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Cadmium in PDB 3q2h: ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4

Protein crystallography data

The structure of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4, PDB code: 3q2h was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.70 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.859, 63.328, 110.844, 90.00, 91.24, 90.00
R / Rfree (%) 23.6 / 29.7

Other elements in 3q2h:

The structure of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Nickel (Ni) 14 atoms
Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 (pdb code 3q2h). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4, PDB code: 3q2h:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3q2h

Go back to Cadmium Binding Sites List in 3q2h
Cadmium binding site 1 out of 4 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:80.5
occ:1.00
OD1 A:ASP92 1.8 89.0 1.0
OD2 A:ASP213 2.2 76.8 1.0
OE1 A:GLU9 2.6 65.7 1.0
OE2 A:GLU9 2.6 65.3 1.0
CG A:ASP92 2.7 93.0 1.0
O A:ASP92 2.8 96.7 1.0
CD A:GLU9 2.9 65.3 1.0
CG A:ASP213 3.3 75.8 1.0
OD2 A:ASP92 3.3 89.3 1.0
OD1 A:ASP213 3.7 72.4 1.0
CB A:ASP92 3.8 95.2 1.0
C A:ASP92 3.8 96.5 1.0
O A:ASP94 4.0 90.4 1.0
NI A:NI601 4.0 53.3 1.0
NE2 A:GLN216 4.0 93.9 1.0
O A:HOH349 4.1 71.0 1.0
CA A:ASP92 4.1 95.3 1.0
O A:HIS97 4.1 71.4 1.0
O A:LYS214 4.3 78.8 1.0
CG A:GLU9 4.4 63.8 1.0
CB A:ASP213 4.5 77.4 1.0
OE1 A:GLN216 4.6 94.9 1.0
CD2 A:HIS97 4.7 79.0 1.0
CD A:GLN216 4.8 93.0 1.0
O A:HOH328 4.8 56.5 1.0
O A:ASP213 4.9 77.3 1.0
CB A:HIS97 4.9 76.5 1.0

Cadmium binding site 2 out of 4 in 3q2h

Go back to Cadmium Binding Sites List in 3q2h
Cadmium binding site 2 out of 4 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:87.4
occ:1.00
OE1 A:GLU63 1.9 44.3 1.0
O A:HOH351 2.2 58.4 1.0
OE1 A:GLU68 2.8 56.6 1.0
CD A:GLU63 3.1 68.2 1.0
O A:HOH357 3.3 65.9 1.0
CD A:GLU68 3.5 65.0 1.0
OE2 A:GLU63 3.9 73.9 1.0
CG A:GLU63 4.0 71.5 1.0
OE2 A:GLU68 4.2 67.7 1.0
CG A:GLU68 4.2 65.8 1.0
CB A:GLU68 4.2 65.8 1.0
NI A:NI609 4.7 83.7 1.0

Cadmium binding site 3 out of 4 in 3q2h

Go back to Cadmium Binding Sites List in 3q2h
Cadmium binding site 3 out of 4 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:89.7
occ:1.00
OD1 A:ASP231 2.2 63.8 1.0
ND1 B:HIS28 2.3 72.9 1.0
O A:HOH332 2.8 66.3 1.0
CG A:ASP231 2.9 70.2 1.0
OD2 A:ASP231 2.9 73.1 1.0
CE1 B:HIS28 3.2 73.2 1.0
CG B:HIS28 3.3 73.7 1.0
CB B:HIS28 3.7 74.1 1.0
CA B:HIS28 4.2 75.3 1.0
ND2 A:ASN233 4.3 75.4 1.0
CG A:ARG234 4.3 68.4 1.0
NE2 B:HIS28 4.3 76.3 1.0
CB A:ASN233 4.3 71.3 1.0
CB A:ASP231 4.4 71.3 1.0
CD2 B:HIS28 4.4 76.4 1.0
CD A:ARG234 4.6 71.1 1.0
CG A:ASN233 4.8 75.0 1.0

Cadmium binding site 4 out of 4 in 3q2h

Go back to Cadmium Binding Sites List in 3q2h
Cadmium binding site 4 out of 4 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd605

b:0.8
occ:1.00
OE2 B:GLU9 2.5 0.1 1.0
OE1 B:GLU9 2.8 0.3 1.0
OD1 B:ASP92 2.8 0.2 1.0
OD1 B:ASP213 2.8 0.8 1.0
OD2 B:ASP213 2.9 0.0 1.0
CD B:GLU9 3.0 0.9 1.0
CG B:ASP213 3.2 0.7 1.0
O B:ASP92 3.4 0.5 1.0
CG B:ASP92 3.6 0.8 1.0
O B:LYS214 3.7 0.2 1.0
OD2 B:ASP92 4.0 0.5 1.0
O B:HIS97 4.1 0.6 1.0
O B:HOH302 4.1 50.2 1.0
NI B:NI606 4.2 88.5 1.0
O B:ASP94 4.3 0.1 1.0
C B:LYS214 4.4 0.1 1.0
C B:ASP92 4.5 0.8 1.0
CG B:GLU9 4.5 0.3 1.0
CB B:ASP92 4.6 0.2 1.0
CB B:ASP213 4.7 0.2 1.0
N B:LYS214 4.7 0.7 1.0
CA B:ASP92 4.8 0.7 1.0
CA B:PRO215 4.8 0.8 1.0
N B:PRO215 4.9 0.5 1.0
CB B:HIS97 5.0 0.8 1.0

Reference:

C.De Savi, A.Pape, J.G.Cumming, A.Ting, P.D.Smith, J.N.Burrows, M.Mills, C.Davies, S.Lamont, D.Milne, C.Cook, P.Moore, Y.Sawyer, S.Gerhardt. The Design and Synthesis of Novel N-Hydroxyformamide Inhibitors of Adam-TS4 For the Treatment of Osteoarthritis Bioorg.Med.Chem.Lett. V. 21 1376 2011.
ISSN: ISSN 0960-894X
PubMed: 21300546
DOI: 10.1016/J.BMCL.2011.01.036
Page generated: Sat Dec 12 08:22:58 2020

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