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Sodium 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
Cadmium (Cd) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4, PDB code: 3q2h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3q2h

Go back to Sodium Binding Sites List in 3q2h
Sodium 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 Sodium with other atoms in the Na 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:Na701

b:76.7
occ:1.00
O A:THR117 2.2 67.2 1.0
O A:LEU109 2.4 75.2 1.0
OE2 A:GLU137 2.4 70.4 1.0
OD2 A:ASP108 2.6 70.8 1.0
O A:CYS115 2.7 77.9 1.0
CG A:ASP108 2.9 72.2 1.0
OD1 A:ASP108 3.1 62.2 1.0
N A:LEU109 3.2 70.9 1.0
C A:THR117 3.4 67.1 1.0
C A:LEU109 3.4 73.5 1.0
C A:CYS115 3.5 79.3 1.0
CD A:GLU137 3.5 65.4 1.0
N A:THR117 3.7 71.9 1.0
CA A:LEU109 3.8 71.1 1.0
NA A:NA703 3.8 66.0 1.0
C A:ASP108 3.8 70.6 1.0
OE1 A:GLU137 3.9 69.8 1.0
C A:ASP116 4.0 74.8 1.0
CA A:THR117 4.0 68.9 1.0
CB A:ASP108 4.1 71.6 1.0
CA A:ASP108 4.1 70.2 1.0
N A:ASP116 4.2 78.7 1.0
CB A:LEU109 4.2 69.3 1.0
CA A:ASP116 4.3 77.8 1.0
CA A:CYS115 4.3 81.0 1.0
CB A:THR117 4.4 68.0 1.0
O A:ASP116 4.4 75.1 1.0
N A:LEU118 4.5 65.5 1.0
CB A:CYS115 4.5 81.8 1.0
N A:CYS110 4.6 74.7 1.0
O A:ASP108 4.8 71.5 1.0
CG A:GLU137 4.8 60.9 1.0
CD2 A:LEU118 4.8 62.9 1.0
CA A:LEU118 4.9 63.5 1.0

Sodium binding site 2 out of 4 in 3q2h

Go back to Sodium Binding Sites List in 3q2h
Sodium 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 Sodium with other atoms in the Na 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:Na703

b:66.0
occ:1.00
OD2 A:ASP108 2.4 70.8 1.0
O A:CYS115 2.6 77.9 1.0
OD1 A:ASP108 2.7 62.2 1.0
CG A:ASP108 2.8 72.2 1.0
C A:CYS115 3.7 79.3 1.0
NA A:NA701 3.8 76.7 1.0
CB A:CYS115 4.1 81.8 1.0
CB A:ASP108 4.3 71.6 1.0
OD1 A:ASP116 4.4 84.5 1.0
CA A:CYS115 4.5 81.0 1.0
N A:ASP116 4.6 78.7 1.0
CA A:ASP116 4.7 77.8 1.0

Sodium binding site 3 out of 4 in 3q2h

Go back to Sodium Binding Sites List in 3q2h
Sodium 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 Sodium with other atoms in the Na 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
B:Na702

b:0.2
occ:1.00
OD1 B:ASP108 2.4 96.0 1.0
OE2 B:GLU137 2.7 92.8 1.0
O B:THR117 2.7 0.4 1.0
O B:LEU109 2.9 0.9 1.0
CG B:ASP108 3.2 0.5 1.0
NA B:NA704 3.3 71.5 1.0
N B:THR117 3.5 0.4 1.0
C B:THR117 3.6 0.1 1.0
N B:LEU109 3.6 0.8 1.0
OD2 B:ASP108 3.7 0.9 1.0
CD B:GLU137 3.8 91.5 1.0
O B:CYS115 3.8 0.2 1.0
C B:LEU109 3.9 0.5 1.0
C B:ASP116 4.0 0.8 1.0
C B:ASP108 4.1 0.9 1.0
CA B:THR117 4.1 1.0 1.0
C B:CYS115 4.1 0.4 1.0
CA B:LEU109 4.2 0.6 1.0
CA B:ASP108 4.3 99.6 1.0
CA B:ASP116 4.3 0.6 1.0
CB B:ASP108 4.3 99.8 1.0
N B:ASP116 4.4 0.5 1.0
OE1 B:GLU137 4.4 95.3 1.0
N B:LEU118 4.6 99.2 1.0
CB B:LEU109 4.6 0.4 1.0
CD2 B:LEU118 4.6 94.1 1.0
O B:ASP116 4.7 0.4 1.0
O B:ASP108 4.8 0.1 1.0
CA B:LEU118 4.9 96.5 1.0
SG B:CYS115 4.9 0.7 1.0
CA B:CYS115 5.0 0.7 1.0
CG B:GLU137 5.0 86.0 1.0

Sodium binding site 4 out of 4 in 3q2h

Go back to Sodium Binding Sites List in 3q2h
Sodium 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 Sodium with other atoms in the Na 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:Na704

b:71.5
occ:1.00
OD2 B:ASP108 2.3 0.9 1.0
O B:CYS115 2.8 0.2 1.0
OD1 B:ASP108 3.0 96.0 1.0
CG B:ASP108 3.0 0.5 1.0
NA B:NA702 3.3 0.2 1.0
C B:CYS115 3.9 0.4 1.0
CA B:ASP116 4.5 0.6 1.0
CB B:ASP108 4.5 99.8 1.0
N B:ASP116 4.6 0.5 1.0
OE2 B:GLU137 4.8 92.8 1.0
CB B:CYS115 5.0 0.7 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: Tue Dec 15 06:22:15 2020

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