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Calcium in PDB 3hy7: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat, PDB code: 3hy7 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) 26.31 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.606, 44.464, 76.349, 90.00, 89.81, 90.00
R / Rfree (%) 17.3 / 22.4

Other elements in 3hy7:

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat 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 Marimastat (pdb code 3hy7). 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 Marimastat, PDB code: 3hy7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3hy7

Go back to Calcium Binding Sites List in 3hy7
Calcium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat


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 Marimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:11.5
occ:1.00
 O A:CYS471 2.3 13.7 1.0
OD1 A:ASP474 2.4 17.6 1.0
OE1 A:GLU270 2.4 13.9 1.0
O A:HOH5001 2.4 9.9 1.0
OD1 A:ASP360 2.5 10.9 1.0
OD2 A:ASP360 2.6 10.3 1.0
OD1 A:ASP353 2.7 13.7 1.0
OD2 A:ASP353 2.7 17.1 1.0
CG A:ASP360 2.9 11.7 1.0
CG A:ASP353 3.0 16.5 1.0
CD A:GLU270 3.4 12.5 1.0
CG A:ASP474 3.4 17.5 1.0
C A:CYS471 3.6 13.3 1.0
CA A:CA903 3.7 13.3 1.0
OD2 A:ASP474 3.8 20.2 1.0
CG A:GLU270 4.2 12.2 1.0
OE2 A:GLU270 4.3 14.8 1.0
CB A:ASP360 4.4 11.6 1.0
CA A:LEU472 4.4 12.2 1.0
N A:LEU472 4.5 12.1 1.0
O A:HOH5072 4.5 26.8 1.0
CB A:ASP353 4.5 17.2 1.0
CA A:CYS471 4.5 13.2 1.0
O A:GLN268 4.6 13.3 1.0
CB A:GLU270 4.6 12.6 1.0
O A:ASP474 4.7 14.9 1.0
CD2 A:HIS358 4.7 13.1 1.0
CB A:CYS471 4.7 13.7 1.0
O A:HOH5011 4.8 12.7 1.0
CB A:ASP474 4.8 14.7 1.0
C A:LEU472 4.8 12.4 1.0
N A:ASP474 4.9 13.8 1.0
NE2 A:HIS358 5.0 15.0 1.0

Calcium binding site 2 out of 6 in 3hy7

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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 Marimastat


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 Marimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:13.3
occ:1.00
 O A:ASP353 2.3 17.4 1.0
OD2 A:ASP474 2.3 20.2 1.0
O A:HOH5025 2.3 16.2 1.0
O A:HOH5013 2.4 14.6 1.0
OD1 A:ASP353 2.5 13.7 1.0
OE1 A:GLU270 2.5 13.9 1.0
OE2 A:GLU270 2.5 14.8 1.0
CD A:GLU270 2.9 12.5 1.0
CG A:ASP474 3.3 17.5 1.0
C A:ASP353 3.4 17.8 1.0
CG A:ASP353 3.5 16.5 1.0
OD1 A:ASP474 3.6 17.6 1.0
CA A:CA902 3.7 11.5 1.0
CA A:ASP353 4.0 17.6 1.0
CB A:ASP353 4.1 17.2 1.0
O A:HOH5052 4.3 20.1 1.0
O A:LEU475 4.4 18.6 1.0
CG A:GLU270 4.4 12.2 1.0
OD2 A:ASP353 4.4 17.1 1.0
O A:HOH5055 4.4 26.7 1.0
CD2 A:HIS358 4.4 13.1 1.0
N A:ASP354 4.6 18.0 1.0
O A:HIS355 4.6 19.6 1.0
O A:HOH5095 4.6 35.4 1.0
CB A:ASP474 4.7 14.7 1.0
O A:HIS358 4.7 14.0 1.0
O A:HOH5001 4.8 9.9 1.0
CB A:HIS358 4.9 14.3 1.0
CA A:ASP354 4.9 18.7 1.0
CG A:HIS358 5.0 14.0 1.0

