Krypton in PDB 8rxi: Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton

All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton:
1.12.7.2;

The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton, PDB code: 8rxi was solved by K.Bikbaev, T.Harand, L.Scheuenstuhl, P.Carpentier, I.Span, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.90 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.6, 87.967, 89.71, 90, 90, 90
R / Rfree (%)	15.4 / 18.1

The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton also contains other interesting chemical elements:

Iron

(Fe)

13 atoms

The binding sites of Krypton atom in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton (pdb code 8rxi). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 2 binding sites of Krypton where determined in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton, PDB code: 8rxi:
Jump to Krypton binding site number: 1; 2;

Krypton binding site 1 out of 2 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 1 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr501 b:20.2 occ:0.40 HD21 A:LEU307 2.8 16.5 1.0 HD2 A:PHE372 3.1 16.4 1.0 HE2 A:PHE160 3.1 17.3 1.0 HD2 A:PHE160 3.2 16.2 1.0 HA A:LEU307 3.2 13.6 1.0 HB3 A:ALA306 3.3 12.4 1.0 HE2 A:PHE372 3.4 16.9 1.0 HG A:LEU307 3.4 15.3 1.0 CD2 A:LEU307 3.5 17.1 1.0 HB2 A:ALA310 3.5 15.2 1.0 HD23 A:LEU307 3.5 16.5 1.0 CE2 A:PHE160 3.5 17.6 1.0 HB2 A:ALA306 3.6 12.4 1.0 CD2 A:PHE160 3.6 16.7 1.0 HB1 A:ALA310 3.7 15.2 1.0 C A:ALA306 3.7 12.9 1.0 N A:LEU307 3.8 12.6 1.0 O A:ALA306 3.8 12.6 1.0 CD2 A:PHE372 3.8 17.0 1.0 CB A:ALA306 3.8 12.5 1.0 CG A:LEU307 3.9 15.2 1.0 CA A:LEU307 3.9 14.1 1.0 CE2 A:PHE372 3.9 17.5 1.0 CB A:ALA310 4.0 15.8 1.0 H A:LEU307 4.1 13.0 1.0 HB3 A:ALA310 4.3 15.2 1.0 HD22 A:LEU307 4.3 16.5 1.0 CA A:ALA306 4.4 12.0 1.0 HG13 A:VAL347 4.4 14.7 1.0 CB A:LEU307 4.5 13.2 1.0 SD A:MET303 4.6 15.6 1.0 HG13 A:VAL345 4.6 18.4 1.0 CZ A:PHE160 4.6 17.4 1.0 KR A:KR502 4.7 27.0 0.4 HB1 A:ALA306 4.7 12.4 1.0 CG A:PHE160 4.7 14.1 1.0 O A:MET303 4.8 12.4 1.0 H A:ALA310 4.9 13.7 1.0 HA A:ALA306 5.0 12.3 1.0 HB3 A:PHE160 5.0 13.3 1.0 HZ A:PHE160 5.0 16.9 1.0

Krypton binding site 2 out of 2 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 2 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Kr502 b:27.0 occ:0.40 HB3 A:ALA310 2.9 15.2 1.0 HG13 A:VAL340 3.0 24.7 1.0 HG21 A:VAL345 3.1 17.7 1.0 HE2 A:PHE160 3.2 17.3 1.0 HG21 A:VAL340 3.2 23.5 1.0 HD12 A:LEU164 3.3 27.5 1.0 HG23 A:VAL161 3.3 16.4 1.0 HD11 A:LEU164 3.3 27.5 1.0 HD13 A:LEU164 3.5 27.6 1.0 CD1 A:LEU164 3.6 29.2 1.0 HG21 A:VAL314 3.6 19.6 1.0 HB2 A:ALA310 3.6 15.2 1.0 CB A:ALA310 3.7 15.8 1.0 HB A:VAL340 3.8 23.7 1.0 CE2 A:PHE160 3.8 17.6 1.0 HG13 A:VAL345 3.9 18.4 1.0 CG1 A:VAL340 3.9 25.3 1.0 HD2 A:PHE160 3.9 16.2 1.0 CG2 A:VAL340 4.0 23.5 1.0 CG2 A:VAL345 4.0 18.0 1.0 CB A:VAL340 4.1 23.4 1.0 HB1 A:ALA310 4.2 15.2 1.0 CG2 A:VAL161 4.2 16.9 1.0 CD2 A:PHE160 4.2 16.7 1.0 HG22 A:VAL161 4.2 16.4 1.0 HG23 A:VAL345 4.3 17.7 1.0 HG12 A:VAL340 4.3 24.7 1.0 HG22 A:VAL314 4.3 19.6 1.0 CG2 A:VAL314 4.4 18.9 1.0 HG21 A:VAL161 4.5 16.4 1.0 HG22 A:VAL340 4.5 23.5 1.0 HG11 A:VAL340 4.6 24.6 1.0 HG22 A:VAL345 4.6 17.7 1.0 HG23 A:VAL340 4.7 23.5 1.0 KR A:KR501 4.7 20.2 0.4 CG1 A:VAL345 4.7 19.1 1.0 O A:ALA310 4.7 15.6 1.0 HA A:VAL161 4.7 14.6 1.0 C A:ALA310 4.7 15.2 1.0 CA A:ALA310 4.8 13.9 1.0 CZ A:PHE160 4.8 17.4 1.0 CB A:VAL345 4.8 17.0 1.0 HD21 A:LEU307 4.9 16.5 1.0 HG11 A:VAL345 4.9 18.4 1.0 HG23 A:VAL314 4.9 19.6 1.0 HB A:VAL345 4.9 17.6 1.0 HZ A:PHE160 5.0 16.9 1.0

K.Bikbaev, T.Harand, L.Scheuenstuhl, P.Carpentier, M.A.Martini, J.A.Birrell, I.Span. Krypton Derivatization of [Fefe] Hydrogenase From Desulfovibrio Desulfuricans Reveals Its Gas Channel To Be Published.