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Calcium in PDB 6yjm: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm was solved by A.Goepfert, P.Leonard, N.Triballeau, D.Fleury, P.Mollat, M.Lamers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.47 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.32, 80.24, 51.05, 90, 90.2, 90
R / Rfree (%) 21.3 / 25.6

Other elements in 6yjm:

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 also contains other interesting chemical elements:

Fluorine (F) 4 atoms
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 the Inhibitor GLPG1972 (pdb code 6yjm). 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 the Inhibitor GLPG1972, PDB code: 6yjm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6yjm

Go back to Calcium Binding Sites List in 6yjm
Calcium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:12.5
occ:1.00
 OD1 A:ASP474 2.3 13.6 1.0
O A:CYS471 2.4 12.5 1.0
OE2 A:GLU270 2.4 12.6 1.0
OD1 A:ASP360 2.5 15.6 1.0
O A:HOH608 2.5 11.1 1.0
OD2 A:ASP360 2.5 8.4 1.0
OD1 A:ASP353 2.6 15.6 1.0
OD2 A:ASP353 2.8 15.8 1.0
CG A:ASP360 2.8 13.1 1.0
CG A:ASP353 3.0 18.0 1.0
CG A:ASP474 3.4 16.3 1.0
CD A:GLU270 3.4 10.5 1.0
C A:CYS471 3.6 9.1 1.0
CA A:CA503 3.7 14.4 1.0
OD2 A:ASP474 3.7 18.4 1.0
OE1 A:GLU270 4.0 12.1 1.0
O A:HOH609 4.2 11.9 1.0
CB A:ASP360 4.3 11.4 1.0
CA A:LEU472 4.4 12.4 1.0
N A:LEU472 4.4 12.9 1.0
CG A:GLU270 4.5 17.2 1.0
O A:GLN268 4.5 11.8 1.0
CB A:GLU270 4.5 13.4 1.0
O A:ASP474 4.5 20.2 1.0
CB A:ASP353 4.5 10.7 1.0
CA A:CYS471 4.6 8.9 1.0
CB A:ASP474 4.7 15.7 1.0
C A:LEU472 4.8 13.4 1.0
N A:ASP474 4.8 10.9 1.0
CB A:CYS471 4.8 15.6 1.0

Calcium binding site 2 out of 6 in 6yjm

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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 the Inhibitor GLPG1972


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 the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:14.4
occ:1.00
 O A:ASP353 2.4 18.7 1.0
OD2 A:ASP474 2.4 18.4 1.0
O A:HOH612 2.4 16.8 1.0
O A:HOH610 2.4 14.0 1.0
OE1 A:GLU270 2.5 12.1 1.0
OE2 A:GLU270 2.5 12.6 1.0
OD1 A:ASP353 2.6 15.6 1.0
CD A:GLU270 2.8 10.5 1.0
CG A:ASP474 3.4 16.3 1.0
C A:ASP353 3.4 18.6 1.0
CG A:ASP353 3.5 18.0 1.0
CA A:CA502 3.7 12.5 1.0
OD1 A:ASP474 3.7 13.6 1.0
CA A:ASP353 3.8 13.7 1.0
O A:HOH641 4.0 9.4 1.0
CB A:ASP353 4.0 10.7 1.0
CG A:GLU270 4.2 17.2 1.0
O A:HIS358 4.3 8.2 1.0
O A:HIS355 4.4 12.0 1.0
OD2 A:ASP353 4.4 15.8 1.0
O A:LEU475 4.4 19.8 1.0
N A:ASP354 4.6 15.7 1.0
CD2 A:HIS358 4.7 10.9 1.0
CB A:ASP474 4.7 15.7 1.0
CB A:GLU270 4.9 13.4 1.0
CB A:HIS358 5.0 10.6 1.0
OD1 A:ASP360 5.0 15.6 1.0

Calcium binding site 3 out of 6 in 6yjm

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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 the Inhibitor GLPG1972


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 the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:21.5
occ:1.00
 OD1 A:ASP369 2.3 15.4 1.0
O A:CYS376 2.4 20.2 1.0
O A:LEU370 2.4 16.4 1.0
O A:THR378 2.4 18.3 1.0
O A:HOH639 2.4 12.1 1.0
OE1 A:GLU398 2.5 15.6 1.0
CD A:GLU398 3.3 17.3 1.0
N A:LEU370 3.4 12.7 1.0
C A:CYS376 3.4 17.4 1.0
C A:LEU370 3.4 13.6 1.0
OE2 A:GLU398 3.5 15.1 1.0
CG A:ASP369 3.6 23.0 1.0
C A:THR378 3.6 14.1 1.0
CA A:LEU370 3.9 8.9 1.0
C A:ASP369 3.9 16.9 1.0
N A:THR378 4.0 13.5 1.0
CA A:CYS376 4.1 18.3 1.0
C A:ASP377 4.1 17.0 1.0
CA A:ASP369 4.2 16.4 1.0
CB A:CYS376 4.2 19.7 1.0
CA A:THR378 4.3 15.3 1.0
OD2 A:ASP369 4.4 25.0 1.0
CB A:LEU370 4.4 10.2 1.0
N A:ASP377 4.4 16.7 1.0
CB A:ASP369 4.5 22.6 1.0
O A:ASP377 4.5 15.7 1.0
CA A:ASP377 4.6 18.9 1.0
N A:CYS371 4.6 13.1 1.0
CD2 A:LEU379 4.6 10.7 1.0
N A:LEU379 4.6 10.7 1.0
O A:ASP369 4.7 21.9 1.0
CB A:THR378 4.7 16.6 1.0
CG A:GLU398 4.8 16.7 1.0
CA A:LEU379 4.9 13.8 1.0
O A:HOH642 4.9 15.5 1.0