Calcium binding site 3 out of 6 in 3hy7

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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 Marimastat


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 Marimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:18.4
occ:1.00
 O A:HOH5020 2.3 19.8 1.0
OE1 A:GLU398 2.3 15.1 1.0
O A:THR378 2.3 17.6 1.0
OD1 A:ASP369 2.3 21.3 1.0
O A:CYS376 2.4 21.3 1.0
O A:LEU370 2.4 20.3 1.0
CD A:GLU398 3.3 16.0 1.0
N A:LEU370 3.3 20.7 1.0
C A:LEU370 3.4 20.8 1.0
C A:CYS376 3.5 21.8 1.0
C A:THR378 3.5 17.5 1.0
OE2 A:GLU398 3.5 18.0 1.0
CG A:ASP369 3.6 22.6 1.0
CA A:LEU370 3.8 20.9 1.0
C A:ASP369 3.9 20.9 1.0
N A:THR378 3.9 19.1 1.0
C A:ASP377 4.0 20.0 1.0
CA A:ASP369 4.1 20.4 1.0
CA A:THR378 4.2 18.7 1.0
CB A:LEU370 4.3 21.4 1.0
CA A:CYS376 4.3 22.2 1.0
N A:ASP377 4.4 21.4 1.0
O A:ASP377 4.4 19.9 1.0
OD2 A:ASP369 4.4 24.5 1.0
CA A:ASP377 4.4 21.0 1.0
CB A:ASP369 4.5 20.7 1.0
O A:HOH5193 4.5 33.0 1.0
N A:LEU379 4.5 16.9 1.0
N A:CYS371 4.6 20.9 1.0
O A:ASP369 4.6 21.7 1.0
CB A:THR378 4.6 18.8 1.0
CG A:GLU398 4.6 14.2 1.0
CB A:CYS376 4.7 22.2 1.0
CA A:LEU379 4.8 15.8 1.0
O A:HOH5069 4.8 31.8 1.0
CD2 A:LEU379 4.8 19.1 1.0
CB A:GLU398 5.0 15.5 1.0

Calcium binding site 4 out of 6 in 3hy7

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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 Marimastat


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 Marimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:11.7
occ:1.00
 O B:CYS471 2.3 11.0 1.0
O B:HOH5006 2.3 11.4 1.0
OD1 B:ASP474 2.4 16.6 1.0
OE1 B:GLU270 2.5 12.2 1.0
OD1 B:ASP360 2.5 12.3 1.0
OD2 B:ASP353 2.6 14.3 1.0
OD2 B:ASP360 2.6 10.7 1.0
OD1 B:ASP353 2.7 14.6 1.0
CG B:ASP360 2.9 11.4 1.0
CG B:ASP353 3.0 17.7 1.0
CG B:ASP474 3.2 16.9 1.0
OD2 B:ASP474 3.3 20.2 1.0
CD B:GLU270 3.5 13.8 1.0
C B:CYS471 3.6 11.9 1.0
CA B:CA903 3.8 14.5 1.0
CG B:GLU270 4.2 12.9 1.0
CB B:ASP360 4.4 11.4 1.0
CA B:LEU472 4.4 12.0 1.0
N B:LEU472 4.4 11.7 1.0
OE2 B:GLU270 4.4 15.3 1.0
O B:HOH5043 4.5 21.6 1.0
CB B:ASP353 4.5 18.1 1.0
CA B:CYS471 4.5 11.6 1.0
O B:ASP474 4.6 15.3 1.0
O B:HOH5009 4.6 12.3 1.0
O B:GLN268 4.7 12.7 1.0
CB B:ASP474 4.7 15.4 1.0
CB B:CYS471 4.7 11.3 1.0
CB B:GLU270 4.7 12.9 1.0
O B:HOH5062 4.9 20.7 1.0
CD2 B:HIS358 5.0 13.6 1.0
N B:ASP474 5.0 14.2 1.0
C B:LEU472 5.0 12.7 1.0

