A:ASP474 3.6 13.7 1.0
CA A:CA902 3.7 7.9 1.0
CA A:ASP353 4.0 11.7 1.0
CB A:ASP353 4.1 10.7 1.0
O A:LEU475 4.3 11.4 1.0
OD2 A:ASP353 4.3 12.3 1.0
CG A:GLU270 4.3 7.8 1.0
O A:HOH5021 4.3 13.4 1.0
O A:HIS358 4.5 9.5 1.0
O A:HIS355 4.5 13.8 1.0
O A:HOH5124 4.5 22.0 1.0
N A:ASP354 4.6 13.3 1.0
CB A:ASP474 4.6 10.6 1.0
CD2 A:HIS358 4.7 12.1 1.0
O A:HOH5150 4.7 23.6 1.0
O A:HOH5001 4.8 9.4 1.0
CB A:HIS358 4.9 9.9 1.0
CA A:ASP354 5.0 14.6 1.0

Calcium binding site 3 out of 6 in 3hyg

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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:13.2
occ:1.00
 O A:THR378 2.3 12.1 1.0
OD1 A:ASP369 2.3 19.4 1.0
O A:CYS376 2.3 16.8 1.0
OE1 A:GLU398 2.3 11.7 1.0
O A:LEU370 2.4 16.3 1.0
O A:HOH5030 2.4 17.2 1.0
CD A:GLU398 3.3 12.5 1.0
N A:LEU370 3.4 16.7 1.0
C A:CYS376 3.4 17.8 1.0
C A:LEU370 3.4 16.5 1.0
C A:THR378 3.5 12.9 1.0
CG A:ASP369 3.5 19.9 1.0
OE2 A:GLU398 3.6 16.2 1.0
C A:ASP369 3.9 17.7 1.0
CA A:LEU370 3.9 16.6 1.0
O A:HOH5156 3.9 27.4 1.0
N A:THR378 4.0 14.8 1.0
C A:ASP377 4.1 15.4 1.0
CA A:ASP369 4.1 17.6 1.0
CA A:CYS376 4.2 19.0 1.0
CA A:THR378 4.2 14.5 1.0
O A:ASP377 4.3 14.8 1.0
CB A:LEU370 4.4 17.0 1.0
CB A:CYS376 4.4 19.2 1.0
OD2 A:ASP369 4.4 21.5 1.0
N A:ASP377 4.4 16.8 1.0
CB A:ASP369 4.4 18.2 1.0
N A:LEU379 4.5 11.2 1.0
CA A:ASP377 4.6 16.8 1.0
O A:ASP369 4.6 18.1 1.0
N A:CYS371 4.6 17.1 1.0
CD2 A:LEU379 4.6 13.5 1.0
CG A:GLU398 4.7 12.2 1.0
CA A:LEU379 4.7 10.4 1.0
CB A:THR378 4.8 15.8 1.0
O A:HOH5047 4.8 22.5 1.0

Calcium binding site 4 out of 6 in 3hyg

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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:6.9
occ:1.00
 O B:CYS471 2.4 6.8 1.0
OE1 B:GLU270 2.4 8.2 1.0
OD1 B:ASP474 2.5 12.7 1.0
O B:HOH6010 2.5 8.0 1.0
OD1 B:ASP360 2.5 6.8 1.0
OD2 B:ASP360 2.6 7.0 1.0
OD1 B:ASP353 2.6 9.6 1.0
OD2 B:ASP353 2.6 9.8 1.0
CG B:ASP360 2.9 5.9 1.0
CG B:ASP353 3.0 11.0 1.0
CG B:ASP474 3.2 12.0 1.0
OD2 B:ASP474 3.2 16.2 1.0
CD B:GLU270 3.4 9.7 1.0
C B:CYS471 3.6 6.0 1.0
CA B:CA903 3.8 10.3 1.0
CG B:GLU270 4.1 7.3 1.0
OE2 B:GLU270 4.4 11.8 1.0
CB B:ASP360 4.4 6.5 1.0
CA B:LEU472 4.4 6.9 1.0
N B:LEU472 4.4 6.0 1.0
O B:HOH6021 4.5 12.8 1.0
CB B:ASP353 4.5 12.1 1.0
O B:ASP474 4.6 10.4 1.0
CA B:CYS471 4.6 6.0 1.0
O B:GLN268 4.6 7.5 1.0
CB B:GLU270 4.6 6.8 1.0
CB B:ASP474 4.7 10.3 1.0
CB B:CYS471 4.8 6.6 1.0
O B:HOH6011 4.8 8.1 1.0
CD2 B:HIS358 4.9 15.5 1.0
C B:LEU472 4.9 7.3 1.0
N B:ASP474 5.0 8.1 1.0

