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Iodine in PDB 2yd9: Crystal Structure of the N-Terminal IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma

Enzymatic activity of Crystal Structure of the N-Terminal IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma

All present enzymatic activity of Crystal Structure of the N-Terminal IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma, PDB code: 2yd9 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) 44.16 / 2.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.699, 90.043, 143.283, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 28.9

Other elements in 2yd9:

The structure of Crystal Structure of the N-Terminal IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the N-Terminal IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma (pdb code 2yd9). 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 IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma, PDB code: 2yd9:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 2yd9

Go back to Iodine Binding Sites List in 2yd9
Iodine binding site 1 out of 4 in the Crystal Structure of the N-Terminal IG1-3 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 IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1319

b:44.1
occ:0.30
 OG A:SER189 3.0 33.0 1.0
CD2 A:LEU155 3.7 30.0 1.0
CB A:SER189 3.8 34.4 1.0
CB A:ALA191 3.9 30.6 1.0
CD1 A:LEU187 4.9 30.7 1.0
CG A:LEU155 4.9 30.4 1.0

Iodine binding site 2 out of 4 in 2yd9

Go back to Iodine Binding Sites List in 2yd9
Iodine binding site 2 out of 4 in the Crystal Structure of the N-Terminal IG1-3 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 IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1320

b:47.8
occ:0.50
 CG1 A:VAL230 3.7 37.8 1.0
CA A:GLY257 3.7 34.6 1.0
O A:HOH2013 3.9 40.5 1.0
N A:GLY257 3.9 35.5 1.0
C A:GLY257 4.0 35.6 1.0
NH1 A:ARG233 4.0 59.0 1.0
CB A:VAL230 4.2 38.0 1.0
N A:SER258 4.4 36.2 1.0
O A:GLY257 4.4 36.7 1.0
CG2 A:VAL230 4.5 40.4 1.0
CB A:SER258 4.8 39.1 1.0
C A:VAL256 4.8 34.4 1.0
CG2 A:VAL256 4.9 36.3 1.0
CB A:VAL256 4.9 36.4 1.0
CZ A:ARG233 5.0 60.4 1.0

Iodine binding site 3 out of 4 in 2yd9

Go back to Iodine Binding Sites List in 2yd9
Iodine binding site 3 out of 4 in the Crystal Structure of the N-Terminal IG1-3 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 IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1321

b:46.4
occ:0.40
 NE2 A:GLN228 2.5 40.0 1.0
OG A:SER258 3.8 41.4 1.0
CD A:GLN228 3.8 40.7 1.0
CA A:PRO259 3.8 37.7 1.0
N A:MET260 4.0 39.1 1.0
C A:PRO259 4.3 37.5 1.0
CG A:GLN228 4.3 39.9 1.0
CA A:SER258 4.3 36.6 1.0
CB A:SER258 4.5 39.1 1.0
CB A:PRO259 4.6 38.5 1.0
N A:PRO259 4.6 36.3 1.0
O A:GLY257 4.7 36.7 1.0
OE1 A:GLN228 4.8 42.8 1.0
CB A:MET260 4.8 41.4 1.0
C A:SER258 4.9 36.3 1.0
CA A:MET260 5.0 38.3 1.0

Iodine binding site 4 out of 4 in 2yd9

Go back to Iodine Binding Sites List in 2yd9
Iodine binding site 4 out of 4 in the Crystal Structure of the N-Terminal IG1-3 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 IG1-3 Module of Human Receptor Protein Tyrosine Phosphatase Sigma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1322

b:43.0
occ:0.70
 N A:LEU155 3.6 32.7 1.0
N A:GLN142 3.6 40.7 1.0
NZ A:LYS144 3.6 40.5 1.0
CE A:LYS144 3.7 38.4 1.0
CA A:PRO141 3.9 38.7 1.0
CB A:LEU155 4.0 29.8 1.0
CG A:LEU155 4.1 30.4 1.0
O A:THR153 4.1 31.7 1.0
O A:GLN142 4.2 40.5 1.0
C A:PRO141 4.2 39.9 1.0
CA A:MET154 4.3 31.8 1.0
CA A:LEU155 4.4 31.0 1.0
C A:MET154 4.4 32.4 1.0
CB A:PRO141 4.4 37.6 1.0
CB A:GLN142 4.5 45.0 1.0
CA A:GLN142 4.5 42.2 1.0
O A:LEU155 4.7 28.9 1.0
CD1 A:LEU155 4.8 31.1 1.0
C A:GLN142 4.8 40.6 1.0
O A:GLY140 4.8 36.5 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 Jan 24 17:24:49 2021

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