Nickel 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:
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Nickel 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 Nickel atom.
In total 14 binding sites of Nickel where determined in the
ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4, PDB code: 3q2h:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 1 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni 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:Ni503
b:99.6
occ:1.00
|
CD2
|
B:HIS61
|
2.4
|
93.7
|
1.0
|
OE1
|
A:GLU242
|
2.5
|
83.9
|
1.0
|
NE2
|
B:HIS61
|
2.6
|
92.9
|
1.0
|
CD
|
A:GLU242
|
3.1
|
82.7
|
1.0
|
OE2
|
A:GLU242
|
3.2
|
89.0
|
1.0
|
CG
|
B:HIS61
|
3.7
|
96.6
|
1.0
|
CE1
|
B:HIS61
|
3.9
|
95.0
|
1.0
|
CB
|
B:ALA19
|
4.2
|
80.7
|
1.0
|
O
|
B:HOH310
|
4.3
|
89.4
|
1.0
|
ND1
|
B:HIS61
|
4.4
|
96.9
|
1.0
|
CG
|
A:GLU242
|
4.6
|
77.4
|
1.0
|
CA
|
B:ALA19
|
4.7
|
79.8
|
1.0
|
O
|
B:ALA19
|
4.7
|
77.5
|
1.0
|
CB
|
B:HIS61
|
4.7
|
98.8
|
1.0
|
C
|
B:ALA19
|
4.9
|
78.3
|
1.0
|
O
|
B:GLY23
|
4.9
|
72.5
|
1.0
|
C
|
B:GLY23
|
5.0
|
71.1
|
1.0
|
|
Nickel binding site 2 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 2 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni 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:Ni504
b:60.4
occ:1.00
|
OD1
|
B:ASP231
|
2.2
|
75.7
|
1.0
|
O
|
A:HOH334
|
2.3
|
57.0
|
1.0
|
ND1
|
A:HIS28
|
2.4
|
56.6
|
1.0
|
OD2
|
B:ASP231
|
2.9
|
72.8
|
1.0
|
CG
|
B:ASP231
|
2.9
|
70.3
|
1.0
|
CE1
|
A:HIS28
|
3.2
|
59.4
|
1.0
|
CG
|
A:HIS28
|
3.4
|
57.4
|
1.0
|
CB
|
A:HIS28
|
3.8
|
56.0
|
1.0
|
CA
|
A:HIS28
|
4.3
|
55.7
|
1.0
|
NE2
|
A:HIS28
|
4.3
|
57.4
|
1.0
|
CG
|
B:ARG234
|
4.3
|
62.3
|
1.0
|
ND2
|
B:ASN233
|
4.4
|
62.6
|
1.0
|
CB
|
B:ASP231
|
4.4
|
69.7
|
1.0
|
CB
|
B:ASN233
|
4.4
|
61.6
|
1.0
|
CD2
|
A:HIS28
|
4.5
|
58.0
|
1.0
|
O
|
B:HOH309
|
4.6
|
83.3
|
1.0
|
CD
|
B:ARG234
|
4.6
|
63.9
|
1.0
|
CG
|
B:ASN233
|
5.0
|
63.6
|
1.0
|
|
Nickel binding site 3 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 3 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni 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:Ni601
b:53.3
occ:1.00
|
O
|
A:HOH328
|
1.9
|
56.5
|
1.0
|
OD2
|
A:ASP99
|
2.1
|
67.3
|
1.0
|
OD2
|
A:ASP92
|
2.2
|
89.3
|
1.0
|
O
|
A:CYS210
|
2.2
|
68.1
|
1.0
|
OE1
|
A:GLU9
|
2.2
|
65.7
|
1.0
|
OD1
|
A:ASP213
|
2.3
|
72.4
|
1.0
|
OD1
|
A:ASP99
|
2.5
|
66.4
|
1.0
|
CG
|
A:ASP99
|
2.7
|
64.6
|
1.0
|
CG
|
A:ASP92
|
3.3
|
93.0
|
1.0
|
CG
|
A:ASP213
|
3.3
|
75.8
|
1.0
|
CD
|
A:GLU9
|
3.4
|
65.3
|
1.0
|
C
|
A:CYS210
|
3.4
|
69.1
|
1.0
|
OD2
|
A:ASP213
|
3.7
|
76.8
|
1.0
