Xenon in PDB 5o27: Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure

The structure of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure, PDB code: 5o27 was solved by N.Colloc'h, T.Prange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.31
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.811, 89.811, 114.333, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 20.4

The structure of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Xenon atom in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure (pdb code 5o27). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 8 binding sites of Xenon where determined in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure, PDB code: 5o27:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Xenon binding site 1 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe203 b:52.7 occ:0.40 CE A:LYS67 3.8 28.8 1.0 NZ A:LYS67 4.4 29.8 1.0 CD A:LYS67 4.9 24.4 1.0

Xenon binding site 2 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe204 b:38.2 occ:0.70 OG A:SER55 3.4 20.9 1.0 N A:ALA29 3.6 17.0 1.0 CD2 A:LEU56 3.7 32.0 1.0 XE A:XE207 3.7 53.1 0.4 CG A:LEU56 3.8 28.5 1.0 CA A:ALA29 3.8 20.5 1.0 C A:PHE28 3.9 19.4 1.0 CD2 A:PHE32 3.9 23.9 1.0 CD1 A:LEU56 4.0 34.4 1.0 CE2 A:PHE32 4.0 25.7 1.0 O A:PHE28 4.1 19.4 1.0 O A:PRO52 4.1 21.5 1.0 CB A:ALA29 4.2 23.3 1.0 CB A:PHE28 4.3 20.3 1.0 CE2 A:PHE61 4.5 21.6 1.0 O A:THR25 4.6 23.6 1.0 CZ A:PHE61 4.7 20.2 1.0 CA A:PHE28 4.7 21.0 1.0 CB A:SER55 4.7 21.6 1.0 C A:PRO52 4.8 22.3 1.0

Xenon binding site 3 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe205 b:46.1 occ:0.90 CG A:TRP140 3.9 47.2 1.0 CB A:TRP140 4.0 40.1 1.0 CD1 A:TRP140 4.0 51.1 1.0 CG A:LEU136 4.3 48.5 1.0 CD2 A:TRP140 4.3 42.1 1.0 CD1 A:TYR137 4.4 31.2 1.0 CA A:TYR137 4.4 33.7 1.0 CG2 A:ILE72 4.5 32.9 1.0 CD2 A:LEU136 4.5 43.1 1.0 CG1 A:ILE72 4.5 34.1 1.0 CD2 A:LEU113 4.5 40.5 1.0 NE1 A:TRP140 4.5 47.3 1.0 CB A:ALA75 4.5 49.3 1.0 CZ3 A:TRP133 4.6 30.9 1.0 XE A:XE206 4.7 46.2 0.7 CE2 A:TRP140 4.8 47.6 1.0 N A:TYR137 4.8 36.8 1.0 CB A:TYR137 4.9 33.0 1.0 CD1 A:LEU136 4.9 50.4 1.0 CE3 A:TRP140 5.0 37.5 1.0 CB A:ILE72 5.0 30.4 1.0

Xenon binding site 4 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe206 b:46.2 occ:0.70 CD1 A:ILE72 3.7 30.6 1.0 CG1 A:VAL109 3.8 31.2 1.0 CG1 A:ILE72 3.9 34.1 1.0 CE1 A:TYR137 4.0 33.4 1.0 CMC A:HEM201 4.1 32.1 1.0 CBC A:HEM201 4.1 36.6 1.0 CD2 A:LEU113 4.1 40.5 1.0 CD1 A:TYR137 4.3 31.2 1.0 CH2 A:TRP140 4.4 46.9 1.0 CZ3 A:TRP140 4.6 36.6 1.0 CZ2 A:TRP140 4.6 43.2 1.0 XE A:XE205 4.7 46.1 0.9 CB A:LEU113 4.9 28.4 1.0 CG A:LEU113 4.9 31.0 1.0 CE3 A:TRP140 4.9 37.5 1.0 CE2 A:TRP140 4.9 47.6 1.0

