Xenon in PDB 3g46: Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity

The structure of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity, PDB code: 3g46 was solved by J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, W.E.Royer Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.30 / 0.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.536, 43.487, 82.853, 90.00, 122.25, 90.00
R / Rfree (%)	12.9 / 15.6

The structure of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Xenon atom in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity (pdb code 3g46). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 8 binding sites of Xenon where determined in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity, PDB code: 3g46:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Xenon binding site 1 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe149 b:15.0 occ:0.90 XE A:XE149 0.0 15.0 0.9 XE A:XE149 3.4 19.4 0.1 CE2 A:TRP135 3.8 10.5 1.0 CD2 A:TRP135 3.9 10.3 1.0 CZ2 A:TRP135 4.0 12.1 1.0 CE3 A:TRP135 4.0 11.6 1.0 CH2 A:TRP135 4.1 13.5 1.0 CZ3 A:TRP135 4.1 12.8 1.0 CG2 A:ILE118 4.1 12.3 1.0 CG2 A:ILE25 4.2 17.0 1.0 CD1 A:LEU77 4.4 12.3 1.0 NE1 A:TRP135 4.4 10.7 1.0 CG A:TRP135 4.5 10.4 1.0 CG1 A:ILE118 4.5 11.4 1.0 CZ3 A:TRP22 4.6 12.8 1.0 CD2 A:LEU122 4.6 13.7 1.0 CG A:LEU122 4.7 12.5 1.0 CD1 A:TRP135 4.7 10.5 1.0 CE3 A:TRP22 4.7 11.4 1.0 CD1 A:LEU36 4.7 21.3 0.7 CG1 A:ILE25 4.7 14.1 1.0 CB A:ILE25 4.8 13.1 1.0 CB A:ILE118 4.8 11.0 1.0 CD1 A:ILE118 4.9 12.6 1.0

Xenon binding site 2 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe149 b:19.4 occ:0.10 XE A:XE149 0.0 19.4 0.1 CD1 A:LEU36 2.2 21.3 0.7 CG A:LEU36 2.7 15.9 0.7 CD2 A:LEU36 3.2 18.7 0.7 XE A:XE149 3.4 15.0 0.9 CG2 A:ILE25 3.7 17.0 1.0 CD2 A:LEU36 3.9 10.2 0.3 SD A:MET74 3.9 13.2 1.0 O A:ASN32 3.9 10.7 1.0 CE A:MET74 3.9 16.0 1.0 CG1 A:VAL121 4.0 16.8 1.0 CB A:LEU36 4.0 11.2 0.3 CB A:LEU36 4.1 11.9 0.7 CD1 A:LEU36 4.2 8.6 0.3 CG A:LEU36 4.2 8.4 0.3 CB A:ASN32 4.5 11.8 1.0 C A:ASN32 4.5 10.8 1.0 CB A:VAL121 4.6 13.8 1.0 CD1 A:LEU77 4.7 12.3 1.0 CG2 A:VAL121 5.0 15.7 1.0

Xenon binding site 3 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe150 b:13.8 occ:0.60 CD2 A:LEU77 3.7 11.4 1.0 CG2 A:VAL139 3.8 11.3 1.0 CE2 A:PHE80 3.8 13.2 1.0 CBB A:HEM147 3.9 14.0 1.0 CA A:VAL139 3.9 9.8 1.0 CD2 A:PHE80 4.0 11.9 1.0 N A:VAL139 4.0 10.1 1.0 CG A:LEU138 4.1 11.3 1.0 CG2 A:VAL142 4.2 11.4 1.0 C A:LEU138 4.3 10.3 1.0 CD2 A:LEU138 4.3 12.3 1.0 O A:LEU138 4.4 10.8 1.0 CAB A:HEM147 4.5 10.9 1.0 CB A:VAL139 4.5 10.3 1.0 CMB A:HEM147 4.7 10.4 1.0 CE2 A:PHE111 4.7 10.2 1.0 CB A:LEU138 4.8 10.6 1.0 CZ A:PHE111 4.9 11.0 1.0

Xenon binding site 4 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe151 b:10.9 occ:0.06 CMB A:HEM147 3.4 10.4 1.0 C2B A:HEM147 3.4 9.5 1.0 CZ A:PHE111 3.5 11.0 1.0 CB A:PHE97 3.5 10.5 1.0 C1B A:HEM147 3.7 9.1 1.0 CE1 A:PHE111 3.8 10.8 1.0 CE1 A:HIS101 3.9 8.1 1.0 CZ A:PHE80 3.9 13.2 1.0 CHB A:HEM147 3.9 8.7 1.0 CG1 A:VAL142 4.1 11.9 1.0 CE2 A:PHE80 4.1 13.2 1.0 C3B A:HEM147 4.1 9.6 1.0 CG2 A:VAL142 4.1 11.4 1.0 CG A:PHE97 4.2 10.4 1.0 ND1 A:HIS101 4.2 8.7 1.0 NB A:HEM147 4.4 8.1 1.0 C4B A:HEM147 4.6 8.9 1.0 CE2 A:PHE111 4.6 10.2 1.0 CD2 A:PHE97 4.7 12.3 1.0 CB A:VAL142 4.7 9.6 1.0 NE2 A:HIS101 4.7 8.0 1.0 CA A:PHE97 4.8 8.9 1.0 C A:PHE97 4.8 9.0 1.0 CD1 A:PHE97 4.8 12.1 1.0 CAB A:HEM147 4.8 10.9 1.0 O A:PHE97 4.8 9.5 1.0 C4A A:HEM147 4.9 8.4 1.0