Calcium binding site 5 out of 6 in 3hy7

Go back to Calcium Binding Sites List in 3hy7
Calcium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat


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 Marimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:14.5
occ:1.00
 O B:ASP353 2.3 19.1 1.0
OD2 B:ASP474 2.3 20.2 1.0
O B:HOH5071 2.4 19.7 1.0
O B:HOH5024 2.4 14.0 1.0
OD1 B:ASP353 2.4 14.6 1.0
OE1 B:GLU270 2.5 12.2 1.0
OE2 B:GLU270 2.7 15.3 1.0
CD B:GLU270 2.9 13.8 1.0
C B:ASP353 3.4 19.3 1.0
CG B:ASP353 3.5 17.7 1.0
CG B:ASP474 3.5 16.9 1.0
CA B:CA902 3.8 11.7 1.0
OD1 B:ASP474 4.0 16.6 1.0
CA B:ASP353 4.1 18.7 1.0
CB B:ASP353 4.2 18.1 1.0
OD2 B:ASP353 4.4 14.3 1.0
CG B:GLU270 4.4 12.9 1.0
NH2 B:ARG477 4.5 22.2 1.0
N B:ASP354 4.5 19.5 1.0
O B:HIS358 4.5 13.5 1.0
CB B:ASP474 4.6 15.4 1.0
O B:HIS355 4.7 20.7 1.0
CA B:ASP354 4.7 20.6 1.0
O B:HOH5006 4.8 11.4 1.0
CD2 B:HIS358 4.9 13.6 1.0
O B:HOH5040 4.9 23.4 1.0

Calcium binding site 6 out of 6 in 3hy7

Go back to Calcium Binding Sites List in 3hy7
Calcium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat


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 Marimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:14.8
occ:1.00
 O B:THR378 2.3 14.7 1.0
OE2 B:GLU398 2.3 13.6 1.0
OD1 B:ASP369 2.3 15.5 1.0
O B:HOH5019 2.4 14.1 1.0
O B:CYS376 2.4 17.7 1.0
O B:LEU370 2.4 14.2 1.0
N B:LEU370 3.2 13.7 1.0
CD B:GLU398 3.3 13.8 1.0
C B:LEU370 3.4 13.7 1.0
C B:CYS376 3.5 18.0 1.0
C B:THR378 3.5 15.3 1.0
CG B:ASP369 3.6 15.9 1.0
OE1 B:GLU398 3.7 14.1 1.0
CA B:LEU370 3.7 14.0 1.0
C B:ASP369 3.8 14.3 1.0
N B:THR378 4.0 16.6 1.0
O B:HOH5145 4.0 27.4 1.0
C B:ASP377 4.1 17.0 1.0
CA B:ASP369 4.1 14.2 1.0
CB B:LEU370 4.1 13.9 1.0
CA B:THR378 4.2 16.9 1.0
CA B:CYS376 4.3 18.3 1.0
O B:ASP377 4.4 15.9 1.0
N B:ASP377 4.4 17.9 1.0
OD2 B:ASP369 4.4 18.8 1.0
CB B:ASP369 4.5 14.8 1.0
O B:ASP369 4.5 12.9 1.0
CB B:CYS376 4.6 18.5 1.0
CA B:ASP377 4.6 17.9 1.0
N B:LEU379 4.6 14.1 1.0
CB B:THR378 4.6 16.9 1.0
N B:CYS371 4.6 14.1 1.0
CG B:GLU398 4.7 12.2 1.0
CA B:LEU379 4.8 13.8 1.0
O B:HOH5169 4.9 45.4 1.0
CD2 B:LEU379 4.9 16.9 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 Dec 12 04:14:48 2020

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