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Iodine in PDB 5cnk: MGLUR3 with Glutamate

Protein crystallography data

The structure of MGLUR3 with Glutamate, PDB code: 5cnk was solved by J.A.Monn, D.K.Clawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.38 / 3.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.344, 80.004, 206.861, 90.00, 130.73, 90.00
R / Rfree (%) 22.1 / 25.8

Iodine Binding Sites:

The binding sites of Iodine atom in the MGLUR3 with Glutamate (pdb code 5cnk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the MGLUR3 with Glutamate, PDB code: 5cnk:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 5cnk

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Iodine binding site 1 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:53.5
occ:1.00
 OD1 A:ASP63 3.2 69.0 1.0
NZ A:LYS358 3.7 11.2 1.0
NE2 A:GLN67 3.7 58.0 1.0
CE1 A:PHE354 4.0 40.6 1.0
CZ A:PHE354 4.1 39.7 1.0
CE2 A:PHE337 4.2 31.2 1.0
CB A:GLU62 4.2 38.7 1.0
CD1 A:TYR384 4.4 52.8 1.0
CG A:GLN67 4.4 51.1 1.0
O A:GLU62 4.4 47.2 1.0
CE A:LYS358 4.4 30.7 1.0
C A:GLU62 4.5 45.8 1.0
CG A:ASP63 4.5 66.5 1.0
CD A:GLN67 4.5 63.2 1.0
OE2 A:GLU62 4.6 80.0 1.0
CD A:LYS358 4.7 32.0 1.0
CZ A:PHE337 4.7 29.9 1.0
N A:ASP63 4.8 43.4 1.0
O A:ASN383 4.8 52.0 1.0
CA A:GLU62 4.9 37.4 1.0
CB A:TYR384 4.9 48.2 1.0

Iodine binding site 2 out of 10 in 5cnk

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Iodine binding site 2 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:45.8
occ:1.00
 OG A:SER152 3.4 53.7 1.0
N A:SER152 3.7 30.1 1.0
CB A:SER152 3.7 36.0 1.0
NE A:ARG277 3.7 33.0 1.0
N A:TYR222 3.9 43.9 1.0
CB A:TYR222 3.9 43.6 1.0
N A:SER151 4.1 27.7 1.0
N A:ASP221 4.3 39.2 1.0
CB A:TYR150 4.3 36.6 1.0
CA A:SER152 4.3 31.0 1.0
CG A:ARG277 4.5 20.1 1.0
CD1 A:TYR150 4.5 42.0 1.0
NH2 A:ARG277 4.5 40.6 1.0
CD A:ARG277 4.5 15.4 1.0
CA A:TYR222 4.5 42.3 1.0
CZ A:ARG277 4.6 48.4 1.0
OXT A:GGL601 4.6 35.4 1.0
C A:SER151 4.6 31.2 1.0
CB A:SER151 4.6 25.3 1.0
CA A:SER151 4.7 26.0 1.0
C A:TYR150 4.7 35.0 1.0
CA A:TYR150 4.8 34.6 1.0
C A:ASP221 4.8 49.1 1.0
C A:GLY220 4.8 40.6 1.0
CG A:TYR150 4.8 39.3 1.0
CA A:ASP221 4.8 41.4 1.0
CA A:GLY220 4.9 37.8 1.0
CB A:ASP221 4.9 44.2 1.0

Iodine binding site 3 out of 10 in 5cnk

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Iodine binding site 3 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:69.5
occ:1.00
 OG1 A:THR98 3.2 49.8 1.0
N A:SER149 3.4 43.4 1.0
CG2 A:VAL153 3.6 34.2 1.0
N A:TYR150 3.7 35.3 1.0
CB A:SER149 3.7 44.0 1.0
CG2 A:THR98 3.8 45.2 1.0
CB A:THR98 3.8 49.2 1.0
CG1 A:VAL153 3.8 34.5 1.0
CD2 A:TYR150 3.9 41.2 1.0
CB A:PRO46 3.9 24.2 1.0
CD A:PRO46 3.9 24.1 1.0
N A:PRO46 4.0 23.6 1.0
CA A:SER149 4.0 41.4 1.0
CG A:PRO46 4.0 28.3 1.0
CA A:GLY148 4.3 45.6 1.0
CB A:VAL153 4.3 34.8 1.0
C A:GLY148 4.3 48.9 1.0
C A:SER149 4.3 41.2 1.0
CA A:PRO46 4.3 23.2 1.0
OG A:SER149 4.4 49.0 1.0
C A:PHE45 4.4 30.3 1.0
CB A:TYR150 4.5 36.6 1.0
CG A:TYR150 4.6 39.3 1.0
CA A:TYR150 4.6 34.6 1.0
CE2 A:TYR150 4.7 43.5 1.0
CA A:PHE45 4.9 28.7 1.0
O A:TYR150 4.9 35.2 1.0
O A:LEU44 4.9 30.8 1.0