Xenon binding site 5 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe149 b:12.3 occ:0.70 CD2 B:LEU77 3.7 9.2 1.0 CG2 B:VAL139 3.8 8.9 1.0 CE2 B:PHE80 3.9 12.4 1.0 CBB B:HEM147 3.9 12.5 1.0 CD2 B:PHE80 3.9 10.9 1.0 CA B:VAL139 3.9 8.0 1.0 N B:VAL139 4.0 7.8 1.0 CG B:LEU138 4.1 8.8 1.0 C B:LEU138 4.2 8.1 1.0 CG2 B:VAL142 4.3 10.2 1.0 O B:LEU138 4.3 8.5 1.0 CD2 B:LEU138 4.3 10.2 1.0 CB B:VAL139 4.5 8.4 1.0 CAB B:HEM147 4.6 9.8 1.0 CB B:LEU138 4.7 8.4 1.0 CE1 B:PHE111 4.7 10.3 1.0 CMB B:HEM147 4.9 10.1 1.0 CZ3 B:TRP135 4.9 11.2 1.0 CZ B:PHE111 4.9 10.6 1.0 CE3 B:TRP135 5.0 9.6 1.0

Xenon binding site 6 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe150 b:13.9 occ:0.90 XE B:XE150 0.0 13.9 0.9 XE B:XE150 3.2 22.8 0.1 CE2 B:TRP135 3.8 8.7 1.0 CZ2 B:TRP135 3.9 10.0 1.0 CD2 B:TRP135 3.9 8.1 1.0 CH2 B:TRP135 4.0 10.9 1.0 CE3 B:TRP135 4.1 9.6 1.0 CZ3 B:TRP135 4.1 11.2 1.0 CG2 B:ILE118 4.1 9.5 1.0 CG2 B:ILE25 4.1 12.8 1.0 NE1 B:TRP135 4.4 8.6 1.0 CZ3 B:TRP22 4.4 9.9 1.0 CG1 B:ILE118 4.5 8.9 1.0 CD1 B:LEU77 4.5 9.8 1.0 CE3 B:TRP22 4.5 9.2 1.0 CD2 B:LEU122 4.6 9.9 1.0 CG B:TRP135 4.6 8.0 1.0 CG B:LEU122 4.7 9.0 1.0 CB B:ILE25 4.7 10.2 1.0 CB B:ILE118 4.8 8.8 1.0 CG1 B:ILE25 4.8 12.4 1.0 CD1 B:TRP135 4.8 7.8 1.0 CD1 B:ILE118 4.8 10.4 1.0

Xenon binding site 7 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe150 b:22.8 occ:0.09 XE B:XE150 0.0 22.8 0.1 XE B:XE150 3.2 13.9 0.9 SD B:MET74 3.7 10.2 1.0 CG2 B:ILE25 3.8 12.8 1.0 CD2 B:LEU36 3.8 13.7 1.0 CE B:MET74 3.8 12.8 1.0 CD1 B:LEU36 4.0 15.1 1.0 CG1 B:VAL121 4.0 13.3 1.0 CG B:LEU36 4.2 10.5 1.0 CB B:LEU36 4.2 8.9 1.0 CD1 B:LEU77 4.3 9.8 1.0 O B:ASN32 4.4 9.2 1.0 CB B:VAL121 4.6 10.6 1.0 CZ3 B:TRP22 4.7 9.9 1.0 C B:ASN32 4.9 8.6 1.0 CB B:ASN32 4.9 9.3 1.0 CG2 B:VAL121 4.9 12.2 1.0

Xenon binding site 8 out of 8 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloroform Bound to the XE4 Cavity within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe151 b:12.3 occ:0.04 CZ B:PHE111 3.2 10.6 1.0 CB B:PHE97 3.4 10.4 1.0 CE2 B:PHE111 3.5 10.6 1.0 CMB B:HEM147 3.5 10.1 1.0 C2B B:HEM147 3.6 8.9 1.0 C1B B:HEM147 3.7 8.5 1.0 CE1 B:HIS101 3.8 8.2 1.0 ND1 B:HIS101 4.0 8.4 1.0 CG1 B:VAL142 4.0 11.0 1.0 CZ B:PHE80 4.1 11.9 1.0 CHB B:HEM147 4.1 9.3 1.0 C3B B:HEM147 4.2 8.4 1.0 CG B:PHE97 4.2 10.5 1.0 CE2 B:PHE80 4.3 12.4 1.0 CG2 B:VAL142 4.4 10.2 1.0 O B:PHE97 4.4 9.8 1.0 NB B:HEM147 4.4 7.8 1.0 CE1 B:PHE111 4.4 10.3 1.0 C B:PHE97 4.4 8.9 1.0 CA B:PHE97 4.5 9.0 1.0 C4B B:HEM147 4.6 8.1 1.0 NE2 B:HIS101 4.6 7.5 1.0 CD2 B:PHE111 4.7 9.8 1.0 CB B:VAL142 4.8 9.3 1.0 CD1 B:PHE97 4.8 11.6 1.0 CAB B:HEM147 4.9 9.8 1.0 N B:ALA98 5.0 9.4 1.0 CD2 B:PHE97 5.0 13.4 1.0 C4A B:HEM147 5.0 8.2 1.0

J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, W.E.Royer. Ligand Migration and Cavities Within Scapharca Dimeric Hbi: Studies By Time-Resolved Crystallo-Graphy, Xe Binding, and Computational Analysis. Structure V. 17 1494 2009.
ISSN: ISSN 0969-2126
PubMed: 19913484
DOI: 10.1016/J.STR.2009.09.004