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Iodine in PDB 4uyu: Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A

Enzymatic activity of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A

All present enzymatic activity of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A:
3.1.1.1;

Protein crystallography data

The structure of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A, PDB code: 4uyu was solved by M.Zebisch, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.78 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.220, 177.564, 60.991, 90.00, 90.00, 90.00
R / Rfree (%) 20.838 / 24.346

Other elements in 4uyu:

The structure of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine atom in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A (pdb code 4uyu). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A, PDB code: 4uyu:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 4uyu

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Iodine binding site 1 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1453

b:50.5
occ:0.90
 OG A:SER117 3.4 31.3 1.0
NE A:ARG119 3.9 37.7 1.0
N A:ALA175 3.9 27.5 1.0
CD A:ARG119 3.9 34.1 1.0
CB A:ARG119 4.0 29.8 1.0
C A:ASN174 4.0 28.9 1.0
CA A:ALA175 4.1 26.6 1.0
CB A:ALA175 4.2 26.1 1.0
CB A:ASN174 4.2 32.0 1.0
CA A:TRP172 4.3 28.6 1.0
O A:TYR171 4.3 29.1 1.0
O A:ASN174 4.4 28.8 1.0
CB A:SER117 4.4 33.4 1.0
CA A:ASN174 4.5 30.3 1.0
N A:ASN174 4.5 30.0 1.0
CD1 A:TRP172 4.6 30.5 1.0
CG A:ARG119 4.6 31.8 1.0
O A:TRP172 4.6 27.7 1.0
C A:TRP172 4.6 28.4 1.0
CB A:TRP172 4.8 28.9 1.0

Iodine binding site 2 out of 11 in 4uyu

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Iodine binding site 2 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1454

b:51.6
occ:1.00
 NH2 A:ARG119 3.6 41.5 1.0
CZ A:ARG119 3.9 40.8 1.0
CE A:LYS224 4.0 45.7 1.0
CB A:ARG119 4.0 29.8 1.0
N A:ARG119 4.1 27.2 1.0
C A:ARG118 4.1 27.6 1.0
CG2 A:VAL225 4.2 27.2 1.0
NE A:ARG119 4.2 37.7 1.0
CA A:ARG119 4.2 28.0 1.0
O A:ARG118 4.2 25.6 1.0
CB A:LYS224 4.3 36.2 1.0
CB A:ARG118 4.4 29.3 1.0
CB A:VAL225 4.4 27.2 1.0
NH1 A:ARG119 4.6 39.8 1.0
CG A:ARG119 4.7 31.8 1.0
N A:VAL225 4.7 28.6 1.0
CA A:ARG118 4.8 28.5 1.0
NZ A:LYS224 4.8 48.7 1.0

Iodine binding site 3 out of 11 in 4uyu

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Iodine binding site 3 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1455

b:0.9
occ:1.00
 NH1 A:ARG139 3.5 37.5 1.0
CG A:ARG139 4.0 40.6 1.0
CD A:ARG139 4.1 40.2 1.0
CB A:ARG139 4.2 42.9 1.0
O A:TYR129 4.3 40.8 1.0
CG2 A:THR282 4.5 57.4 1.0
OG1 A:THR282 4.5 56.0 1.0
CB A:THR282 4.6 57.9 1.0
CZ A:ARG139 4.6 38.3 1.0
CB A:TRP128 4.7 39.8 1.0
NE A:ARG139 4.8 38.5 1.0
CA A:ARG139 4.8 44.0 1.0

Iodine binding site 4 out of 11 in 4uyu

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Iodine binding site 4 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1457

b:96.3
occ:1.00
 CB A:CYS445 3.7 57.6 1.0
CD A:PRO441 4.2 65.0 1.0
CA A:CYS445 4.7 57.9 1.0
CB A:CYS440 4.8 61.1 1.0
SG A:CYS445 4.9 57.5 1.0
CB A:TRP442 5.0 71.7 1.0

Iodine binding site 5 out of 11 in 4uyu

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Iodine binding site 5 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1458

b:88.5
occ:1.00
 NE2 A:GLN248 3.5 32.9 1.0
CG A:GLN248 4.1 32.9 1.0
CG A:GLN209 4.1 35.5 1.0
CD1 A:LEU252 4.2 34.7 1.0
CD A:ARG213 4.2 49.7 1.0
CD A:GLN248 4.3 33.1 1.0
CD A:GLN209 4.3 38.3 1.0
CD2 A:LEU252 4.3 35.4 1.0
OE1 A:GLN209 4.5 42.4 1.0
CB A:ARG213 4.5 41.1 1.0
CG A:LEU252 4.6 35.5 1.0
NE2 A:GLN209 4.8 39.4 1.0
CG A:ARG213 4.9 46.3 1.0

