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Calcium in PDB 3b8z: High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)

Protein crystallography data

The structure of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2), PDB code: 3b8z was solved by H.-S.Shieh, J.M.Williams, 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) 26.53 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.057, 44.487, 76.380, 90.00, 90.07, 90.00
R / Rfree (%) 18.5 / 21.4

Other elements in 3b8z:

The structure of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) (pdb code 3b8z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2), PDB code: 3b8z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3b8z

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Calcium binding site 1 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:9.0
occ:1.00
 O A:HOH905 2.4 11.1 1.0
O A:CYS471 2.4 10.0 1.0
OE1 A:GLU270 2.4 9.7 1.0
OD1 A:ASP474 2.4 15.5 1.0
OD1 A:ASP360 2.5 9.7 1.0
OD2 A:ASP360 2.5 8.5 1.0
OD2 A:ASP353 2.6 12.8 1.0
OD1 A:ASP353 2.6 11.5 1.0
CG A:ASP360 2.8 8.8 1.0
CG A:ASP353 3.0 11.6 1.0
CG A:ASP474 3.4 14.3 1.0
CD A:GLU270 3.4 11.5 1.0
C A:CYS471 3.6 10.1 1.0
CA A:CA903 3.8 10.9 1.0
OD2 A:ASP474 3.8 15.8 1.0
CG A:GLU270 4.2 10.3 1.0
OE2 A:GLU270 4.3 11.5 1.0
O A:HOH961 4.3 19.7 1.0
CB A:ASP360 4.4 9.2 1.0
CA A:LEU472 4.4 10.5 1.0
N A:LEU472 4.5 9.8 1.0
CB A:ASP353 4.5 13.8 1.0
CA A:CYS471 4.6 10.6 1.0
O A:GLN268 4.6 10.8 1.0
CB A:GLU270 4.6 9.6 1.0
O A:ASP474 4.7 12.0 1.0
O A:HOH913 4.7 12.0 1.0
CB A:CYS471 4.8 11.3 1.0
CB A:ASP474 4.8 12.3 1.0
CD2 A:HIS358 4.8 14.2 1.0
N A:ASP474 4.9 11.6 1.0
C A:LEU472 4.9 11.0 1.0

Calcium binding site 2 out of 6 in 3b8z

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Calcium binding site 2 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:10.9
occ:1.00
 O A:HOH916 2.3 13.7 1.0
OD2 A:ASP474 2.3 15.8 1.0
O A:ASP353 2.3 13.7 1.0
O A:HOH919 2.4 13.4 1.0
OE1 A:GLU270 2.4 9.7 1.0
OD1 A:ASP353 2.5 11.5 1.0
OE2 A:GLU270 2.5 11.5 1.0
CD A:GLU270 2.8 11.5 1.0
CG A:ASP474 3.3 14.3 1.0
C A:ASP353 3.4 14.8 1.0
CG A:ASP353 3.4 11.6 1.0
OD1 A:ASP474 3.6 15.5 1.0
CA A:CA902 3.8 9.0 1.0
CA A:ASP353 4.0 14.0 1.0
CB A:ASP353 4.1 13.8 1.0
O A:HOH917 4.3 16.4 1.0
OD2 A:ASP353 4.3 12.8 1.0
CG A:GLU270 4.3 10.3 1.0
O A:LEU475 4.4 14.2 1.0
O A:HIS355 4.5 16.3 1.0
O A:HIS358 4.5 11.8 1.0
O A:HOH959 4.5 23.2 1.0
N A:ASP354 4.6 15.4 1.0
O A:HOH1056 4.6 23.7 1.0
CD2 A:HIS358 4.7 14.2 1.0
CB A:ASP474 4.7 12.3 1.0
O A:HOH905 4.8 11.1 1.0
CB A:HIS358 4.9 12.3 1.0
CA A:ASP354 5.0 16.3 1.0

