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Iodine in PDB 2yd2: Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma

Enzymatic activity of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma

All present enzymatic activity of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma, PDB code: 2yd2 was solved by C.H.Coles, Y.Shen, A.P.Tenney, C.Siebold, G.C.Sutton, W.Lu, J.T.Gallagher, E.Y.Jones, J.G.Flanagan, A.R.Aricescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.237 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.400, 29.490, 61.580, 90.00, 92.61, 90.00
R / Rfree (%) 19.62 / 26.02

Other elements in 2yd2:

The structure of Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma (pdb code 2yd2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma, PDB code: 2yd2:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 2yd2

Go back to Iodine Binding Sites List in 2yd2
Iodine binding site 1 out of 4 in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma


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 the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1230

b:66.0
occ:1.00
 N A:ASN222 3.7 20.0 1.0
N A:LEU143 4.0 33.4 1.0
CB A:LEU143 4.0 31.1 1.0
CA A:LEU143 4.0 29.2 1.0
CA A:ALA221 4.2 18.4 1.0
CB A:ASN222 4.5 35.3 1.0
OD1 A:ASN222 4.5 40.5 1.0
CD1 A:LEU143 4.5 34.5 1.0
C A:ALA221 4.5 23.4 1.0
CA A:ASN222 4.7 27.9 1.0
O A:PRO220 4.7 26.0 1.0
CG A:ASN222 4.8 39.2 1.0
C A:GLN142 4.8 47.0 1.0
CB A:ALA221 4.8 17.7 1.0
CG A:LEU143 4.9 32.9 1.0

Iodine binding site 2 out of 4 in 2yd2

Go back to Iodine Binding Sites List in 2yd2
Iodine binding site 2 out of 4 in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma


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 the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1231

b:53.0
occ:1.00
 N A:SER212 3.6 16.1 1.0
CG A:PRO162 3.9 18.5 1.0
CA A:ASN211 4.0 16.0 1.0
CB A:SER212 4.1 9.4 1.0
CB A:ASN211 4.1 13.1 1.0
CB A:PRO162 4.1 16.4 1.0
C A:ASN211 4.1 19.8 1.0
OG A:SER212 4.2 20.8 1.0
CA A:SER212 4.3 12.9 1.0
CD A:PRO162 4.4 15.8 1.0

Iodine binding site 3 out of 4 in 2yd2

Go back to Iodine Binding Sites List in 2yd2
Iodine binding site 3 out of 4 in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma


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 the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1232

b:62.9
occ:1.00
 NZ A:LYS204 3.5 61.9 1.0
NE2 A:GLN94 3.6 33.3 1.0
CZ A:PHE172 4.1 16.0 1.0
O A:HOH2023 4.2 35.1 1.0
CE1 A:PHE172 4.2 16.9 1.0
CE A:LYS204 4.4 58.5 1.0
CD A:LYS204 4.5 50.5 1.0
CD A:GLN94 4.6 39.1 1.0
CG A:PRO220 4.6 24.1 1.0
OE1 A:GLN94 4.6 45.5 1.0
NH2 A:ARG92 4.7 15.6 1.0

Iodine binding site 4 out of 4 in 2yd2

Go back to Iodine Binding Sites List in 2yd2
Iodine binding site 4 out of 4 in the Crystal Structure of the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma


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 the N-Terminal IG1-2 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1233

b:62.7
occ:1.00
 N A:LYS40 3.4 16.1 1.0
N A:VAL53 3.5 24.0 1.0
CA A:PRO39 3.8 20.9 1.0
C A:PRO39 4.1 21.4 1.0
CA A:PHE52 4.1 21.9 1.0
O A:SER51 4.1 11.2 1.0
O A:LYS40 4.2 30.9 1.0
CB A:LYS40 4.3 31.8 1.0
O A:VAL53 4.3 17.9 1.0
C A:PHE52 4.3 24.2 1.0
CA A:LYS40 4.3 21.7 1.0
NE2 A:GLN42 4.4 32.9 1.0
CB A:VAL53 4.4 29.2 1.0
CA A:VAL53 4.4 23.6 1.0
CB A:PRO39 4.5 23.2 1.0
CG2 A:VAL53 4.5 27.2 1.0
CG A:LYS40 4.6 39.5 1.0
O A:GLU38 4.7 35.0 1.0
CD1 A:PHE52 4.7 20.2 1.0
C A:LYS40 4.8 24.9 1.0
C A:VAL53 4.8 20.4 1.0
CD A:GLN42 4.9 37.4 1.0
CB A:PHE52 4.9 21.7 1.0
N A:PRO39 4.9 22.4 1.0
C A:SER51 5.0 15.6 1.0

Reference:

C.H.Coles, Y.Shen, A.P.Tenney, C.Siebold, G.C.Sutton, W.Lu, J.T.Gallagher, E.Y.Jones, J.G.Flanagan, A.R.Aricescu. Proteoglycan-Specific Molecular Switch For Rptp Sigma Clustering and Neuronal Extension. Science V. 332 484 2011.
ISSN: ISSN 0036-8075
PubMed: 21454754
DOI: 10.1126/SCIENCE.1200840
Page generated: Sun Aug 11 14:37:45 2024

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