Calcium binding site 4 out of 6 in 6yjm

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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 the Inhibitor GLPG1972


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 the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:10.8
occ:1.00
 O B:CYS471 2.4 16.0 1.0
OE1 B:GLU270 2.4 13.6 1.0
OD2 B:ASP360 2.4 7.9 1.0
OD1 B:ASP360 2.5 6.8 1.0
OD1 B:ASP474 2.5 11.3 1.0
O B:HOH605 2.7 8.7 1.0
OD2 B:ASP353 2.8 12.7 1.0
CG B:ASP360 2.8 9.2 1.0
OD1 B:ASP353 2.9 14.1 1.0
CG B:ASP353 3.2 12.3 1.0
CD B:GLU270 3.4 14.4 1.0
CG B:ASP474 3.5 14.4 1.0
CA B:CA503 3.6 15.9 1.0
C B:CYS471 3.7 13.2 1.0
OD2 B:ASP474 3.7 16.9 1.0
OE2 B:GLU270 4.0 19.2 1.0
CB B:ASP360 4.3 8.4 1.0
CA B:LEU472 4.4 12.2 1.0
O B:GLN268 4.4 9.9 1.0
CG B:GLU270 4.4 13.6 1.0
N B:LEU472 4.5 9.5 1.0
CB B:GLU270 4.5 11.7 1.0
O B:ASP474 4.6 22.7 1.0
CB B:ASP353 4.6 15.0 1.0
CA B:CYS471 4.7 12.6 1.0
O B:HOH619 4.8 11.5 1.0
CB B:ASP474 4.8 9.8 1.0
C B:LEU472 4.8 11.1 1.0
CB B:CYS471 4.9 9.4 1.0
N B:ASP474 4.9 20.2 1.0

Calcium binding site 5 out of 6 in 6yjm

Go back to Calcium Binding Sites List in 6yjm
Calcium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:15.9
occ:1.00
 OD2 B:ASP474 2.4 16.9 1.0
O B:ASP353 2.5 20.2 1.0
O B:HOH614 2.5 20.2 1.0
O B:HOH607 2.5 13.3 1.0
OE1 B:GLU270 2.5 13.6 1.0
OE2 B:GLU270 2.5 19.2 1.0
OD1 B:ASP353 2.6 14.1 1.0
CD B:GLU270 2.8 14.4 1.0
CG B:ASP474 3.4 14.4 1.0
CG B:ASP353 3.4 12.3 1.0
C B:ASP353 3.6 18.0 1.0
CA B:CA502 3.6 10.8 1.0
OD1 B:ASP474 3.7 11.3 1.0
CA B:ASP353 4.0 18.2 1.0
O B:HOH615 4.1 15.4 1.0
CB B:ASP353 4.1 15.0 1.0
CG B:GLU270 4.2 13.6 1.0
OD2 B:ASP353 4.2 12.7 1.0
O B:HIS358 4.3 13.7 1.0
O B:LEU475 4.4 19.1 1.0
O B:HIS355 4.4 18.2 1.0
N B:ASP354 4.7 19.3 1.0
CB B:ASP474 4.7 9.8 1.0
CB B:GLU270 5.0 11.7 1.0
CD2 B:HIS358 5.0 12.4 1.0
O B:HOH605 5.0 8.7 1.0

Calcium binding site 6 out of 6 in 6yjm

Go back to Calcium Binding Sites List in 6yjm
Calcium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:20.0
occ:1.00
 O B:THR378 2.3 17.1 1.0
O B:CYS376 2.4 16.6 1.0
OD1 B:ASP369 2.4 24.6 1.0
O B:LEU370 2.4 18.6 1.0
OE1 B:GLU398 2.5 14.6 1.0
O B:HOH630 2.6 23.5 1.0
CD B:GLU398 3.4 19.6 1.0
C B:CYS376 3.4 18.2 1.0
N B:LEU370 3.5 15.6 1.0
C B:THR378 3.5 10.5 1.0
C B:LEU370 3.5 19.8 1.0
OE2 B:GLU398 3.5 20.1 1.0
CG B:ASP369 3.6 25.1 1.0
N B:THR378 3.9 18.8 1.0
CA B:LEU370 4.0 16.6 1.0
O B:HOH642 4.0 24.6 1.0
C B:ASP369 4.0 20.9 1.0
C B:ASP377 4.0 17.9 1.0
CA B:THR378 4.2 15.8 1.0
CA B:CYS376 4.2 14.7 1.0
CB B:CYS376 4.3 22.8 1.0
CA B:ASP369 4.3 21.3 1.0
O B:ASP377 4.4 19.9 1.0
N B:ASP377 4.4 15.6 1.0
CB B:LEU370 4.4 16.8 1.0
OD2 B:ASP369 4.4 34.3 1.0
CA B:ASP377 4.5 16.9 1.0
N B:LEU379 4.5 12.6 1.0
CB B:ASP369 4.6 22.1 1.0
CD2 B:LEU379 4.6 15.8 1.0
CB B:THR378 4.7 15.4 1.0
N B:CYS371 4.7 21.4 1.0
CG B:GLU398 4.8 14.7 1.0
O B:ASP369 4.8 22.4 1.0
CA B:LEU379 4.8 11.9 1.0

Reference:

P.Leonard, N.Triballeau, P.Mollat. Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 To Be Published.
Page generated: Thu Jul 18 22:25:51 2024

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