Calcium binding site 3 out of 6 in 3b8z

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Calcium binding site 3 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:13.8
occ:1.00
 OD1 A:ASP369 2.3 19.3 1.0
O A:CYS376 2.3 17.5 1.0
OE1 A:GLU398 2.3 14.7 1.0
O A:LEU370 2.3 16.3 1.0
O A:THR378 2.4 13.6 1.0
O A:HOH925 2.4 20.4 1.0
CD A:GLU398 3.3 13.8 1.0
N A:LEU370 3.3 17.1 1.0
C A:LEU370 3.4 17.1 1.0
C A:CYS376 3.4 18.2 1.0
CG A:ASP369 3.5 19.8 1.0
C A:THR378 3.6 13.9 1.0
OE2 A:GLU398 3.6 17.3 1.0
C A:ASP369 3.8 17.5 1.0
CA A:LEU370 3.8 17.0 1.0
N A:THR378 4.0 14.8 1.0
C A:ASP377 4.1 16.2 1.0
CA A:ASP369 4.1 17.5 1.0
O A:HOH1088 4.1 32.6 1.0
CA A:CYS376 4.2 19.1 1.0
CA A:THR378 4.2 13.9 1.0
CB A:LEU370 4.3 17.4 1.0
OD2 A:ASP369 4.3 22.0 1.0
O A:ASP377 4.3 16.6 1.0
N A:ASP377 4.4 17.5 1.0
CB A:ASP369 4.4 17.8 1.0
CB A:CYS376 4.5 19.1 1.0
CA A:ASP377 4.5 17.2 1.0
O A:ASP369 4.5 18.4 1.0
N A:CYS371 4.6 17.4 1.0
CB A:THR378 4.6 13.9 1.0
N A:LEU379 4.7 13.7 1.0
CG A:GLU398 4.7 13.4 1.0
O A:HOH1001 4.7 26.1 1.0
CD2 A:LEU379 4.8 16.0 1.0
CA A:LEU379 5.0 13.8 1.0

Calcium binding site 4 out of 6 in 3b8z

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Calcium binding site 4 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:10.9
occ:1.00
 O B:CYS471 2.3 10.7 1.0
OE1 B:GLU270 2.5 13.9 1.0
OD1 B:ASP474 2.5 16.8 1.0
OD1 B:ASP360 2.5 10.3 1.0
O B:HOH913 2.5 12.3 1.0
OD2 B:ASP360 2.6 10.4 1.0
OD1 B:ASP353 2.6 15.2 1.0
OD2 B:ASP353 2.6 13.5 1.0
CG B:ASP360 2.9 9.4 1.0
CG B:ASP353 3.0 17.3 1.0
CG B:ASP474 3.2 17.9 1.0
OD2 B:ASP474 3.2 21.4 1.0
CD B:GLU270 3.5 14.6 1.0
C B:CYS471 3.6 9.8 1.0
CA B:CA903 3.8 15.2 1.0
CG B:GLU270 4.2 13.1 1.0
CB B:ASP360 4.4 9.7 1.0
OE2 B:GLU270 4.4 16.4 1.0
O B:HOH938 4.4 18.4 1.0
CA B:LEU472 4.4 9.8 1.0
N B:LEU472 4.4 9.2 1.0
CB B:ASP353 4.5 18.6 1.0
CA B:CYS471 4.6 9.6 1.0
O B:ASP474 4.6 14.7 1.0
O B:GLN268 4.6 11.8 1.0
CB B:ASP474 4.7 14.6 1.0
CB B:GLU270 4.7 11.1 1.0
CB B:CYS471 4.8 9.4 1.0
CD2 B:HIS358 4.8 17.9 1.0
O B:HOH928 4.8 11.4 1.0
C B:LEU472 5.0 10.4 1.0
N B:ASP474 5.0 13.4 1.0