Xenon binding site 5 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe207 b:53.1 occ:0.40 O A:HOH318 3.5 32.1 1.0 XE A:XE204 3.7 38.2 0.7 CB A:PRO52 3.9 22.9 1.0 CD1 A:LEU56 3.9 34.4 1.0 N A:GLU53 4.1 22.6 1.0 CB A:ALA29 4.2 23.3 1.0 C A:PRO52 4.2 22.3 1.0 CA A:GLU53 4.4 24.7 1.0 O A:PRO52 4.4 21.5 1.0 CA A:ALA29 4.5 20.5 1.0 CA A:PRO52 4.7 23.6 1.0 CB A:GLU53 4.8 24.4 1.0 CG A:LEU56 4.9 28.5 1.0

Xenon binding site 6 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe208 b:49.7 occ:0.35 CB A:ASP73 3.8 49.1 1.0 O A:MET69 3.9 34.5 1.0 OD1 A:ASP73 3.9 59.3 1.0 C A:MET69 4.1 36.8 1.0 CG A:ASP73 4.1 58.6 1.0 CB A:PRO20 4.3 33.6 1.0 CG A:PRO20 4.3 34.8 1.0 CB A:MET69 4.3 29.9 1.0 CD2 A:LEU70 4.4 54.5 1.0 XE A:XE209 4.4 46.3 0.2 N A:LEU70 4.4 33.1 1.0 CZ2 A:TRP13 4.5 46.3 1.0 CA A:LEU70 4.5 33.4 1.0 CB A:SER17 4.6 49.9 1.0 CA A:MET69 4.8 26.8 1.0 CG A:LEU70 4.8 53.0 1.0 O A:SER17 4.9 47.3 1.0

Xenon binding site 7 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe209 b:46.3 occ:0.20 CG A:PRO20 3.8 34.8 1.0 O A:ARG66 3.9 28.0 1.0 CB A:ARG66 4.0 27.5 1.0 CA A:ARG66 4.0 27.0 1.0 CG A:ARG66 4.1 26.7 0.4 CG A:ARG66 4.1 27.5 0.6 CG A:LEU70 4.1 53.0 1.0 CB A:PRO20 4.2 33.6 1.0 CD A:ARG66 4.4 27.5 0.4 XE A:XE208 4.4 49.7 0.3 C A:ARG66 4.4 26.4 1.0 CD1 A:LEU70 4.4 56.7 1.0 CD2 A:LEU70 4.5 54.5 1.0 NH1 A:ARG66 4.5 21.4 0.4 CB A:MET69 4.8 29.9 1.0 N A:LEU70 5.0 33.1 1.0 CD A:ARG66 5.0 29.1 0.6

Xenon binding site 8 out of 8 in the Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Crystal Structure of Murine Neuroglobin Mutant V140W Under 30 Bar Xenon Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe211 b:47.0 occ:0.60 CE2 A:PHE106 3.4 99.5 1.0 CHC A:HEM201 3.7 21.6 1.0 CE A:MET144 3.8 53.7 1.0 CZ A:PHE106 3.9 90.0 1.0 CBB A:HEM201 3.9 31.4 1.0 C1C A:HEM201 4.1 25.3 1.0 CG A:HIS96 4.2 23.0 1.0 CD2 A:PHE106 4.2 83.7 1.0 CD2 A:HIS96 4.2 27.2 1.0 CG1 A:VAL101 4.2 32.3 1.0 C4B A:HEM201 4.3 25.9 1.0 CMC A:HEM201 4.3 32.1 1.0 CB A:HIS96 4.4 25.1 1.0 C2C A:HEM201 4.4 28.3 1.0 ND1 A:HIS96 4.7 25.6 1.0 C3B A:HEM201 4.7 31.9 1.0 NE2 A:HIS96 4.7 24.8 1.0 CAB A:HEM201 4.7 27.6 1.0 CH2 A:TRP140 4.9 46.9 1.0 CE1 A:PHE106 4.9 85.1 1.0 CG2 A:VAL101 4.9 34.3 1.0 CE1 A:HIS96 5.0 24.5 1.0 CB A:VAL101 5.0 35.0 1.0

N.Colloc'h, P.Carpentier, L.C.Montemiglio, B.Vallone, T.Prange. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas Under Pressure. Biophys. J. V. 113 2199 2017.
ISSN: ESSN 1542-0086
PubMed: 29108649
DOI: 10.1016/J.BPJ.2017.10.014