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Iodine in PDB 7f5o: Crystal Structure of PTPN2 Catalytic Domain

Enzymatic activity of Crystal Structure of PTPN2 Catalytic Domain

All present enzymatic activity of Crystal Structure of PTPN2 Catalytic Domain:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of PTPN2 Catalytic Domain, PDB code: 7f5o was solved by J.P.Singh, M.-J.Lin, S.-F.Hsu, C.-C.Lee, T.-C.Meng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.094, 68.187, 72.683, 111.54, 102.66, 92.34
R / Rfree (%) 19.9 / 24.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of PTPN2 Catalytic Domain (pdb code 7f5o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of PTPN2 Catalytic Domain, PDB code: 7f5o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 7f5o

Go back to Iodine Binding Sites List in 7f5o
Iodine binding site 1 out of 6 in the Crystal Structure of PTPN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of PTPN2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:8.6
occ:1.00
 N A:PHE183 3.6 8.0 1.0
NE A:ARG222 3.6 5.0 1.0
N A:ARG222 3.7 5.6 1.0
CA A:GLY221 3.7 6.4 1.0
NE2 A:GLN264 3.9 8.1 1.0
CG A:ARG222 3.9 5.0 1.0
O A:HOH593 3.9 3.7 1.0
CA A:PHE183 4.0 8.1 1.0
C A:GLY221 4.2 5.9 1.0
CD1 A:PHE183 4.2 9.8 1.0
CD A:ARG222 4.3 5.1 1.0
CZ A:ARG222 4.3 5.1 1.0
NH1 A:ARG222 4.3 5.4 1.0
N A:GLY221 4.4 6.8 1.0
CE1 A:PHE183 4.5 10.5 1.0
OG A:SER217 4.6 4.7 1.0
CG A:PHE183 4.6 8.9 1.0
CB A:ARG222 4.6 5.1 1.0
C A:ASP182 4.6 9.4 1.0
CA A:ASP182 4.7 10.1 1.0
CB A:GLN260 4.8 11.1 1.0
CD A:GLN264 4.8 9.3 1.0
CA A:ARG222 4.8 5.4 1.0
OE1 A:GLN264 4.8 9.9 1.0
CG A:GLN260 4.9 12.2 1.0
CB A:PHE183 5.0 7.8 1.0
SG A:CYS216 5.0 4.8 1.0

Iodine binding site 2 out of 6 in 7f5o

Go back to Iodine Binding Sites List in 7f5o
Iodine binding site 2 out of 6 in the Crystal Structure of PTPN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of PTPN2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:23.8
occ:1.00
 O A:HOH649 3.6 16.9 1.0
N A:ILE115 3.7 8.0 1.0
CE1 A:HIS176 3.8 8.1 1.0
CG1 A:ILE115 3.9 11.4 1.0
CA A:ARG114 4.0 7.5 1.0
CB A:ARG114 4.1 9.4 1.0
O A:HOH529 4.1 22.4 1.0
CB A:ILE115 4.3 9.6 1.0
C A:ARG114 4.3 7.2 1.0
NE2 A:HIS176 4.4 7.6 1.0
CG A:ARG114 4.4 12.1 1.0
CZ A:ARG114 4.5 25.0 1.0
NH1 A:ARG114 4.5 27.7 1.0
NE A:ARG114 4.6 20.2 1.0
CA A:ILE115 4.7 8.8 1.0
NH2 A:ARG114 4.9 27.9 1.0
ND1 A:HIS176 5.0 7.6 1.0

Iodine binding site 3 out of 6 in 7f5o

Go back to Iodine Binding Sites List in 7f5o
Iodine binding site 3 out of 6 in the Crystal Structure of PTPN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of PTPN2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:23.0
occ:1.00
 O A:HOH534 3.6 11.5 1.0
CB A:TYR48 3.8 4.7 1.0
N A:ASP50 3.9 7.0 1.0
CB A:ASP50 4.0 10.2 1.0
CG2 A:VAL51 4.1 7.8 1.0
CA A:ASP50 4.2 7.4 1.0
C A:ASP50 4.3 7.2 1.0
CG A:TYR48 4.4 4.5 1.0
N A:VAL51 4.4 6.4 1.0
N A:ARG49 4.6 6.3 1.0
O A:ASP50 4.8 8.2 1.0
CA A:TYR48 4.8 5.0 1.0
C A:TYR48 4.8 5.7 1.0
OD2 A:ASP50 4.9 12.6 1.0
CD1 A:TYR48 4.9 4.7 1.0
CG A:ASP50 5.0 11.3 1.0