|
OD1
|
A:ASP92
|
3.7
|
89.0
|
1.0
|
CG
|
A:GLU9
|
3.9
|
63.8
|
1.0
|
CD
|
A:CD501
|
4.0
|
80.5
|
1.0
|
CB
|
A:ASP99
|
4.2
|
60.8
|
1.0
|
O
|
A:ASP213
|
4.2
|
77.3
|
1.0
|
CB
|
A:GLU9
|
4.2
|
62.2
|
1.0
|
N
|
A:LEU211
|
4.3
|
68.7
|
1.0
|
O
|
A:HOH336
|
4.3
|
75.3
|
1.0
|
O
|
A:TYR7
|
4.3
|
67.9
|
1.0
|
CA
|
A:LEU211
|
4.3
|
67.8
|
1.0
|
CA
|
A:CYS210
|
4.4
|
70.3
|
1.0
|
OE2
|
A:GLU9
|
4.4
|
65.3
|
1.0
|
CB
|
A:ASP213
|
4.6
|
77.4
|
1.0
|
CB
|
A:CYS210
|
4.7
|
68.9
|
1.0
|
CB
|
A:ASP92
|
4.7
|
95.2
|
1.0
|
N
|
A:ASP213
|
4.7
|
76.8
|
1.0
|
C
|
A:LEU211
|
4.8
|
70.5
|
1.0
|
N
|
A:GLU9
|
4.9
|
63.1
|
1.0
|
C
|
A:ASP213
|
5.0
|
78.2
|
1.0
|
|
Nickel binding site 4 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 4 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni 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
|
A:Ni607
b:88.8
occ:1.00
|
NE2
|
A:HIS61
|
2.4
|
66.6
|
1.0
|
O
|
A:HOH330
|
2.9
|
66.9
|
1.0
|
CD2
|
A:HIS61
|
3.0
|
68.6
|
1.0
|
O
|
A:HOH356
|
3.3
|
87.6
|
1.0
|
CE1
|
A:HIS61
|
3.6
|
68.7
|
1.0
|
OE1
|
B:GLU242
|
3.9
|
79.8
|
1.0
|
CD
|
B:GLU242
|
4.0
|
77.0
|
1.0
|
CG
|
B:GLU242
|
4.2
|
72.1
|
1.0
|
CG
|
A:HIS61
|
4.3
|
69.3
|
1.0
|
CB
|
A:ALA19
|
4.3
|
59.4
|
1.0
|
O
|
B:HOH1
|
4.4
|
75.9
|
1.0
|
ND1
|
A:HIS61
|
4.5
|
70.7
|
1.0
|
O
|
A:ALA19
|
4.6
|
59.4
|
1.0
|
OE2
|
B:GLU242
|
4.6
|
79.5
|
1.0
|
O
|
A:GLY23
|
4.6
|
58.7
|
1.0
|
CA
|
A:ALA19
|
4.8
|
59.7
|
1.0
|
C
|
A:GLY23
|
4.8
|
59.7
|
1.0
|
CB
|
B:GLU242
|
4.9
|
69.6
|
1.0
|
C
|
A:ALA19
|
4.9
|
60.1
|
1.0
|
|
Nickel binding site 5 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 5 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni609
b:83.7
occ:1.00
|
OE2
|
A:GLU68
|
2.4
|
67.7
|
1.0
|
O
|
A:HOH358
|
2.6
|
78.1
|
1.0
|
OE1
|
A:GLU68
|
2.8
|
56.6
|
1.0
|
CD
|
A:GLU68
|
2.9
|
65.0
|
1.0
|
O
|
A:VAL69
|
3.7
|
69.4
|
1.0
|
CG
|
A:GLU68
|
4.4
|
65.8
|
1.0
|
CG
|
A:GLU63
|
4.6
|
71.5
|
1.0
|
CD
|
A:CD502
|
4.7
|
87.4
|
1.0
|
C
|
A:VAL69
|
4.7
|
67.9
|
1.0
|
N
|
A:VAL69
|
4.7
|
66.1
|
1.0
|
O
|
A:HOH351
|
5.0
|
58.4
|
1.0
|
|
Nickel binding site 6 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 6 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni611
b:61.3
occ:1.00
|
O
|
A:HOH319
|
1.9
|
40.6
|
1.0
|
NE2
|
A:HIS176
|
2.3
|
82.0
|
1.0
|
CE1
|
A:HIS176
|
3.2
|
80.7
|
1.0
|
CD2
|
A:HIS176
|
3.3
|
80.6
|
1.0
|
ND1
|
A:HIS176
|
4.3
|
79.3
|
1.0
|
CG
|
A:HIS176
|
4.4
|
79.6
|
1.0
|
CD
|
A:PRO193
|
4.5
|
85.5
|
1.0
|
OG
|
A:SER175
|
4.7
|
90.2
|
1.0
|
|
Nickel binding site 7 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 7 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni612
