Krypton in PDB 7q37: Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton

The structure of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton, PDB code: 7q37 was solved by I.Melnikov, M.Rulev, R.Astashkin, K.Kovalev, P.Carpentier, V.Gordeliy, A.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.43 / 2.25
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.897, 40.381, 60.619, 90, 101.36, 90
R / Rfree (%)	17.8 / 24.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Krypton atom in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton (pdb code 7q37). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 19 binding sites of Krypton where determined in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton, PDB code: 7q37:
Jump to Krypton binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Krypton binding site 1 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 1 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr321 b:29.6 occ:0.41 CE A:MET140 2.6 38.6 1.0 CE1 A:PHE81 3.5 35.4 1.0 O A:LEU139 3.7 24.9 1.0 CZ A:PHE81 3.8 37.7 1.0 CB A:LEU139 3.8 25.6 1.0 C A:LEU139 3.9 27.5 1.0 CB A:LEU143 3.9 28.2 1.0 CD2 A:LEU143 3.9 27.2 1.0 CG2 A:ILE165 4.0 24.2 1.0 KR A:KR325 4.2 30.5 0.3 CZ3 A:TRP101 4.2 27.0 1.0 SD A:MET140 4.2 34.0 1.0 N A:MET140 4.3 29.5 1.0 CA A:LEU139 4.4 26.9 1.0 CG A:LEU143 4.4 29.2 1.0 CD1 A:PHE81 4.5 33.1 1.0 CA A:MET140 4.5 29.0 1.0 CE3 A:TRP101 4.6 25.4 1.0 CZ3 A:TRP169 4.6 29.5 1.0 CG A:LEU139 4.8 26.2 1.0 CD2 A:LEU139 4.8 26.4 1.0 CD1 A:LEU143 4.9 30.5 1.0 CH2 A:TRP101 4.9 27.1 1.0 CE3 A:TRP169 4.9 30.4 1.0 CE2 A:PHE81 5.0 36.8 1.0 CH2 A:TRP169 5.0 30.7 1.0

Krypton binding site 2 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 2 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr322 b:31.0 occ:0.44 O A:VAL98 3.1 35.1 1.0 CB A:PHE81 3.5 32.2 1.0 O A:PRO78 3.5 26.9 1.0 N A:GLY102 3.5 22.8 1.0 CA A:GLY102 3.7 24.4 1.0 CA A:PRO78 3.8 29.0 1.0 CB A:PRO78 3.9 28.2 1.0 CD2 A:PHE81 3.9 34.3 1.0 CG1 A:VAL98 3.9 39.6 1.0 CA A:VAL98 4.0 34.5 1.0 C A:VAL98 4.0 34.1 1.0 C A:PRO78 4.1 28.3 1.0 CG A:PHE81 4.2 32.7 1.0 C4 A:LFA305 4.3 62.9 1.0 C A:TRP101 4.3 25.4 1.0 N A:VAL82 4.4 36.5 1.0 CB A:TRP101 4.4 24.1 1.0 CB A:VAL98 4.4 36.9 1.0 CA A:PHE81 4.6 30.9 1.0 C A:PHE81 4.6 30.4 1.0 CG2 A:VAL82 4.7 39.4 1.0 CG2 A:VAL98 4.8 37.4 1.0 CA A:TRP101 4.9 25.8 1.0 O A:TRP101 5.0 24.9 1.0 CD1 A:LEU85 5.0 29.3 1.0