Iodine binding site 4 out of 10 in 5cnk

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Iodine binding site 4 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:93.0
occ:1.00
 NE2 B:HIS346 3.2 59.6 1.0
OD2 A:ASP257 3.4 61.3 1.0
CD1 B:TYR343 3.6 52.0 1.0
N A:TYR256 3.6 37.3 1.0
CE1 B:HIS346 3.6 59.3 1.0
CB A:SER255 3.9 49.0 1.0
N A:ASP257 4.0 38.2 1.0
CE1 B:TYR343 4.1 52.1 1.0
CB A:TYR256 4.1 34.8 1.0
CD2 B:HIS346 4.2 59.4 1.0
CA A:TYR256 4.3 35.3 1.0
CA A:SER255 4.4 45.1 1.0
CG A:ASP257 4.4 54.2 1.0
OG A:SER255 4.4 59.5 1.0
C A:SER255 4.5 43.9 1.0
CA B:TYR343 4.5 43.3 1.0
CB A:ASP257 4.5 39.8 1.0
O B:PRO342 4.5 44.4 1.0
CD1 A:TYR256 4.6 38.5 1.0
NH1 A:ARG290 4.7 64.2 1.0
CG B:TYR343 4.7 49.5 1.0
C A:TYR256 4.7 42.2 1.0
O B:TYR343 4.8 51.3 1.0
ND1 B:HIS346 4.8 59.5 1.0
CB B:TYR343 4.9 45.3 1.0
CG A:TYR256 4.9 36.1 1.0
CA A:ASP257 4.9 38.0 1.0

Iodine binding site 5 out of 10 in 5cnk

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Iodine binding site 5 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I601

b:57.4
occ:1.00
 NE2 B:GLN67 3.6 17.0 1.0
OD1 B:ASP63 3.6 68.3 1.0
NZ B:LYS358 3.8 32.6 1.0
CE2 B:PHE337 4.0 35.7 1.0
CZ B:PHE354 4.0 37.4 1.0
CE1 B:PHE354 4.0 37.9 1.0
CD1 B:TYR384 4.2 46.1 1.0
CZ B:PHE337 4.2 33.4 1.0
CG B:GLN67 4.3 13.3 1.0
CB B:GLU62 4.4 38.5 1.0
CD B:GLN67 4.4 21.5 1.0
CE B:LYS358 4.4 30.3 1.0
O B:GLU62 4.4 39.8 1.0
C B:GLU62 4.5 38.8 1.0
CD B:LYS358 4.6 40.8 1.0
CG B:ASP63 4.7 62.7 1.0
OE2 B:GLU62 4.7 35.2 1.0
N B:ASP63 4.8 32.3 1.0
CB B:TYR384 4.9 40.6 1.0
O B:ASN383 5.0 40.5 1.0
CA B:ASP63 5.0 31.8 1.0
CE1 B:TYR384 5.0 46.1 1.0
CA B:GLU62 5.0 37.0 1.0

