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Calcium in PDB 2rjp: Crystal Structure of ADAMTS4 with Inhibitor Bound

Enzymatic activity of Crystal Structure of ADAMTS4 with Inhibitor Bound

All present enzymatic activity of Crystal Structure of ADAMTS4 with Inhibitor Bound:
3.4.24.82;

Protein crystallography data

The structure of Crystal Structure of ADAMTS4 with Inhibitor Bound, PDB code: 2rjp was solved by L.Mosyak, M.Stahl, W.Somers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.566, 82.618, 99.326, 90.00, 90.63, 90.00
R / Rfree (%) 20.6 / 26.7

Other elements in 2rjp:

The structure of Crystal Structure of ADAMTS4 with Inhibitor Bound also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of ADAMTS4 with Inhibitor Bound (pdb code 2rjp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of ADAMTS4 with Inhibitor Bound, PDB code: 2rjp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 2rjp

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Calcium binding site 1 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:52.8
occ:1.00
 O A:CYS327 2.2 57.7 1.0
O A:LEU321 2.3 53.8 1.0
OE1 A:GLU349 2.3 55.1 1.0
O A:THR329 2.4 54.1 1.0
OD1 A:ASP320 2.5 52.8 1.0
CD A:GLU349 3.2 53.8 1.0
C A:CYS327 3.4 57.6 1.0
OE2 A:GLU349 3.4 55.4 1.0
C A:LEU321 3.4 53.8 1.0
C A:THR329 3.6 54.2 1.0
CG A:ASP320 3.7 51.6 1.0
N A:LEU321 3.7 52.5 1.0
N A:THR329 4.1 55.6 1.0
CA A:LEU321 4.1 53.1 1.0
C A:ASP328 4.1 56.5 1.0
C A:ASP320 4.2 51.8 1.0
CA A:CYS327 4.2 57.6 1.0
CA A:THR329 4.3 54.8 1.0
N A:ASP328 4.3 57.4 1.0
OD2 A:ASP320 4.4 50.9 1.0
CA A:ASP328 4.4 57.0 1.0
CB A:CYS327 4.4 57.5 1.0
O A:ASP328 4.4 56.6 1.0
CA A:ASP320 4.5 51.3 1.0
N A:CYS322 4.5 54.7 1.0
CD2 A:LEU330 4.6 52.8 1.0
CB A:LEU321 4.6 52.8 1.0
N A:LEU330 4.6 53.4 1.0
CG A:GLU349 4.6 51.0 1.0
CB A:ASP320 4.7 51.4 1.0
CB A:THR329 4.7 54.7 1.0
CA A:LEU330 4.8 52.7 1.0
CA A:CYS322 4.8 55.3 1.0
O A:ASP320 4.8 51.6 1.0
CB A:GLU349 5.0 49.3 1.0

Calcium binding site 2 out of 12 in 2rjp

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Calcium binding site 2 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:39.3
occ:1.00
 OE1 A:GLU221 2.4 46.1 1.0
OD2 A:ASP304 2.4 58.5 1.0
O A:CYS423 2.4 50.7 1.0
OD1 A:ASP426 2.4 55.1 1.0
OD2 A:ASP311 2.5 46.4 1.0
OD1 A:ASP311 3.0 46.2 1.0
CG A:ASP311 3.1 46.6 1.0
CG A:ASP426 3.2 54.2 1.0
CG A:ASP304 3.2 57.8 1.0
OD2 A:ASP426 3.3 55.3 1.0
OD1 A:ASP304 3.4 57.5 1.0
CD A:GLU221 3.5 45.8 1.0
C A:CYS423 3.6 50.5 1.0
CG A:GLU221 4.1 45.2 1.0
CA A:LEU424 4.2 50.8 1.0
CA A:CA4 4.2 49.8 1.0
N A:LEU424 4.3 50.4 1.0
O A:PHE219 4.4 44.2 1.0
O A:ASP426 4.4 53.4 1.0
OE2 A:GLU221 4.5 46.7 1.0
CB A:ASP311 4.6 46.4 1.0
CB A:ASP426 4.6 53.1 1.0
C A:LEU424 4.6 51.0 1.0
CA A:CYS423 4.6 50.4 1.0
CB A:ASP304 4.7 57.4 1.0
CB A:GLU221 4.7 45.3 1.0
N A:ASP426 4.7 52.5 1.0
N A:LEU425 4.9 51.5 1.0
CB A:CYS423 4.9 50.2 1.0