Krypton binding site 3 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 3 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr323 b:32.6 occ:0.31 O A:VAL201 3.5 30.2 1.0 CG A:LEU23 3.5 32.2 1.0 CG1 A:VAL201 3.6 36.7 1.0 CD1 A:LEU23 3.6 33.1 1.0 CD2 A:LEU23 3.7 35.5 1.0 CG2 A:VAL205 3.8 32.1 1.0 CA A:GLY19 3.9 22.2 1.0 CD2 A:PHE22 3.9 48.0 1.0 CA A:VAL201 3.9 34.4 1.0 C3 A:LFA313 4.0 46.2 1.0 O A:GLY19 4.1 23.9 1.0 N A:VAL205 4.1 29.8 1.0 C A:VAL201 4.2 29.9 1.0 CA A:GLY204 4.2 28.9 1.0 CB A:VAL201 4.3 34.9 1.0 C A:GLY204 4.3 26.8 1.0 CE2 A:PHE22 4.3 47.4 1.0 C A:GLY19 4.4 24.9 1.0 CG2 A:VAL201 4.7 33.8 1.0 CA A:VAL205 4.8 30.7 1.0 C4 A:LFA313 4.8 48.8 1.0 SG A:CYS45 4.9 30.9 1.0 CB A:VAL205 4.9 32.4 1.0 N A:GLY204 4.9 27.3 1.0 CB A:LEU23 5.0 29.1 1.0 CG A:PHE22 5.0 49.9 1.0 O A:LYS200 5.0 30.8 1.0

Krypton binding site 4 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 4 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr324 b:30.8 occ:0.34 OG1 A:THR193 2.9 22.6 1.0 O A:THR5 3.1 25.4 1.0 CB A:THR193 3.5 25.0 1.0 CB A:LEU8 3.6 44.9 1.0 O A:GLU189 3.6 28.0 1.0 CG2 A:THR5 3.7 35.7 1.0 CD2 A:PHE9 3.7 28.8 1.0 N A:PHE9 3.7 27.4 1.0 CG A:PHE9 3.7 27.1 1.0 CE2 A:PHE9 3.8 27.6 1.0 CD1 A:PHE9 3.9 28.6 1.0 CG2 A:THR193 3.9 25.2 1.0 C A:GLU189 4.0 25.2 1.0 CZ A:PHE9 4.0 24.8 1.0 CE1 A:PHE9 4.0 25.6 1.0 C A:THR5 4.0 29.4 1.0 C A:LEU8 4.1 33.4 1.0 CA A:VAL190 4.1 26.6 1.0 CA A:THR5 4.1 34.5 1.0 N A:VAL190 4.2 28.5 1.0 CA A:PHE9 4.3 28.5 1.0 CA A:LEU8 4.4 38.1 1.0 CB A:PHE9 4.5 27.9 1.0 CB A:THR5 4.5 34.0 1.0 CB A:GLU189 4.6 31.1 1.0 CD1 A:LEU8 4.7 54.1 1.0 CG2 A:VAL190 4.7 30.2 1.0 CG A:LEU8 4.8 53.9 1.0 O A:LEU8 4.8 33.7 1.0 CA A:GLU189 4.9 28.7 1.0 CA A:THR193 4.9 24.2 1.0 O A:VAL190 4.9 23.4 1.0 N A:LEU8 5.0 35.6 1.0 NH1 A:ARG69 5.0 28.7 1.0

Krypton binding site 5 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 5 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr325 b:30.5 occ:0.35 CE A:MET140 3.2 38.6 1.0 CE3 A:TRP169 3.4 30.4 1.0 CD1 A:LEU139 3.6 26.9 1.0 CZ3 A:TRP169 3.6 29.5 1.0 CD2 A:TYR136 3.6 37.4 1.0 CB A:LEU139 3.7 25.6 1.0 SD A:MET108 3.7 29.0 1.0 CE A:MET108 3.9 28.1 1.0 CA A:TYR136 4.0 29.9 1.0 O A:TYR136 4.0 24.8 1.0 CG A:TYR136 4.1 31.4 1.0 CE2 A:TYR136 4.2 37.4 1.0 KR A:KR321 4.2 29.6 0.4 CG A:LEU139 4.3 26.2 1.0 CB A:TYR136 4.4 31.5 1.0 SD A:MET140 4.4 34.0 1.0 C19 A:RET301 4.5 27.1 1.0 C A:TYR136 4.5 24.8 1.0 CG A:MET140 4.5 32.6 1.0 CD2 A:TRP169 4.6 29.4 1.0 CZ A:PHE81 4.8 37.7 1.0 CH2 A:TRP169 4.9 30.7 1.0 N A:MET140 5.0 29.5 1.0 CA A:LEU139 5.0 26.9 1.0 CD1 A:TYR136 5.0 32.5 1.0