b:86.0
occ:1.00
|
O
|
A:HOH365
|
2.2
|
79.7
|
1.0
|
OD1
|
A:ASP243
|
2.5
|
72.9
|
1.0
|
OE2
|
A:GLU242
|
2.8
|
89.0
|
1.0
|
CE1
|
B:HIS61
|
3.1
|
95.0
|
1.0
|
CG
|
A:ASP243
|
3.5
|
77.4
|
1.0
|
CD
|
A:GLU242
|
3.7
|
82.7
|
1.0
|
NE2
|
B:HIS61
|
3.8
|
92.9
|
1.0
|
CG
|
A:GLU242
|
3.9
|
77.4
|
1.0
|
OD2
|
A:ASP243
|
4.0
|
81.1
|
1.0
|
ND1
|
B:HIS61
|
4.2
|
96.9
|
1.0
|
NZ
|
B:LYS27
|
4.4
|
80.8
|
1.0
|
CA
|
A:ASP243
|
4.4
|
75.4
|
1.0
|
N
|
A:ASP243
|
4.5
|
74.0
|
1.0
|
CB
|
A:ASP243
|
4.5
|
76.9
|
1.0
|
CB
|
B:VAL59
|
4.6
|
95.4
|
1.0
|
CG2
|
B:VAL59
|
4.7
|
93.2
|
1.0
|
CE
|
B:LYS27
|
4.8
|
81.9
|
1.0
|
C
|
A:GLU242
|
4.8
|
72.9
|
1.0
|
O
|
A:GLU242
|
4.8
|
72.9
|
1.0
|
CB
|
A:GLU242
|
4.9
|
72.0
|
1.0
|
OE1
|
A:GLU242
|
4.9
|
83.9
|
1.0
|
|
Nickel binding site 8 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 8 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni613
b:91.2
occ:1.00
|
ND1
|
A:HIS246
|
2.4
|
85.4
|
1.0
|
CE1
|
A:HIS246
|
3.2
|
87.4
|
1.0
|
CG
|
A:HIS246
|
3.4
|
81.7
|
1.0
|
CB
|
A:HIS246
|
3.8
|
79.2
|
1.0
|
OE1
|
B:GLN220
|
4.2
|
0.5
|
1.0
|
NE2
|
A:HIS246
|
4.3
|
88.4
|
1.0
|
CD2
|
A:HIS246
|
4.5
|
85.1
|
1.0
|
CB
|
A:ALA232
|
4.7
|
75.4
|
1.0
|
O
|
A:HOH346
|
4.9
|
66.9
|
1.0
|
|
Nickel binding site 9 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 9 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni615
b:0.5
occ:1.00
|
NE2
|
A:HIS273
|
3.1
|
84.4
|
1.0
|
CD2
|
A:HIS273
|
3.2
|
79.6
|
1.0
|
O
|
A:THR271
|
4.4
|
73.8
|
1.0
|
CE1
|
A:HIS273
|
4.4
|
85.9
|
1.0
|
CG
|
A:HIS273
|
4.6
|
80.6
|
1.0
|
|
Nickel binding site 10 out
of 14 in 3q2h
Go back to
Nickel Binding Sites List in 3q2h
Nickel binding site 10 out
of 14 in the ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of ADAMTS1 in Complex with N-Hydroxyformamide Inhibitors of Adam-TS4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni604
b:87.8
occ:1.00
|
O
|
B:HOH311
|
1.7
|
77.2
|
1.0
|
OE2
|
B:GLU242
|
2.3
|
79.5
|
1.0
|
OD1
|
B:ASP243
|
2.7
|
68.8
|
1.0
|
OE1
|
B:GLU242
|
2.8
|
79.8
|
1.0
|
CD
|
B:GLU242
|
2.9
|
77.0
|
1.0
|
CE1
|
A:HIS61
|
3.1
|
68.7
|
1.0
|
CG
|
B:ASP243
|
3.8
|
70.2
|
1.0
|
ND1
|
A:HIS61
|
4.0
|
70.7
|
1.0
|
NE2
|
A:HIS61
|
4.1
|
66.6
|
1.0
|
OD2
|
B:ASP243
|
4.2
|
74.3
|
1.0
|
CG
|
B:GLU242
|
4.4
|
72.1
|
1.0
|
NZ
|
A:LYS27
|
4.5
|
68.5
|
1.0
|
CB
|
A:VAL59
|
4.6
|
58.8
|
1.0
|
O
|
B:HOH1
|
4.6
|
75.9
|
1.0
|
CG1
|
A:VAL59
|
4.9
|
57.7
|
1.0
|
CE
|
A:LYS27
|
4.9
|
66.4
|
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: Wed Oct 9 17:42:59 2024
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