Iodine binding site 6 out of 11 in 4uyu

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Iodine binding site 6 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1453

b:53.1
occ:1.00
 O B:HOH2011 3.4 33.2 1.0
NE B:ARG119 3.6 43.1 1.0
OG B:SER117 3.8 41.6 1.0
N B:ALA175 3.8 33.4 1.0
CD B:ARG119 3.9 42.0 1.0
C B:ASN174 4.0 33.8 1.0
CB B:ASN174 4.1 33.9 1.0
CA B:ALA175 4.1 33.5 1.0
CB B:ARG119 4.2 40.6 1.0
CA B:TRP172 4.3 33.1 1.0
CB B:ALA175 4.3 33.4 1.0
O B:TYR171 4.3 34.2 1.0
CA B:ASN174 4.4 33.1 1.0
N B:ASN174 4.4 32.9 1.0
CB B:SER117 4.4 42.6 1.0
O B:ASN174 4.4 35.3 1.0
O B:TRP172 4.5 32.5 1.0
C B:TRP172 4.5 32.9 1.0
CG B:ARG119 4.7 41.6 1.0
CD1 B:TRP172 4.7 33.5 1.0
CZ B:ARG119 4.8 44.5 1.0
CB B:TRP172 4.9 32.9 1.0

Iodine binding site 7 out of 11 in 4uyu

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Iodine binding site 7 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1454

b:68.0
occ:1.00
 CD B:LYS224 3.8 59.9 1.0
CG2 B:VAL225 3.9 47.0 1.0
CB B:ARG119 4.0 40.6 1.0
NH2 B:ARG119 4.0 45.9 1.0
CB B:LYS224 4.1 53.2 1.0
N B:ARG119 4.1 40.7 1.0
CZ B:ARG119 4.1 44.5 1.0
C B:ARG118 4.2 42.8 1.0
CA B:ARG119 4.3 39.7 1.0
CB B:VAL225 4.3 46.4 1.0
O B:ARG118 4.4 42.2 1.0
NE B:ARG119 4.4 43.1 1.0
NH1 B:ARG119 4.5 43.4 1.0
CG B:ARG119 4.6 41.6 1.0
CG B:LYS224 4.6 57.7 1.0
N B:VAL225 4.6 46.9 1.0
CB B:ARG118 4.7 47.5 1.0
CA B:ARG118 4.9 44.0 1.0

Iodine binding site 8 out of 11 in 4uyu

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Iodine binding site 8 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1455

b:74.7
occ:0.50
 OE2 B:GLU247 3.0 68.7 1.0
N B:ARG244 3.8 45.5 1.0
N B:GLU304 3.9 57.0 1.0
CA B:PRO303 4.0 49.0 1.0
CA B:ARG244 4.1 47.9 1.0
CD B:GLU247 4.1 68.4 1.0
CB B:ASP243 4.1 44.2 1.0
C B:ASP243 4.1 45.0 1.0
CB B:PRO303 4.2 48.2 1.0
CB B:ARG244 4.2 50.8 1.0
NH2 B:ARG305 4.4 82.5 1.0
C B:PRO303 4.4 53.0 1.0
O B:ASP243 4.5 46.3 1.0
NH2 B:ARG244 4.6 65.5 1.0
OE1 B:GLU247 4.7 72.4 1.0
CA B:ASP243 4.7 43.7 1.0
CB B:GLU304 4.8 65.4 1.0
CZ B:ARG244 4.9 65.4 1.0
CA B:GLU304 4.9 61.6 1.0
NE B:ARG244 4.9 62.6 1.0

Iodine binding site 9 out of 11 in 4uyu

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Iodine binding site 9 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1456

b:95.4
occ:1.00
 NE B:ARG139 3.8 50.9 1.0
CG B:ARG139 3.9 49.2 1.0
CD B:ARG139 4.3 48.9 1.0
O B:TYR129 4.4 43.7 1.0
CB B:TRP128 4.5 41.0 1.0
CB B:ARG139 4.6 50.6 1.0
CZ B:ARG139 4.8 51.5 1.0
NH2 B:ARG139 4.8 49.3 1.0
CG2 B:THR282 4.9 63.4 1.0
CB B:THR282 4.9 63.7 1.0

Iodine binding site 10 out of 11 in 4uyu

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Iodine binding site 10 out of 11 in the Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of the Wnt Deacylase Notum - Crystal Form I Iodide Complex - 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1457

b:71.0
occ:0.50
 NE2 B:GLN248 3.3 46.5 1.0
CD1 B:LEU252 4.0 59.7 1.0
CD B:ARG213 4.1 68.2 1.0
CG B:GLN209 4.1 45.6 1.0
NH1 B:ARG213 4.2 78.3 1.0
CD B:GLN209 4.2 47.2 1.0
CD B:GLN248 4.2 47.7 1.0
CG B:GLN248 4.3 49.2 1.0
OE1 B:GLN209 4.5 47.8 1.0
CB B:ARG213 4.6 57.1 1.0
NE2 B:GLN209 4.6 48.5 1.0
CG B:LEU252 4.6 60.9 1.0
CD2 B:LEU252 4.7 61.5 1.0
CG B:ARG213 4.8 63.2 1.0

Reference:

S.Kakugawa, P.F.Langton, M.Zebisch, S.A.Howell, T.-H.Chang, Y.Liu, T.Feizi, G.Bineva, N.O'reilly, A.P.Snijders, E.Y.Jones, J.-P.Vincent. Notum Deacylates Wnt Proteins to Suppress Signalling Activity Nature 2015.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14259
Page generated: Sun Dec 13 19:37:13 2020

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