Atomistry » Calcium » PDB 3hjb-3hz3 » 3hy7
Atomistry »
  Calcium »
    PDB 3hjb-3hz3 »
      3hy7 »

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

Go back to Calcium Binding Sites List in 3hy7
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

Go back to Calcium Binding Sites List in 3hy7
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

Go back to Calcium Binding Sites List in 3hy7
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy