Iodine in PDB 4pvq: Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein

All present enzymatic activity of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein:
3.4.19.5; 3.5.1.1;

The structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein, PDB code: 4pvq was solved by J.Nomme, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.13
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.220, 59.220, 298.500, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 22.2

The structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iodine atom in the Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein (pdb code 4pvq). 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 Sulfate-Bound Human L-Asparaginase Protein, PDB code: 4pvq:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein


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 Sulfate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:58.7 occ:0.50 I A:IOD410 3.0 48.0 0.5 CG A:PRO284 3.6 22.2 1.0 N A:GLY10 3.6 22.7 1.0 CA A:LEU166 3.6 35.7 1.0 CD A:PRO284 4.0 22.0 1.0 N A:GLY167 4.1 35.0 1.0 O A:GLY10 4.2 22.7 1.0 CA A:GLY10 4.2 22.7 1.0 C A:LEU166 4.2 35.6 1.0 NH1 A:ARG19 4.3 37.4 1.0 CD1 A:ILE15 4.3 32.6 1.0 N A:LEU166 4.4 35.7 1.0 CB A:LEU166 4.4 36.1 1.0 C A:GLY9 4.6 22.5 1.0 CD1 A:PHE61 4.6 27.8 1.0 CA A:GLY9 4.7 21.6 1.0 C A:GLY10 4.7 23.2 1.0 CG1 A:VAL23 4.8 34.1 1.0 CB A:PRO284 4.9 22.5 1.0 CE1 A:PHE61 4.9 28.5 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein


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 Sulfate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:61.1 occ:0.50 I B:IOD407 3.2 38.9 0.5 O B:PRO113 3.4 23.8 1.0 NZ A:LYS227 3.4 17.5 1.0 CE A:LYS227 3.8 16.7 1.0 CB A:GLU223 3.8 16.9 1.0 CG A:GLU223 3.9 16.4 1.0 C B:PRO113 4.1 24.0 1.0 SG B:CYS115 4.2 25.6 1.0 CE1 A:HIS221 4.7 17.8 1.0 CA B:PRO113 4.8 24.4 1.0 O A:HOH541 4.9 22.2 1.0 N B:HIS114 4.9 23.5 1.0 O B:HIS114 5.0 22.9 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein


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 Sulfate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:48.0 occ:0.50 N A:GLY167 2.9 35.0 1.0 O A:GLY167 2.9 33.8 1.0 I A:IOD408 3.0 58.7 0.5 N A:ASN62 3.3 26.9 1.0 CB A:LEU166 3.6 36.1 1.0 CA A:LEU166 3.6 35.7 1.0 C A:LEU166 3.7 35.6 1.0 C A:GLY167 3.7 33.9 1.0 CA A:PHE61 3.8 28.1 1.0 CA A:GLY167 3.8 34.2 1.0 CB A:ASN62 3.9 26.1 1.0 N A:GLY10 3.9 22.7 1.0 C A:PHE61 4.0 27.7 1.0 CB A:PHE61 4.1 28.0 1.0 CD1 A:PHE61 4.1 27.8 1.0 CA A:ASN62 4.2 26.3 1.0 CG1 A:VAL169 4.4 28.4 1.0 CA A:GLY10 4.5 22.7 1.0 CG A:PHE61 4.5 27.7 1.0 O A:GLU60 4.6 28.2 1.0 C A:GLY9 4.9 22.5 1.0 CA A:GLY9 4.9 21.6 1.0 O A:LEU166 4.9 35.6 1.0 N A:PHE61 5.0 28.4 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein


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 Sulfate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:I407 b:38.9 occ:0.50 I A:IOD409 3.2 61.1 0.5 OG B:SER88 3.4 16.6 1.0 CE A:LYS227 3.6 16.7 1.0 NZ A:LYS227 3.8 17.5 1.0 CA B:SER88 3.8 17.2 1.0 N B:ALA89 3.8 17.1 1.0 CB B:SER88 4.0 17.5 1.0 SG B:CYS115 4.1 25.6 1.0 O B:ALA89 4.2 17.2 1.0 C B:SER88 4.4 17.7 1.0 O B:HOH515 4.4 15.6 1.0 O B:MET109 4.5 23.2 1.0 CD A:LYS227 4.7 15.7 1.0 CG B:MET109 4.8 25.2 1.0 CA B:ALA89 5.0 16.7 1.0 N B:SER88 5.0 17.3 1.0 C B:ALA89 5.0 16.9 1.0

J.Nomme, Y.Su, M.Konrad, A.Lavie. Structures of Apo and Product-Bound Human L-Asparaginase: Insights Into the Mechanism of Autoproteolysis and Substrate Hydrolysis. Biochemistry V. 51 6816 2012.
ISSN: ISSN 0006-2960
PubMed: 22861376
DOI: 10.1021/BI300870G