Iodine binding site 6 out of 10 in 5cnk

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Iodine binding site 6 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I602

b:84.3
occ:1.00
 N B:SER149 3.3 29.1 1.0
OG1 B:THR98 3.3 50.9 1.0
CG2 B:VAL153 3.5 34.8 1.0
CB B:SER149 3.6 35.0 1.0
N B:TYR150 3.6 21.3 1.0
CG2 B:THR98 3.8 48.7 1.0
CG1 B:VAL153 3.8 35.1 1.0
CA B:SER149 3.9 28.3 1.0
CB B:THR98 3.9 49.2 1.0
CD2 B:TYR150 4.0 21.8 1.0
CD B:PRO46 4.0 15.4 1.0
CB B:PRO46 4.1 16.2 1.0
N B:PRO46 4.1 15.1 1.0
CG B:PRO46 4.2 19.1 1.0
CA B:GLY148 4.2 34.1 1.0
C B:GLY148 4.2 34.2 1.0
CB B:VAL153 4.3 35.2 1.0
C B:SER149 4.3 28.2 1.0
C B:PHE45 4.4 22.2 1.0
CB B:TYR150 4.5 19.8 1.0
CA B:PRO46 4.5 14.4 1.0
OG B:SER149 4.6 49.1 1.0
CA B:TYR150 4.6 19.5 1.0
CG B:TYR150 4.7 20.4 1.0
CA B:PHE45 4.7 20.7 1.0
O B:LEU44 4.8 24.5 1.0
O B:TYR150 4.8 21.7 1.0
N B:GLY148 4.9 36.0 1.0
CE2 B:TYR150 4.9 22.9 1.0
N B:PHE45 5.0 21.4 1.0
O B:PHE45 5.0 24.3 1.0

Iodine binding site 7 out of 10 in 5cnk

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Iodine binding site 7 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I603

b:51.4
occ:1.00
 NE B:ARG277 3.4 3.0 1.0
OG B:SER152 3.6 42.5 1.0
N B:SER152 3.9 28.3 1.0
CB B:TYR222 3.9 46.9 1.0
CB B:SER152 3.9 33.7 1.0
N B:TYR222 4.0 47.1 1.0
CG B:ARG277 4.1 26.6 1.0
CD B:ARG277 4.2 7.4 1.0
N B:SER151 4.2 20.7 1.0
CB B:TYR150 4.3 19.8 1.0
NH2 B:ARG277 4.3 24.1 1.0
CZ B:ARG277 4.3 26.6 1.0
CD1 B:TYR150 4.4 21.6 1.0
N B:ASP221 4.5 51.4 1.0
CA B:SER152 4.5 29.2 1.0
O B:HOH704 4.6 3.0 1.0
CA B:TYR222 4.6 46.6 1.0
CB B:SER151 4.8 25.1 1.0
C B:TYR150 4.8 22.7 1.0
CG B:TYR150 4.8 20.4 1.0
C B:SER151 4.8 30.2 1.0
CA B:SER151 4.8 21.5 1.0
CA B:TYR150 4.9 19.5 1.0
CA B:GLY220 5.0 48.9 1.0

Iodine binding site 8 out of 10 in 5cnk

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Iodine binding site 8 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I601

b:62.0
occ:1.00
 OD1 C:ASP63 3.3 82.7 1.0
NE2 C:GLN67 3.5 27.8 1.0
NZ C:LYS358 3.8 22.9 1.0
CE2 C:PHE337 4.0 50.1 1.0
CZ C:PHE354 4.1 53.6 1.0
CE1 C:PHE354 4.1 54.8 1.0
CD1 C:TYR384 4.2 56.9 1.0
CZ C:PHE337 4.3 47.2 1.0
CG C:GLN67 4.3 38.9 1.0
CE C:LYS358 4.4 21.6 1.0
CB C:GLU62 4.4 42.1 1.0
CD C:GLN67 4.4 47.6 1.0
O C:GLU62 4.5 41.3 1.0
CG C:ASP63 4.5 78.8 1.0
C C:GLU62 4.6 43.0 1.0
CD C:LYS358 4.6 34.2 1.0
OE2 C:GLU62 4.7 78.5 1.0
N C:ASP63 4.9 40.7 1.0
CB C:TYR384 4.9 52.5 1.0
O C:ASN383 5.0 56.8 1.0
CE1 C:TYR384 5.0 57.5 1.0