Krypton binding site 6 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 6 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr326 b:63.2 occ:0.63 CD2 A:PHE184 3.3 90.4 1.0 CE2 A:PHE184 3.9 90.2 1.0 CG A:PHE184 4.2 93.5 1.0 O A:ALA178 4.3 35.7 1.0 CB A:PHE184 4.4 89.2 1.0 CG1 A:VAL181 4.4 77.8 1.0 CB A:VAL181 4.4 72.4 1.0 CG2 A:ILE187 4.5 36.5 1.0 CB A:ALA178 4.6 33.1 1.0 CA A:ALA178 4.7 38.4 1.0 C A:ALA178 4.9 37.7 1.0

Krypton binding site 7 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 7 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr327 b:30.2 occ:0.20 C4 A:HEX317 2.9 56.5 1.0 O A:VAL167 3.5 27.6 1.0 CG1 A:ILE171 3.8 30.9 1.0 C3 A:LFA309 3.9 52.1 1.0 C5 A:LFA309 4.1 52.6 1.0 CG1 A:VAL167 4.1 33.2 1.0 CD1 A:ILE171 4.4 32.5 1.0 C3 A:HEX317 4.4 56.2 1.0 C A:VAL167 4.5 28.8 1.0 C4 A:LFA309 4.6 56.0 1.0 CB A:ILE170 4.8 33.5 1.0 KR A:KR328 4.9 33.4 0.1 N A:ILE171 4.9 24.8 1.0

Krypton binding site 8 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 8 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr328 b:33.4 occ:0.11 C1 A:LFA309 3.6 47.7 1.0 CD1 A:LEU174 4.3 37.1 1.0 CD2 A:LEU191 4.6 32.3 1.0 C2 A:LFA309 4.8 46.6 1.0 KR A:KR327 4.9 30.2 0.2 CG1 A:ILE171 4.9 30.9 1.0 C3 A:LFA309 5.0 52.1 1.0

Krypton binding site 9 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 9 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr329 b:43.0 occ:0.31 OG A:SER26 3.3 49.1 1.0 CD1 A:PHE22 3.9 55.8 1.0 N A:SER26 3.9 35.9 1.0 CE1 A:PHE22 3.9 56.1 1.0 O A:HOH419 4.0 41.3 1.0 O A:PHE22 4.1 34.4 1.0 CB A:ALA25 4.1 37.1 1.0 CA A:SER26 4.1 37.0 1.0 C A:ALA25 4.2 36.8 1.0 CB A:SER26 4.3 38.3 1.0 O A:ALA25 4.6 37.1 1.0 CA A:ALA25 4.8 36.9 1.0 CG A:PHE22 4.9 49.9 1.0 CZ A:PHE22 5.0 54.5 1.0

Krypton binding site 10 out of 19 in the Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 10 of Crystal Structure of Proton Pump Mar Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr330 b:32.8 occ:0.07 C3 A:LFA308 2.5 59.7 1.0 C4 A:LFA308 3.5 66.7 1.0 C2 A:LFA309 3.6 46.6 1.0 C1 A:LFA309 3.7 47.7 1.0 CG2 A:ILE194 3.8 29.9 1.0 CD1 A:ILE194 4.4 34.8 1.0 C5 A:LFA308 4.8 59.8 1.0 CD1 A:ILE198 4.8 37.1 1.0 CG1 A:ILE194 4.9 32.9 1.0 KR A:KR333 4.9 30.6 0.2 CB A:ILE194 5.0 29.1 1.0

I.Melnikov, P.Orekhov, M.Rulev, K.Kovalev, R.Astashkin, D.Bratanov, Y.Ryzhykau, T.Balandin, S.Bukhdruker, I.Okhrimenko, V.Borshchevskiy, G.Bourenkov, C.Mueller-Dieckmann, P.Van Der Linden, P.Carpentier, G.Leonard, V.Gordeliy, A.Popov. High-Pressure Crystallography Shows Noble Gas Intervention Into Protein-Lipid Interaction and Suggests A Model For Anaesthetic Action. Commun Biol V. 5 360 2022.
ISSN: ESSN 2399-3642
PubMed: 35422073
DOI: 10.1038/S42003-022-03233-Y