Xenon in PDB 3ord: Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata

The structure of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata, PDB code: 3ord was solved by V.S.De Serrano, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.50 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.674, 67.805, 68.304, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 28.9

The structure of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Xenon atom in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata (pdb code 3ord). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata, PDB code: 3ord:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe140 b:46.7 occ:0.55 O A:HOH254 3.0 28.5 1.0 CE1 A:PHE21 3.5 21.9 1.0 C1C A:HEM139 3.6 24.1 1.0 CD1 A:PHE21 3.7 20.6 1.0 C2C A:HEM139 3.8 23.3 1.0 NC A:HEM139 3.9 23.8 1.0 CHC A:HEM139 4.0 21.4 1.0 CD2 A:LEU100 4.0 15.9 1.0 C3C A:HEM139 4.1 23.8 1.0 C4C A:HEM139 4.2 23.6 1.0 CG1 A:VAL59 4.2 18.6 1.0 CD1 A:LEU100 4.2 18.5 1.0 CZ A:PHE35 4.2 27.7 1.0 CE2 A:PHE24 4.2 21.9 1.0 CMC A:HEM139 4.3 23.8 1.0 CD2 A:PHE24 4.5 20.0 1.0 C4B A:HEM139 4.5 22.2 1.0 CG A:LEU100 4.7 18.5 1.0 CZ A:PHE21 4.7 22.5 1.0 FE A:HEM139 4.8 25.6 1.0 NB A:HEM139 4.8 23.3 1.0 CE1 A:HIS55 4.9 24.8 0.7 CE2 A:PHE35 5.0 28.6 1.0 NE2 A:HIS55 5.0 24.1 0.7 CAC A:HEM139 5.0 26.4 1.0

Xenon binding site 2 out of 4 in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe141 b:20.1 occ:0.05 O A:ASP79 3.4 26.2 1.0 CD1 A:LEU62 3.5 15.9 1.0 CG2 A:VAL66 3.6 13.7 1.0 CB A:THR82 3.6 33.4 1.0 OD2 A:ASP79 3.8 27.3 1.0 CA A:ASP79 3.9 26.3 1.0 CD2 A:LEU62 3.9 11.6 1.0 CG A:LEU62 4.0 14.2 1.0 CB A:ASP79 4.0 25.9 1.0 C A:ASP79 4.0 26.4 1.0 CG2 A:THR82 4.1 33.9 1.0 CG A:LEU83 4.2 32.2 1.0 CG A:ASP79 4.2 26.0 1.0 OG1 A:THR82 4.2 35.0 1.0 CD2 A:LEU83 4.3 29.7 1.0 NH2 A:ARG69 4.5 14.4 1.0 N A:LEU83 4.6 33.5 1.0 CA A:THR82 4.7 33.5 1.0 C A:THR82 4.8 33.2 1.0 CD1 A:LEU83 4.8 29.5 1.0

Xenon binding site 3 out of 4 in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe140 b:51.8 occ:0.30 O B:HOH256 3.1 27.8 1.0 CE1 B:PHE21 3.1 20.4 1.0 CD1 B:PHE21 3.5 19.6 1.0 C1C B:HEM139 3.7 22.4 1.0 C2C B:HEM139 3.9 23.3 1.0 CZ B:PHE35 4.0 28.7 1.0 NC B:HEM139 4.0 23.6 1.0 CHC B:HEM139 4.0 23.5 1.0 CD2 B:LEU100 4.0 11.1 1.0 CG1 B:VAL59 4.1 12.9 1.0 CD1 B:LEU100 4.2 17.6 1.0 C3C B:HEM139 4.2 23.5 1.0 C4C B:HEM139 4.3 25.2 1.0 CZ B:PHE21 4.3 19.5 1.0 CMC B:HEM139 4.4 22.7 1.0 C4B B:HEM139 4.4 22.9 1.0 CE2 B:PHE24 4.5 15.4 1.0 CE1 B:HIS55 4.7 22.9 1.0 CG B:LEU100 4.7 18.0 1.0 CE2 B:PHE35 4.7 28.7 1.0 CD2 B:PHE24 4.7 16.1 1.0 FE B:HEM139 4.7 25.2 1.0 NB B:HEM139 4.8 24.0 1.0 CG2 B:VAL59 4.8 14.5 1.0 CE1 B:PHE35 4.8 28.4 1.0 CG B:PHE21 4.9 19.2 1.0 CB B:VAL59 5.0 15.1 1.0

Xenon binding site 4 out of 4 in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe141 b:42.3 occ:0.37 CD1 B:LEU62 3.4 6.2 1.0 OD2 B:ASP79 3.5 16.9 1.0 O B:ASP79 3.6 15.8 1.0 CB B:THR82 3.6 23.1 1.0 CG2 B:THR82 3.6 24.8 1.0 CG2 B:VAL66 3.9 10.9 1.0 CD2 B:LEU62 3.9 8.1 1.0 CG B:LEU62 3.9 12.6 1.0 CA B:ASP79 3.9 16.6 1.0 CB B:ASP79 4.1 16.7 1.0 CG B:ASP79 4.1 16.6 1.0 C B:ASP79 4.2 17.1 1.0 OG1 B:THR82 4.3 23.1 1.0 NH2 B:ARG69 4.3 14.6 1.0 CG B:LEU83 4.4 22.7 1.0 N B:LEU83 4.8 24.1 1.0 CD2 B:LEU83 4.8 19.6 1.0 CD1 B:LEU83 4.8 19.0 1.0 CA B:THR82 4.9 22.9 1.0

V.De Serrano, S.Franzen. Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata. Biopolymers V. 98 27 2012.
ISSN: ISSN 0006-3525
PubMed: 23325557
DOI: 10.1002/BIP.21674