Calcium binding site 3 out of 12 in 2rjp

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Calcium binding site 3 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:49.8
occ:1.00
 O A:HOH57 2.4 31.4 1.0
OD1 A:ASP304 2.5 57.5 1.0
OD2 A:ASP426 2.7 55.3 1.0
O A:ASP304 2.7 57.6 1.0
OE1 A:GLU221 2.8 46.1 1.0
OE2 A:GLU221 2.8 46.7 1.0
CD A:GLU221 3.2 45.8 1.0
CG A:ASP304 3.5 57.8 1.0
CG A:ASP426 3.8 54.2 1.0
C A:ASP304 3.8 57.5 1.0
OD2 A:ASP304 4.2 58.5 1.0
CA A:CA3 4.2 39.3 1.0
OD1 A:ASP426 4.3 55.1 1.0
O A:ASP306 4.3 55.7 1.0
CA A:ASP304 4.3 57.5 1.0
O A:HIS309 4.4 49.4 1.0
CB A:ASP304 4.4 57.4 1.0
CG A:GLU221 4.7 45.2 1.0
CB A:HIS309 4.7 50.4 1.0
N A:SER305 4.9 57.4 1.0
CB A:ASP426 4.9 53.1 1.0

Calcium binding site 4 out of 12 in 2rjp

Go back to Calcium Binding Sites List in 2rjp
Calcium binding site 4 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:37.4
occ:1.00
 O B:CYS327 2.3 61.0 1.0
OE1 B:GLU349 2.3 50.6 1.0
OD1 B:ASP320 2.3 53.6 1.0
O B:THR329 2.4 57.0 1.0
O B:LEU321 2.5 55.5 1.0
CD B:GLU349 3.2 48.8 1.0
N B:LEU321 3.4 54.2 1.0
OE2 B:GLU349 3.4 48.5 1.0
C B:CYS327 3.5 60.8 1.0
CG B:ASP320 3.5 53.8 1.0
C B:LEU321 3.6 55.4 1.0
C B:THR329 3.6 57.1 1.0
C B:ASP320 3.9 53.7 1.0
CA B:LEU321 4.0 54.9 1.0
N B:THR329 4.0 58.6 1.0
CA B:ASP320 4.2 53.3 1.0
C B:ASP328 4.3 59.7 1.0
CA B:CYS327 4.3 60.9 1.0
CA B:THR329 4.3 57.6 1.0
OD2 B:ASP320 4.4 55.3 1.0
CB B:LEU321 4.4 54.7 1.0
CB B:ASP320 4.5 53.4 1.0
CB B:CYS327 4.5 60.9 1.0
N B:ASP328 4.5 60.6 1.0
CG B:GLU349 4.6 49.0 1.0
CA B:ASP328 4.6 60.3 1.0
N B:LEU330 4.6 56.4 1.0
CB B:THR329 4.7 57.5 1.0
O B:ASP328 4.7 59.9 1.0
O B:ASP320 4.7 53.7 1.0
N B:CYS322 4.8 56.2 1.0
CD2 B:LEU330 4.8 54.7 1.0
CA B:LEU330 4.8 55.5 1.0
CB B:GLU349 4.9 48.3 1.0

Calcium binding site 5 out of 12 in 2rjp

Go back to Calcium Binding Sites List in 2rjp
Calcium binding site 5 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:49.2
occ:1.00
 OE1 B:GLU221 2.3 47.2 1.0
O B:CYS423 2.4 49.5 1.0
OD2 B:ASP304 2.5 56.0 1.0
OD1 B:ASP426 2.6 54.0 1.0
OD1 B:ASP311 2.7 48.2 1.0
OD2 B:ASP311 2.7 48.4 1.0
CG B:ASP311 3.1 48.5 1.0
OD2 B:ASP426 3.2 53.5 1.0
CG B:ASP426 3.2 52.7 1.0
OD1 B:ASP304 3.3 55.6 1.0
CG B:ASP304 3.3 55.8 1.0
CD B:GLU221 3.5 46.5 1.0
C B:CYS423 3.6 49.5 1.0
O B:ASP426 4.1 52.1 1.0
CG B:GLU221 4.2 45.6 1.0
CA B:CA4 4.2 59.8 1.0
CA B:LEU424 4.2 49.4 1.0
O B:PHE219 4.3 43.8 1.0
N B:LEU424 4.4 49.4 1.0
OE2 B:GLU221 4.4 47.2 1.0
CB B:ASP311 4.6 48.1 1.0
CB B:GLU221 4.6 45.6 1.0
CA B:CYS423 4.7 49.5 1.0
CB B:ASP426 4.7 51.6 1.0
CB B:ASP304 4.7 55.8 1.0
N B:ASP426 4.8 50.8 1.0
C B:LEU424 4.8 49.4 1.0
CB B:CYS423 4.8 49.3 1.0
O B:HOH544 4.9 35.7 1.0
C B:ASP426 4.9 52.0 1.0

Calcium binding site 6 out of 12 in 2rjp

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Calcium binding site 6 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:59.8
occ:1.00
 OD1 B:ASP304 2.3 55.6 1.0
OD2 B:ASP426 2.4 53.5 1.0
O B:ASP304 2.6 55.7 1.0
OE2 B:GLU221 2.6 47.2 1.0
OE1 B:GLU221 2.9 47.2 1.0
CD B:GLU221 3.1 46.5 1.0
CG B:ASP304 3.4 55.8 1.0
C B:ASP304 3.7 55.8 1.0
CG B:ASP426 3.7 52.7 1.0
O B:ASP306 4.1 55.5 1.0
OD2 B:ASP304 4.2 56.0 1.0
CA B:ASP304 4.2 55.8 1.0
CA B:CA3 4.2 49.2 1.0
CB B:ASP304 4.2 55.8 1.0
O B:HOH551 4.3 49.0 1.0
OD1 B:ASP426 4.4 54.0 1.0
O B:LYS427 4.6 52.4 1.0
O B:HIS309 4.6 51.3 1.0
CG B:GLU221 4.6 45.6 1.0
CB B:ASP426 4.7 51.6 1.0
N B:SER305 4.8 56.1 1.0
CB B:HIS309 4.9 52.1 1.0

Calcium binding site 7 out of 12 in 2rjp

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Calcium binding site 7 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2

b:42.2
occ:1.00
 O C:CYS327 2.4 49.8 1.0
O C:THR329 2.4 46.7 1.0
OD1 C:ASP320 2.4 43.8 1.0
OE1 C:GLU349 2.5 44.0 1.0
O C:LEU321 2.5 41.8 1.0
CD C:GLU349 3.2 43.0 1.0
OE2 C:GLU349 3.3 45.4 1.0
C C:CYS327 3.6 49.6 1.0
N C:LEU321 3.6 41.9 1.0
C C:LEU321 3.6 41.8 1.0
C C:THR329 3.6 46.9 1.0
CG C:ASP320 3.7 43.6 1.0
C C:ASP328 4.1 48.8 1.0
CA C:LEU321 4.1 41.5 1.0
C C:ASP320 4.1 42.2 1.0
O C:ASP328 4.1 48.8 1.0
N C:THR329 4.3 47.9 1.0
CA C:ASP320 4.4 42.3 1.0
CA C:THR329 4.4 47.2 1.0
CA C:CYS327 4.4 49.7 1.0
OD2 C:ASP320 4.5 44.5 1.0
N C:ASP328 4.5 49.6 1.0
CB C:LEU321 4.6 40.9 1.0
CA C:ASP328 4.6 49.5 1.0
CB C:CYS327 4.6 49.8 1.0
N C:LEU330 4.6 46.4 1.0
CG C:GLU349 4.6 42.5 1.0
CB C:ASP320 4.7 42.4 1.0
N C:CYS322 4.8 42.2 1.0
CB C:THR329 4.8 47.3 1.0
CA C:LEU330 4.8 45.7 1.0
CD2 C:LEU330 4.9 44.5 1.0
O C:ASP320 4.9 42.6 1.0

Calcium binding site 8 out of 12 in 2rjp

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Calcium binding site 8 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3

b:39.7
occ:1.00
 O C:CYS423 2.3 44.2 1.0
OD1 C:ASP426 2.4 49.2 1.0
OE1 C:GLU221 2.4 37.4 1.0
OD1 C:ASP311 2.5 43.0 1.0
OD2 C:ASP311 2.6 42.6 1.0
OD2 C:ASP304 2.6 51.6 1.0
CG C:ASP311 2.9 42.0 1.0
OD1 C:ASP304 2.9 51.6 1.0
CG C:ASP304 3.2 51.7 1.0
CG C:ASP426 3.3 48.2 1.0
OD2 C:ASP426 3.4 47.6 1.0
C C:CYS423 3.5 44.3 1.0
CD C:GLU221 3.6 37.6 1.0
CA C:CA4 4.1 47.3 1.0
CG C:GLU221 4.4 37.5 1.0
N C:LEU424 4.4 44.4 1.0
CA C:LEU424 4.4 44.6 1.0
CB C:ASP311 4.4 41.2 1.0
CA C:CYS423 4.5 44.4 1.0
OE2 C:GLU221 4.5 36.7 1.0
CB C:CYS423 4.6 44.6 1.0
O C:ASP426 4.7 48.4 1.0
CB C:ASP304 4.7 51.7 1.0
O C:PHE219 4.7 39.8 1.0
CB C:ASP426 4.7 47.9 1.0
CB C:GLU221 4.7 38.2 1.0
C C:LEU424 4.9 45.1 1.0
N C:ASP426 5.0 47.1 1.0

