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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:

Fluorine (F) 2 atoms
Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms
Cadmium (Cd) 4 atoms
Sodium (Na) 4 atoms

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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 Dec 16 01:27:16 2020

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