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Iodine in PDB 3lnx: Second Pdz Domain From Human PTP1E

Protein crystallography data

The structure of Second Pdz Domain From Human PTP1E, PDB code: 3lnx was solved by J.Zhang, A.Chang, H.Ke, G.N.Phillips Jr., A.L.Lee, Center For Eukaryoticstructural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.64 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.023, 95.148, 101.989, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.7

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Iodine atom in the Second Pdz Domain From Human PTP1E (pdb code 3lnx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 25 binding sites of Iodine where determined in the Second Pdz Domain From Human PTP1E, PDB code: 3lnx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 25 in 3lnx

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Iodine binding site 1 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I97

b:28.8
occ:1.00
O A:HOH332 3.4 39.7 1.0
O A:HOH180 3.6 43.9 1.0
N A:LEU18 3.6 28.4 1.0
O A:HOH383 3.7 41.9 1.0
O A:LEU78 4.1 28.8 1.0
CG A:LEU18 4.1 30.7 1.0
O A:HOH391 4.1 43.8 1.0
CA A:SER17 4.2 32.5 1.0
CA A:ARG79 4.2 26.0 0.4
CD1 A:LEU18 4.2 29.1 1.0
CB A:LEU18 4.2 24.4 1.0
CA A:ARG79 4.2 25.9 0.6
CG A:ARG79 4.3 32.5 0.6
C A:LEU78 4.3 26.0 1.0
CG A:ARG79 4.3 31.3 0.4
N A:ARG79 4.4 24.8 0.4
C A:SER17 4.4 31.1 1.0
N A:ARG79 4.4 24.4 0.6
OG A:SER17 4.5 35.8 1.0
CA A:LEU18 4.5 27.6 1.0
O A:ASN16 4.6 39.5 1.0
CB A:LEU78 4.7 27.0 1.0
CE A:LYS13 4.7 33.6 1.0
CB A:ARG79 4.8 29.2 0.4
CB A:SER17 4.8 36.5 1.0
CB A:ARG79 4.8 29.9 0.6

Iodine binding site 2 out of 25 in 3lnx

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Iodine binding site 2 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I98

b:35.0
occ:1.00
NE2 F:GLN83 3.6 54.7 1.0
CG F:GLN83 3.7 53.3 1.0
NE2 E:GLN83 3.8 48.1 1.0
CG A:GLN83 3.9 38.8 1.0
CB F:ALA12 4.0 49.6 1.0
CG2 F:VAL84 4.0 39.5 1.0
CG E:GLN83 4.0 44.5 1.0
NE2 A:GLN83 4.1 39.4 1.0
CG2 A:VAL84 4.1 30.6 1.0
CD F:GLN83 4.2 54.5 1.0
CB E:ALA12 4.2 43.8 1.0
CG2 E:VAL84 4.3 39.4 1.0
CB A:ALA12 4.4 32.2 1.0
CD E:GLN83 4.5 48.3 1.0
CD A:GLN83 4.5 38.9 1.0

Iodine binding site 3 out of 25 in 3lnx

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Iodine binding site 3 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I99

b:45.2
occ:1.00
N A:ARG31 3.5 50.1 1.0
CG A:ARG31 3.7 58.9 1.0
CA A:VAL30 3.9 37.4 1.0
CD A:ARG31 3.9 65.5 1.0
O A:SER29 4.2 49.0 1.0
C A:VAL30 4.2 48.2 1.0
CB A:ARG31 4.3 57.7 1.0
CA A:ARG31 4.5 50.5 1.0
CG1 A:VAL30 4.6 40.9 1.0
CB A:VAL30 4.6 36.5 1.0
CG2 A:VAL30 4.8 36.9 1.0
N A:VAL30 4.9 40.1 1.0
C A:SER29 5.0 44.9 1.0

Iodine binding site 4 out of 25 in 3lnx

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Iodine binding site 4 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I100

b:52.9
occ:1.00
O A:HOH312 3.5 36.6 1.0
CG A:LYS72 3.8 38.8 1.0
CA A:LYS72 3.9 28.8 1.0
CB A:LYS72 4.2 31.6 1.0
CB A:VAL75 4.2 24.2 1.0
CD2 A:HIS71 4.3 28.8 1.0
CG1 A:VAL75 4.3 24.8 1.0
CG2 A:VAL75 4.4 24.0 1.0
N A:LYS72 4.6 27.9 1.0
CD A:LYS72 4.8 43.0 1.0
O A:LYS72 4.8 27.9 1.0
C A:LYS72 4.9 26.4 1.0
O A:HIS71 4.9 23.8 1.0
NE2 A:HIS71 4.9 27.8 1.0
C A:HIS71 5.0 23.9 1.0

Iodine binding site 5 out of 25 in 3lnx

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Iodine binding site 5 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I101

b:0.4
occ:1.00
ND2 A:ASN14 3.5 48.1 1.0
OG A:SER48 3.5 43.9 1.0
CB A:SER48 3.6 36.6 1.0
OD1 A:ASN14 3.7 52.7 1.0
O A:HOH483 3.8 36.5 1.0
CG A:ASN14 4.0 47.8 1.0
N E:GLN83 4.1 34.8 1.0
CA E:GLY82 4.1 35.7 1.0
C E:GLY82 4.4 34.6 1.0
O A:HOH166 4.4 38.8 1.0
O E:THR81 4.7 40.1 1.0
CB E:GLN83 4.7 43.1 1.0
CA E:GLN83 4.8 39.0 1.0