Calcium binding site 5 out of 6 in 3hyg

Go back to Calcium Binding Sites List in 3hyg
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:10.3
occ:1.00
 OD2 B:ASP474 2.3 16.2 1.0
O B:HOH6119 2.3 20.2 1.0
O B:ASP353 2.4 14.0 1.0
O B:HOH6037 2.4 13.2 1.0
OD1 B:ASP353 2.4 9.6 1.0
OE1 B:GLU270 2.4 8.2 1.0
OE2 B:GLU270 2.6 11.8 1.0
CD B:GLU270 2.9 9.7 1.0
CG B:ASP353 3.5 11.0 1.0
C B:ASP353 3.5 14.2 1.0
CG B:ASP474 3.5 12.0 1.0
CA B:CA902 3.8 6.9 1.0
CA B:ASP353 4.1 13.2 1.0
OD1 B:ASP474 4.1 12.7 1.0
CB B:ASP353 4.2 12.1 1.0
CG B:GLU270 4.4 7.3 1.0
OD2 B:ASP353 4.4 9.8 1.0
O B:HOH6230 4.5 29.1 1.0
NH2 B:ARG477 4.6 22.2 1.0
N B:ASP354 4.6 14.4 1.0
CB B:ASP474 4.6 10.3 1.0
O B:HIS355 4.7 14.3 1.0
O B:HOH6252 4.8 40.7 1.0
O B:HIS358 4.8 10.9 1.0
O B:HOH6010 4.8 8.0 1.0
CD2 B:HIS358 4.9 15.5 1.0
O B:HOH6057 4.9 16.3 1.0
CA B:ASP354 4.9 16.3 1.0

Calcium binding site 6 out of 6 in 3hyg

Go back to Calcium Binding Sites List in 3hyg
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:6.7
occ:1.00
 OD1 B:ASP369 2.3 8.5 1.0
O B:CYS376 2.3 7.8 1.0
OE2 B:GLU398 2.3 7.8 1.0
O B:THR378 2.3 6.3 1.0
O B:LEU370 2.4 6.9 1.0
O B:HOH6009 2.4 8.9 1.0
N B:LEU370 3.2 7.3 1.0
C B:LEU370 3.3 7.7 1.0
CD B:GLU398 3.4 7.8 1.0
C B:CYS376 3.4 8.4 1.0
C B:THR378 3.5 7.0 1.0
CG B:ASP369 3.5 8.8 1.0
OE1 B:GLU398 3.7 9.1 1.0
C B:ASP369 3.7 8.3 1.0
CA B:LEU370 3.7 7.8 1.0
CA B:ASP369 4.1 7.9 1.0
C B:ASP377 4.1 8.4 1.0
O B:HOH6066 4.1 17.0 1.0
N B:THR378 4.1 7.8 1.0
CA B:CYS376 4.1 9.1 1.0
CB B:LEU370 4.2 8.0 1.0
O B:ASP377 4.2 8.1 1.0
CB B:CYS376 4.3 9.1 1.0
CA B:THR378 4.4 7.7 1.0
OD2 B:ASP369 4.4 10.8 1.0
N B:ASP377 4.4 8.3 1.0
CB B:ASP369 4.4 8.3 1.0
O B:ASP369 4.5 8.5 1.0
N B:LEU379 4.5 6.8 1.0
CA B:ASP377 4.6 8.9 1.0
N B:CYS371 4.6 7.4 1.0
O B:HOH6081 4.7 16.3 1.0
CG B:GLU398 4.7 7.2 1.0
CA B:LEU379 4.7 6.6 1.0
CD2 B:LEU379 4.8 9.4 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 11:17:53 2024

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