Iodine binding site 4 out of 6 in 7f5o

Go back to Iodine Binding Sites List in 7f5o
Iodine binding site 4 out of 6 in the Crystal Structure of PTPN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of PTPN2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:27.4
occ:1.00
 O B:HOH628 3.0 34.6 1.0
N B:PHE183 3.5 33.5 1.0
N B:ARG222 3.6 13.6 1.0
O B:HOH582 3.7 14.6 1.0
NE B:ARG222 3.8 14.8 1.0
OD1 B:ASP182 3.8 29.3 1.0
NE2 B:GLN264 3.8 22.8 1.0
CA B:GLY221 3.9 15.6 1.0
CA B:PHE183 3.9 33.8 1.0
CG B:ARG222 4.0 13.7 1.0
CD1 B:PHE183 4.2 48.5 1.0
C B:GLY221 4.2 14.8 1.0
OG B:SER217 4.4 24.1 1.0
N B:GLY221 4.4 15.2 1.0
NH1 B:ARG222 4.4 14.4 1.0
CD B:ARG222 4.5 13.8 1.0
CZ B:ARG222 4.5 14.6 1.0
CE1 B:PHE183 4.6 48.7 1.0
C B:ASP182 4.6 29.8 1.0
CB B:ARG222 4.6 13.6 1.0
CG B:PHE183 4.6 43.5 1.0
O B:HOH509 4.7 47.3 1.0
CB B:GLN260 4.7 26.2 1.0
OE1 B:GLN264 4.7 25.5 1.0
CD B:GLN264 4.7 26.7 1.0
CA B:ARG222 4.7 13.1 1.0
CA B:ASP182 4.7 29.6 1.0
CG B:ASP182 4.8 32.2 1.0
CG B:GLN260 4.9 28.2 1.0
SG B:CYS216 4.9 14.8 1.0
CB B:PHE183 4.9 37.5 1.0
C B:PHE183 5.0 31.8 1.0

Iodine binding site 5 out of 6 in 7f5o

Go back to Iodine Binding Sites List in 7f5o
Iodine binding site 5 out of 6 in the Crystal Structure of PTPN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of PTPN2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I401

b:25.0
occ:1.00
 O A:HOH558 2.8 47.8 1.0
N C:PHE183 3.4 15.7 1.0
NE C:ARG222 3.7 8.1 1.0
N C:ARG222 3.8 9.1 1.0
O C:HOH619 3.8 8.6 1.0
CA C:GLY221 3.8 8.1 1.0
OD1 C:ASP182 3.8 26.8 1.0
NE2 C:GLN264 3.9 11.2 1.0
OE1 A:GLU65 4.0 19.1 1.0
CG C:ARG222 4.0 8.2 1.0
CA C:PHE183 4.0 14.6 1.0
C C:GLY221 4.3 8.6 1.0
CD C:ARG222 4.3 8.1 1.0
N C:GLY221 4.3 8.2 1.0
C C:ASP182 4.4 15.2 1.0
CZ C:ARG222 4.4 7.6 1.0
CA C:ASP182 4.5 16.0 1.0
NH1 C:ARG222 4.5 7.8 1.0
CG C:PHE183 4.6 16.3 1.0
CB C:ARG222 4.6 8.4 1.0
OG C:SER217 4.6 10.1 1.0
CD1 C:PHE183 4.7 20.1 1.0
CD2 C:PHE183 4.8 17.6 1.0
CA C:ARG222 4.8 8.6 1.0
O C:HOH527 4.8 17.8 1.0
CB C:GLN260 4.8 15.6 1.0
CD C:GLN264 4.9 13.0 1.0
CG C:ASP182 4.9 24.3 1.0
SG C:CYS216 4.9 7.9 1.0
CB C:PHE183 4.9 15.6 1.0
OE1 C:GLN264 5.0 13.6 1.0
CE1 C:PHE183 5.0 19.5 1.0
CG C:GLN260 5.0 17.5 1.0
CE2 C:PHE183 5.0 19.3 1.0

Iodine binding site 6 out of 6 in 7f5o

Go back to Iodine Binding Sites List in 7f5o
Iodine binding site 6 out of 6 in the Crystal Structure of PTPN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of PTPN2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I402

b:31.7
occ:1.00
 O C:HOH643 3.5 17.4 1.0
N C:ILE115 3.6 10.2 1.0
CE1 C:HIS176 3.7 9.3 1.0
CG1 C:ILE115 3.9 14.2 1.0
CA C:ARG114 4.0 10.8 1.0
O C:HOH535 4.0 20.3 1.0
CB C:ARG114 4.0 12.9 1.0
CB C:ILE115 4.3 12.7 1.0
C C:ARG114 4.3 10.1 1.0
CG C:ARG114 4.3 15.3 1.0
NE2 C:HIS176 4.4 8.9 1.0
CZ C:ARG114 4.4 24.7 1.0
NH1 C:ARG114 4.4 26.0 1.0
NE C:ARG114 4.6 22.6 1.0
CA C:ILE115 4.6 11.3 1.0
ND1 C:HIS176 4.8 10.3 1.0
NH2 C:ARG114 4.8 26.1 1.0

Reference:

J.P.Singh, M.J.Lin, S.F.Hsu, W.Peti, C.C.Lee, T.C.Meng. Crystal Structure of Tcptp Unravels An Allosteric Regulatory Role of Helix Alpha 7 in Phosphatase Activity. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34910875
DOI: 10.1021/ACS.BIOCHEM.1C00519
Page generated: Thu Mar 31 03:26:11 2022

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