Iodine binding site 9 out of 10 in 5cnk

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Iodine binding site 9 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I602

b:42.8
occ:1.00
 O C:HOH706 3.0 3.0 1.0
OG C:SER152 3.6 42.3 1.0
NE C:ARG277 3.7 4.2 1.0
CB C:SER152 3.8 33.0 1.0
N C:SER152 3.8 29.5 1.0
CB C:TYR222 3.9 39.4 1.0
N C:TYR222 3.9 42.1 1.0
NH2 C:ARG277 4.0 33.8 1.0
N C:ASP221 4.2 47.8 1.0
CZ C:ARG277 4.3 33.1 1.0
N C:SER151 4.3 27.4 1.0
CA C:SER152 4.4 29.2 1.0
CA C:TYR222 4.5 39.8 1.0
CD2 C:TYR150 4.5 23.9 1.0
CB C:TYR150 4.5 22.2 1.0
CG C:ARG277 4.7 26.6 1.0
CD C:ARG277 4.7 8.0 1.0
CA C:GLY220 4.7 44.0 1.0
CB C:SER151 4.7 30.9 1.0
C C:GLY220 4.7 49.6 1.0
C C:SER151 4.8 33.3 1.0
CA C:ASP221 4.8 48.1 1.0
CA C:SER151 4.8 28.0 1.0
C C:ASP221 4.8 49.3 1.0
CB C:ASP221 4.9 50.7 1.0
C C:TYR150 4.9 28.3 1.0

Iodine binding site 10 out of 10 in 5cnk

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Iodine binding site 10 out of 10 in the MGLUR3 with Glutamate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of MGLUR3 with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I603

b:78.9
occ:1.00
 OG1 C:THR98 3.2 73.2 1.0
N C:SER149 3.5 24.3 1.0
CB C:SER149 3.6 24.6 1.0
CG2 C:VAL153 3.6 27.1 1.0
N C:TYR150 3.7 22.4 1.0
CG2 C:THR98 3.8 68.1 1.0
CG1 C:VAL153 3.8 27.0 1.0
CB C:THR98 3.8 68.4 1.0
CD1 C:TYR150 3.9 23.9 1.0
CB C:PRO46 3.9 20.4 1.0
CD C:PRO46 3.9 18.9 1.0
CA C:SER149 4.0 23.1 1.0
CG C:PRO46 4.0 23.4 1.0
N C:PRO46 4.0 18.3 1.0
CB C:VAL153 4.3 27.6 1.0
C C:SER149 4.4 26.2 1.0
CA C:PRO46 4.4 19.2 1.0
CB C:TYR150 4.5 22.2 1.0
OG C:SER149 4.5 31.3 1.0
C C:PHE45 4.5 24.6 1.0
C C:GLY148 4.5 29.1 1.0
CA C:GLY148 4.6 29.0 1.0
CG C:TYR150 4.7 22.6 1.0
CA C:TYR150 4.7 22.1 1.0
O C:LEU44 4.7 30.7 1.0
CE1 C:TYR150 4.7 26.1 1.0
CA C:PHE45 4.9 25.3 1.0
O C:TYR150 5.0 28.2 1.0

Reference:

J.A.Monn, L.Prieto, L.Taboada, J.Hao, M.R.Reinhard, S.S.Henry, C.D.Beadle, L.Walton, T.Man, H.Rudyk, B.Clark, D.Tupper, S.R.Baker, C.Lamas, C.Montero, A.Marcos, J.Blanco, M.Bures, D.K.Clawson, S.Atwell, F.Lu, J.Wang, M.Russell, B.A.Heinz, X.Wang, J.H.Carter, B.G.Getman, J.T.Catlow, S.Swanson, B.G.Johnson, D.B.Shaw, D.L.Mckinzie. Synthesis and Pharmacological Characterization of C4-(Thiotriazolyl) -Substituted-2-Aminobicyclo[3.1.0]Hexane-2,6-Dicarboxylates. Identification of (1R,2S,4R,5R,6R)-2-Amino-4-(1H-1,2,4-Triazol-3-Ylsulfanyl) Bicyclo[3.1.0]Hexane-2,6-Dicarboxylic Acid (LY2812223), A Highly Potent, Functionally Selective MGLU2 Receptor Agonist. J.Med.Chem. V. 58 7526 2015.
ISSN: ISSN 0022-2623
PubMed: 26313429
DOI: 10.1021/ACS.JMEDCHEM.5B01124
Page generated: Sun Aug 11 20:39:00 2024

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