Atomistry » Xenon, Xe » PDB 1w53-3pk4 » 3ord
Atomistry »
  Xenon, Xe »
    PDB 1w53-3pk4 »
      3ord »

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

Protein crystallography data

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

Other elements in 3ord:

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

Xenon Binding Sites:

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 3ord

Go back to Xenon Binding Sites List in 3ord
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 3ord

Go back to Xenon Binding Sites List in 3ord
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 3ord

Go back to Xenon Binding Sites List in 3ord
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 3ord

Go back to Xenon Binding Sites List in 3ord
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

Reference:

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
Page generated: Sat Oct 12 18:52:16 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy