Chlorine in PDB 4xdd: Apo [Fefe]-Hydrogenase Cpi

All present enzymatic activity of Apo [Fefe]-Hydrogenase Cpi:
1.12.7.2;

The structure of Apo [Fefe]-Hydrogenase Cpi, PDB code: 4xdd was solved by J.Esselborn, E.Hofmann, G.Kurisu, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.96 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.057, 71.807, 103.308, 90.00, 97.93, 90.00
R / Rfree (%)	14.4 / 16.6

The structure of Apo [Fefe]-Hydrogenase Cpi also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	36 atoms

The binding sites of Chlorine atom in the Apo [Fefe]-Hydrogenase Cpi (pdb code 4xdd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Apo [Fefe]-Hydrogenase Cpi, PDB code: 4xdd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:20.2 occ:1.00 HG A:SER232 2.3 24.6 1.0 H A:SER232 2.4 21.6 1.0 HB1 A:ALA230 2.7 25.0 1.0 HD2 A:PRO231 2.7 27.1 1.0 HB2 A:CYS503 3.0 22.2 1.0 HG3 A:PRO354 3.0 21.4 1.0 OG A:SER232 3.1 20.5 1.0 HA2 A:GLY418 3.1 24.1 1.0 HB2 A:SER232 3.2 23.7 1.0 HB2 A:PRO231 3.2 27.8 1.0 HB3 A:CYS503 3.2 22.2 1.0 N A:SER232 3.2 18.0 1.0 O A:HOH1365 3.2 23.4 1.0 O A:HOH1381 3.3 20.2 1.0 HG2 A:PRO231 3.4 24.2 1.0 CD A:PRO231 3.4 22.5 1.0 HA3 A:GLY418 3.5 24.1 1.0 CB A:CYS503 3.5 18.5 1.0 CB A:SER232 3.5 19.8 1.0 CB A:ALA230 3.6 20.9 1.0 N A:PRO231 3.6 19.8 1.0 CG A:PRO231 3.7 20.1 1.0 HB3 A:ALA230 3.7 25.0 1.0 CA A:GLY418 3.7 20.1 1.0 HD3 A:PRO354 3.8 19.7 1.0 CB A:PRO231 3.8 23.2 1.0 CG A:PRO354 3.9 17.8 1.0 CA A:SER232 4.0 17.2 1.0 CA A:PRO231 4.1 19.1 1.0 CD A:PRO354 4.1 16.4 1.0 C A:PRO231 4.1 18.2 1.0 HD2 A:PRO354 4.2 19.7 1.0 C A:ALA230 4.2 18.1 1.0 HB2 A:ALA230 4.2 25.0 1.0 HG2 A:PRO354 4.2 21.4 1.0 SG A:CYS503 4.2 19.0 1.0 O A:HOH1380 4.3 19.4 1.0 HD3 A:PRO231 4.3 27.1 1.0 N A:GLY418 4.3 20.9 1.0 HB3 A:SER232 4.4 23.7 1.0 CA A:ALA230 4.5 19.3 1.0 H A:GLY418 4.5 25.1 1.0 HA A:SER232 4.5 20.6 1.0 HA A:ALA230 4.7 23.2 1.0 HB3 A:PRO231 4.7 27.8 1.0 HG3 A:PRO231 4.7 24.2 1.0 O A:HOH1243 4.8 22.4 1.0 CA A:CYS503 4.8 17.5 1.0 H A:VAL233 4.9 23.5 1.0 C A:CYS503 4.9 19.0 1.0 HB3 A:PHE417 5.0 23.9 1.0 O A:ALA230 5.0 19.2 1.0 HB3 A:PRO354 5.0 22.8 1.0 C A:GLY418 5.0 18.8 1.0

Chlorine binding site 2 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl610 b:32.7 occ:1.00 H A:ALA406 2.5 26.4 1.0 HB3 A:ASP404 2.7 31.0 1.0 HD2 A:PRO405 2.9 33.4 1.0 O A:HOH1281 2.9 35.7 1.0 O A:HOH1333 3.0 46.0 1.0 HB2 A:ALA406 3.0 33.4 1.0 HB3 A:ALA406 3.1 33.4 1.0 HE1 A:PHE266 3.2 27.6 1.0 HE3 A:LYS264 3.3 41.9 1.0 N A:ALA406 3.4 22.0 1.0 CB A:ALA406 3.5 27.8 1.0 HG2 A:PRO405 3.6 33.5 1.0 CD A:PRO405 3.6 27.8 1.0 N A:PRO405 3.7 23.0 1.0 CB A:ASP404 3.7 25.8 1.0 HE2 A:LYS264 3.7 41.9 1.0 HZ1 A:LYS264 3.7 55.9 1.0 CE A:LYS264 3.9 34.9 1.0 C A:ASP404 3.9 23.6 1.0 CE1 A:PHE266 4.0 23.0 1.0 O A:HOH1373 4.0 47.4 1.0 CA A:ALA406 4.0 25.1 1.0 HZ A:PHE266 4.1 27.9 1.0 HB2 A:ASP404 4.1 31.0 1.0 CA A:ASP404 4.1 23.1 1.0 CG A:PRO405 4.1 27.9 1.0 HA A:ASP404 4.1 27.7 1.0 NZ A:LYS264 4.3 46.5 1.0 HB1 A:ALA406 4.3 33.4 1.0 C A:PRO405 4.4 20.9 1.0 HD3 A:PRO405 4.4 33.4 1.0 CZ A:PHE266 4.5 23.3 1.0 CA A:PRO405 4.5 25.3 1.0 O A:ASP404 4.5 24.2 1.0 H A:MET407 4.6 25.2 1.0 HA A:ALA406 4.6 30.1 1.0 CG A:ASP404 4.7 28.4 1.0 HZ2 A:LYS264 4.7 55.9 1.0 HG3 A:PRO405 4.8 33.5 1.0 HZ3 A:LYS264 5.0 55.9 1.0 CB A:PRO405 5.0 29.0 1.0

Chlorine binding site 3 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl606 b:23.6 occ:1.00 HG B:SER232 2.3 29.1 1.0 H B:SER232 2.4 27.5 1.0 HD2 B:PRO231 2.7 30.8 1.0 HB1 B:ALA230 2.7 28.1 1.0 HB2 B:CYS503 2.9 29.4 1.0 HG3 B:PRO354 3.0 27.4 1.0 OG B:SER232 3.0 24.2 1.0 HA2 B:GLY418 3.1 27.7 1.0 HB2 B:PRO231 3.1 28.7 1.0 HB3 B:CYS503 3.1 29.4 1.0 O B:HOH1359 3.2 22.8 1.0 HB2 B:SER232 3.2 27.2 1.0 O B:HOH1341 3.3 27.5 1.0 N B:SER232 3.3 22.9 1.0 HG2 B:PRO231 3.4 29.4 1.0 HA3 B:GLY418 3.4 27.7 1.0 CD B:PRO231 3.4 25.6 1.0 CB B:CYS503 3.4 24.5 1.0 CB B:SER232 3.6 22.7 1.0 CB B:ALA230 3.6 23.5 1.0 N B:PRO231 3.7 21.3 1.0 CG B:PRO231 3.7 24.5 1.0 CA B:GLY418 3.7 23.1 1.0 CB B:PRO231 3.7 23.9 1.0 HB3 B:ALA230 3.8 28.1 1.0 CG B:PRO354 3.8 22.8 1.0 HD3 B:PRO354 3.9 24.6 1.0 CA B:SER232 4.0 23.4 1.0 CA B:PRO231 4.1 21.7 1.0 HG2 B:PRO354 4.1 27.4 1.0 C B:PRO231 4.2 25.7 1.0 CD B:PRO354 4.2 20.5 1.0 SG B:CYS503 4.2 21.7 1.0 C B:ALA230 4.2 22.4 1.0 HB2 B:ALA230 4.2 28.1 1.0 O B:HOH1361 4.3 23.7 1.0 HD3 B:PRO231 4.3 30.8 1.0 HD2 B:PRO354 4.3 24.6 1.0 N B:GLY418 4.3 24.2 1.0 HB3 B:SER232 4.5 27.2 1.0 CA B:ALA230 4.5 24.4 1.0 H B:GLY418 4.5 29.1 1.0 HA B:SER232 4.6 28.0 1.0 HB3 B:PRO231 4.6 28.7 1.0 HG3 B:PRO231 4.7 29.4 1.0 HA B:ALA230 4.7 29.3 1.0 O B:HOH1220 4.7 26.7 1.0 CA B:CYS503 4.8 23.6 1.0 H B:VAL233 4.9 29.7 1.0 HB3 B:PRO354 4.9 23.3 1.0 C B:CYS503 4.9 19.8 1.0 HB3 B:PHE417 4.9 25.0 1.0 C B:GLY418 4.9 23.0 1.0 C B:PHE417 4.9 25.0 1.0 CB B:PRO354 5.0 19.4 1.0 O B:ALA230 5.0 22.6 1.0

Chlorine binding site 4 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl607 b:36.5 occ:1.00 H B:ALA406 2.5 32.3 1.0 HB3 B:ASP404 2.7 36.3 1.0 HD2 B:PRO405 2.9 42.4 1.0 O B:HOH1278 2.9 36.8 1.0 O B:HOH1312 3.0 45.2 1.0 HB2 B:ALA406 3.1 32.2 1.0 HB3 B:ALA406 3.1 32.2 1.0 HE1 B:PHE266 3.1 25.9 1.0 HE3 B:LYS264 3.3 48.0 1.0 N B:ALA406 3.3 26.9 1.0 CB B:ALA406 3.5 26.9 1.0 CD B:PRO405 3.6 35.3 1.0 HG2 B:PRO405 3.6 45.3 1.0 CB B:ASP404 3.6 30.2 1.0 N B:PRO405 3.6 30.6 1.0 HE2 B:LYS264 3.7 48.0 1.0 HZ1 B:LYS264 3.7 58.9 1.0 C B:ASP404 3.8 28.7 1.0 CE B:LYS264 3.9 40.0 1.0 HB2 B:ASP404 3.9 36.3 1.0 CE1 B:PHE266 4.0 21.6 1.0 CA B:ASP404 4.0 25.6 1.0 CA B:ALA406 4.0 27.2 1.0 HZ B:PHE266 4.1 31.4 1.0 HA B:ASP404 4.1 30.8 1.0 CG B:PRO405 4.1 37.8 1.0 O B:HOH1368 4.1 46.3 1.0 NZ B:LYS264 4.3 49.0 1.0 C B:PRO405 4.3 28.5 1.0 HB1 B:ALA406 4.4 32.2 1.0 HD3 B:PRO405 4.4 42.4 1.0 O B:ASP404 4.4 29.8 1.0 CA B:PRO405 4.4 29.1 1.0 CZ B:PHE266 4.5 26.1 1.0 H B:MET407 4.6 32.1 1.0 HA B:ALA406 4.6 32.6 1.0 CG B:ASP404 4.6 39.2 1.0 HZ2 B:LYS264 4.7 58.9 1.0 HG3 B:PRO405 4.8 45.3 1.0 CB B:PRO405 4.9 38.3 1.0 HZ3 B:LYS264 5.0 58.9 1.0

J.Esselborn, N.Muraki, K.Klein, V.Engelbrecht, N.Metzler-Nolte, U.P.Apfel, E.Hofmann, G.Kurisu, T.Happe. A Structural View of Synthetic Cofactor Integration Into [Fefe]-Hydrogenases. Chem Sci V. 7 959 2016.
ISSN: ISSN 2041-6520
PubMed: 29896366
DOI: 10.1039/C5SC03397G