Calcium binding site 5 out of 6 in 3b8z

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Calcium binding site 5 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:15.2
occ:1.00
 OD2 B:ASP474 2.3 21.4 1.0
O B:ASP353 2.4 19.3 1.0
O B:HOH971 2.4 29.8 1.0
OE1 B:GLU270 2.4 13.9 1.0
OD1 B:ASP353 2.4 15.2 1.0
O B:HOH927 2.5 18.2 1.0
OE2 B:GLU270 2.6 16.4 1.0
CD B:GLU270 2.9 14.6 1.0
CG B:ASP353 3.5 17.3 1.0
CG B:ASP474 3.5 17.9 1.0
C B:ASP353 3.5 20.1 1.0
CA B:CA902 3.8 10.9 1.0
CA B:ASP353 4.1 19.5 1.0
OD1 B:ASP474 4.1 16.8 1.0
CB B:ASP353 4.2 18.6 1.0
CG B:GLU270 4.4 13.1 1.0
OD2 B:ASP353 4.4 13.5 1.0
NH2 B:ARG477 4.5 27.1 1.0
CB B:ASP474 4.6 14.6 1.0
N B:ASP354 4.6 21.0 1.0
CD2 B:HIS358 4.7 17.9 1.0
O B:HIS355 4.7 22.0 1.0
O B:HIS358 4.7 15.5 1.0
O B:HOH913 4.8 12.3 1.0
O B:HOH935 4.9 21.7 1.0
CA B:ASP354 5.0 22.5 1.0

Calcium binding site 6 out of 6 in 3b8z

Go back to Calcium Binding Sites List in 3b8z
Calcium binding site 6 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:10.1
occ:1.00
 OD1 B:ASP369 2.3 12.8 1.0
O B:CYS376 2.3 12.2 1.0
O B:THR378 2.4 10.3 1.0
OE2 B:GLU398 2.4 10.7 1.0
O B:LEU370 2.4 11.1 1.0
O B:HOH924 2.4 14.2 1.0
N B:LEU370 3.2 11.6 1.0
C B:LEU370 3.4 11.4 1.0
CD B:GLU398 3.4 11.3 1.0
C B:CYS376 3.4 12.9 1.0
CG B:ASP369 3.5 13.2 1.0
C B:THR378 3.5 10.3 1.0
OE1 B:GLU398 3.7 14.4 1.0
C B:ASP369 3.7 12.2 1.0
CA B:LEU370 3.7 11.9 1.0
O B:HOH974 3.9 25.0 1.0
N B:THR378 4.0 11.5 1.0
C B:ASP377 4.1 12.5 1.0
CA B:ASP369 4.1 11.9 1.0
CB B:LEU370 4.2 12.5 1.0
CA B:CYS376 4.2 13.8 1.0
CA B:THR378 4.2 10.8 1.0
O B:ASP377 4.3 13.5 1.0
OD2 B:ASP369 4.4 14.7 1.0
CB B:ASP369 4.4 12.1 1.0
N B:ASP377 4.4 12.6 1.0
CB B:CYS376 4.4 13.4 1.0
O B:ASP369 4.5 12.2 1.0
CA B:ASP377 4.5 13.2 1.0
CB B:THR378 4.5 11.2 1.0
O B:HOH1031 4.6 25.7 1.0
N B:CYS371 4.6 11.4 1.0
N B:LEU379 4.6 10.0 1.0
CG B:GLU398 4.7 10.8 1.0
CA B:LEU379 4.9 10.1 1.0
CD2 B:LEU379 4.9 13.9 1.0

Reference:

H.S.Shieh, K.J.Mathis, J.M.Williams, R.L.Hills, J.F.Wiese, T.E.Benson, J.R.Kiefer, M.H.Marino, J.N.Carroll, J.W.Leone, A.M.Malfait, E.C.Arner, M.D.Tortorella, A.Tomasselli. High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2). J.Biol.Chem. V. 283 1501 2008.
ISSN: ISSN 0021-9258
PubMed: 17991750
DOI: 10.1074/JBC.M705879200
Page generated: Sat Jul 13 08:10:14 2024

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