Iodine binding site 6 out of 25 in 3lnx

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Iodine binding site 6 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I102

b:84.3
occ:1.00
O A:HOH223 3.3 31.3 1.0
NZ A:LYS91 3.3 35.8 0.7
CD A:PRO1 3.8 32.4 1.0
O A:HOH519 3.8 47.5 1.0
CE A:LYS91 3.9 36.1 0.7
O A:HOH108 3.9 30.5 1.0
N A:PRO1 4.0 29.3 1.0
CE A:LYS91 4.0 35.2 0.3
NZ A:LYS91 4.2 36.9 0.3
CD A:LYS91 4.2 31.8 0.3
CE1 A:HIS53 4.2 38.9 1.0
CG A:PRO1 4.2 33.9 1.0
O A:ARG51 4.3 30.6 1.0
CD A:LYS91 4.4 31.9 0.7
ND1 A:HIS53 4.4 37.6 1.0
NZ C:LYS2 4.4 53.8 1.0
O A:PRO1 4.5 30.3 1.0
CE C:LYS2 4.9 47.6 1.0
CB A:PRO1 5.0 28.9 1.0

Iodine binding site 7 out of 25 in 3lnx

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Iodine binding site 7 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I97

b:28.2
occ:1.00
O B:HOH214 3.5 31.8 1.0
N B:LEU18 3.6 19.8 1.0
O B:HOH143 3.7 36.9 1.0
CG B:LEU18 4.1 22.7 1.0
O B:LEU78 4.1 27.9 1.0
CD1 B:LEU18 4.1 24.6 1.0
CA B:SER17 4.2 21.2 1.0
CB B:LEU18 4.2 18.9 1.0
C B:LEU78 4.3 26.1 1.0
CA B:ARG79 4.4 26.7 1.0
CG B:ARG79 4.4 34.5 1.0
N B:ARG79 4.4 23.8 1.0
C B:SER17 4.4 20.3 1.0
OG B:SER17 4.5 24.2 1.0
CB B:LEU78 4.5 24.5 1.0
O B:ASN16 4.5 22.5 1.0
CA B:LEU18 4.6 20.5 1.0
CE B:LYS13 4.8 22.9 1.0
CB B:SER17 4.9 23.2 1.0
CB B:ARG79 5.0 30.4 1.0

Iodine binding site 8 out of 25 in 3lnx

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Iodine binding site 8 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I98

b:25.1
occ:1.00
O C:HOH249 3.3 45.1 1.0
NE2 C:GLN83 3.6 32.3 1.0
NE2 D:GLN83 3.7 30.1 1.0
NE2 B:GLN83 3.8 28.4 1.0
CG C:GLN83 3.8 27.9 1.0
CG B:GLN83 3.8 24.8 1.0
CG D:GLN83 3.8 29.8 1.0
CG2 C:VAL84 4.0 26.5 1.0
CG2 B:VAL84 4.0 16.8 0.6
CG2 D:VAL84 4.0 25.7 1.0
CB C:ALA12 4.0 22.5 1.0
CB B:ALA12 4.1 21.2 1.0
CB D:ALA12 4.2 26.7 1.0
CD C:GLN83 4.3 30.4 1.0
CD D:GLN83 4.3 31.1 1.0
CD B:GLN83 4.3 28.4 1.0

Iodine binding site 9 out of 25 in 3lnx

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Iodine binding site 9 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I99

b:0.6
occ:1.00
O B:HOH532 3.6 42.8 1.0
ND1 B:HIS71 3.9 35.1 1.0
CA B:LYS72 4.1 28.8 1.0
CE1 B:HIS71 4.1 34.4 1.0
CG2 B:VAL75 4.1 23.1 1.0
CB B:VAL75 4.2 22.9 1.0
CG1 B:VAL75 4.3 25.4 1.0
CG B:LYS72 4.4 42.5 1.0
CB B:LYS72 4.5 31.9 1.0
N B:LYS72 4.7 29.4 1.0
O B:HIS71 5.0 24.3 1.0

Iodine binding site 10 out of 25 in 3lnx

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Iodine binding site 10 out of 25 in the Second Pdz Domain From Human PTP1E


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Second Pdz Domain From Human PTP1E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I100

b:74.3
occ:1.00
O B:HOH124 3.2 32.1 1.0
NZ B:LYS91 3.6 35.5 1.0
CD B:PRO1 3.7 29.8 1.0
CE B:LYS91 3.9 34.2 1.0
N B:PRO1 3.9 28.2 1.0
O B:HOH232 4.0 48.3 1.0
O B:HOH246 4.1 29.2 1.0
O B:ARG51 4.2 23.5 1.0
CG B:PRO1 4.2 29.2 1.0
CE1 B:HIS53 4.3 30.5 1.0
O B:PRO1 4.4 30.9 1.0
NZ F:LYS2 4.4 57.3 1.0
CD B:LYS91 4.5 31.5 1.0
ND1 B:HIS53 4.6 30.9 1.0
CD F:LYS2 4.9 50.8 1.0
CB B:PRO1 5.0 28.6 1.0
CA B:PRO1 5.0 28.0 1.0

Reference:

J.Zhang, P.J.Sapienza, H.Ke, A.Chang, S.R.Hengel, H.Wang, G.N.Phillips, A.L.Lee. Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second Pdz Domain of Protein Tyrosine Phosphatase 1E. Biochemistry V. 49 9280 2010.
ISSN: ISSN 0006-2960
PubMed: 20839809
DOI: 10.1021/BI101131F
Page generated: Sun Dec 13 19:28:15 2020

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