Calcium binding site 9 out of 12 in 2rjp

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Calcium binding site 9 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4

b:47.3
occ:1.00
 OD2 C:ASP426 2.5 47.6 1.0
O C:HOH33 2.5 30.1 1.0
OD1 C:ASP304 2.6 51.6 1.0
OE2 C:GLU221 2.7 36.7 1.0
O C:ASP304 2.7 51.8 1.0
OE1 C:GLU221 2.8 37.4 1.0
CD C:GLU221 3.1 37.6 1.0
C C:ASP304 3.5 51.6 1.0
CG C:ASP426 3.6 48.2 1.0
CG C:ASP304 3.6 51.7 1.0
CA C:CA3 4.1 39.7 1.0
OD1 C:ASP426 4.1 49.2 1.0
O C:ASP306 4.1 49.6 1.0
CA C:ASP304 4.2 51.6 1.0
N C:SER305 4.3 51.4 1.0
OD2 C:ASP304 4.4 51.6 1.0
CB C:ASP304 4.5 51.7 1.0
CG C:GLU221 4.6 37.5 1.0
CA C:SER305 4.7 50.9 1.0
CB C:HIS309 4.7 45.6 1.0
O C:HIS309 4.7 44.9 1.0
CD2 C:HIS309 4.8 46.8 1.0
CB C:ASP426 4.8 47.9 1.0
C C:SER305 4.9 50.6 1.0

Calcium binding site 10 out of 12 in 2rjp

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Calcium binding site 10 out of 12 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2

b:67.3
occ:1.00
 O D:CYS327 2.3 47.8 1.0
O D:THR329 2.4 44.0 1.0
OE1 D:GLU349 2.5 45.2 1.0
OD1 D:ASP320 2.5 45.2 1.0
O D:LEU321 3.1 46.0 1.0
OE2 D:GLU349 3.1 44.3 1.0
CD D:GLU349 3.1 44.5 1.0
CG D:ASP320 3.5 45.3 1.0
C D:CYS327 3.5 47.5 1.0
C D:THR329 3.6 44.1 1.0
N D:LEU321 3.8 45.8 1.0
OD2 D:ASP320 4.0 45.2 1.0
N D:THR329 4.1 45.4 1.0
C D:LEU321 4.1 46.1 1.0
C D:ASP328 4.2 46.1 1.0
CD2 D:LEU330 4.2 42.0 1.0
CA D:THR329 4.4 44.5 1.0
CA D:ASP320 4.4 45.4 1.0
CA D:ASP328 4.4 46.6 1.0
C D:ASP320 4.4 45.6 1.0
N D:ASP328 4.4 47.1 1.0
CA D:LEU321 4.5 45.9 1.0
CA D:CYS327 4.5 47.9 1.0
CB D:ASP320 4.5 45.4 1.0
CB D:CYS327 4.5 47.8 1.0
CG D:GLU349 4.6 43.9 1.0
N D:LEU330 4.6 43.5 1.0
O D:ASP328 4.6 46.2 1.0
CA D:LEU330 4.7 43.1 1.0
CB D:THR329 4.9 44.5 1.0
CB D:LEU321 4.9 45.8 1.0
CB D:GLU349 5.0 43.8 1.0

Reference:

L.Mosyak, K.Georgiadis, T.Shane, K.Svenson, T.Hebert, T.Mcdonagh, S.Mackie, S.Olland, L.Lin, X.Zhong, R.Kriz, E.L.Reifenberg, L.A.Collins-Racie, C.Corcoran, B.Freeman, R.Zollner, T.Marvell, M.Vera, P.E.Sum, E.R.Lavallie, M.Stahl, W.Somers. Crystal Structures of the Two Major Aggrecan Degrading Enzymes, ADAMTS4 and ADAMTS5. Protein Sci. V. 17 16 2008.
ISSN: ISSN 0961-8368
PubMed: 18042673
DOI: 10.1110/PS.073287008
Page generated: Fri Jul 12 16:01:56 2024

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