Atomistry » Calcium » PDB 3hjb-3hz3 » 3hyg
Atomistry »
  Calcium »
    PDB 3hjb-3hz3 »
      3hyg »

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

Go back to Calcium Binding Sites List in 3hyg
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

Go back to Calcium Binding Sites List in 3hyg
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

Go back to Calcium Binding Sites List in 3hyg
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy