Iron in PDB 30jk: Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State

The structure of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State, PDB code: 30jk was solved by J.Duan, A.Rutz, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.07 / 2.15
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	168.42, 168.42, 126.31, 90, 90, 90
R / Rfree (%)	24.9 / 28

The structure of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State also contains other interesting chemical elements:

Chlorine	(Cl)	9 atoms
Zinc	(Zn)	2 atoms
Magnesium	(Mg)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State (pdb code 30jk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State, PDB code: 30jk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:27.0 occ:1.00 FE1 A:402701 0.0 27.0 1.0 C3 A:402701 1.7 23.8 1.0 C4 A:402701 1.8 24.3 1.0 C5 A:402701 1.9 24.4 1.0 S1 A:402701 2.3 22.6 1.0 S2 A:402701 2.3 34.8 1.0 SG A:CYS571 2.3 25.3 1.0 FE2 A:402701 2.6 33.8 1.0 O3 A:402701 3.0 28.1 1.0 O5 A:402701 3.0 25.6 1.0 N4 A:402701 3.0 24.8 1.0 CB A:CYS571 3.4 25.3 1.0 C1 A:402701 3.4 42.2 1.0 C2 A:402701 3.5 29.7 1.0 C7 A:402701 3.7 24.9 1.0 C6 A:402701 3.9 30.2 1.0 N1 A:402701 3.9 36.0 1.0 FE4 A:SF4702 4.0 24.4 1.0 S2 A:SF4702 4.3 24.5 1.0 O7 A:402701 4.7 36.3 1.0 N6 A:402701 4.8 33.4 1.0 CB A:ALA292 4.8 25.1 1.0 CE A:LYS426 4.8 34.3 1.0 CA A:CYS571 4.8 28.1 1.0 SG A:CYS367 4.9 33.6 1.0 CA A:GLY486 5.0 30.6 1.0 CD A:PRO293 5.0 32.1 1.0 CG A:PRO422 5.0 25.1 1.0

Iron binding site 2 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:33.8 occ:1.00 FE2 A:402701 0.0 33.8 1.0 C7 A:402701 1.8 24.9 1.0 C6 A:402701 1.9 30.2 1.0 C5 A:402701 2.0 24.4 1.0 S2 A:402701 2.3 34.8 1.0 S1 A:402701 2.3 22.6 1.0 FE1 A:402701 2.6 27.0 1.0 SG A:CYS367 2.8 33.6 1.0 O5 A:402701 2.9 25.6 1.0 O7 A:402701 2.9 36.3 1.0 N6 A:402701 3.1 33.4 1.0 C1 A:402701 3.5 42.2 1.0 N1 A:402701 3.5 36.0 1.0 C2 A:402701 3.5 29.7 1.0 C3 A:402701 3.7 23.8 1.0 C4 A:402701 3.7 24.3 1.0 CB A:CYS367 3.7 27.4 1.0 CD2 A:PHE485 4.5 30.0 1.0 CG A:PRO392 4.5 23.6 1.0 SG A:CYS571 4.5 25.3 1.0 CD A:PRO392 4.5 31.2 1.0 O3 A:402701 4.6 28.1 1.0 N4 A:402701 4.7 24.8 1.0 NZ A:LYS426 4.7 31.4 1.0 CE A:LYS426 4.7 34.3 1.0 CA A:CYS367 4.9 26.6 1.0 O A:CYS367 4.9 31.9 1.0 CB A:PHE485 4.9 34.5 1.0 CB A:PRO392 5.0 28.6 1.0 C A:CYS367 5.0 31.9 1.0

Iron binding site 3 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:34.0 occ:1.00 FE1 A:SF4702 0.0 34.0 1.0 SG A:CYS423 2.3 40.1 1.0 S3 A:SF4702 2.3 24.5 1.0 S4 A:SF4702 2.3 37.7 1.0 S2 A:SF4702 2.3 24.5 1.0 FE2 A:SF4702 2.7 38.4 1.0 FE3 A:SF4702 2.7 31.0 1.0 FE4 A:SF4702 2.7 24.4 1.0 CB A:CYS423 2.9 28.9 1.0 S1 A:SF4702 3.9 26.3 1.0 CB A:ALA425 4.2 38.5 1.0 O3 A:402701 4.3 28.1 1.0 CA A:CYS423 4.3 36.5 1.0 O A:HOH918 4.4 45.8 1.0 SG A:CYS567 4.6 38.8 1.0 C3 A:402701 4.7 23.8 1.0 SG A:CYS571 4.7 25.3 1.0 N A:CYS423 4.7 32.6 1.0 SG A:CYS368 4.8 36.4 1.0 CG A:LYS426 5.0 26.2 1.0

Iron binding site 4 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:38.4 occ:1.00 FE2 A:SF4702 0.0 38.4 1.0 SG A:CYS567 2.3 38.8 1.0 S1 A:SF4702 2.3 26.3 1.0 S4 A:SF4702 2.3 37.7 1.0 S3 A:SF4702 2.3 24.5 1.0 FE1 A:SF4702 2.7 34.0 1.0 FE3 A:SF4702 2.7 31.0 1.0 FE4 A:SF4702 2.7 24.4 1.0 CB A:CYS567 3.2 33.1 1.0 N A:CYS567 3.8 42.8 1.0 S2 A:SF4702 3.9 24.5 1.0 CA A:CYS567 4.1 37.2 1.0 CA A:GLY574 4.3 28.9 1.0 O A:GLY570 4.4 31.9 1.0 O A:HOH825 4.4 39.7 1.0 CB A:CYS423 4.5 28.9 1.0 CA A:CYS571 4.5 28.1 1.0 CB A:ALA566 4.5 39.3 1.0 SG A:CYS368 4.7 36.4 1.0 C A:ALA566 4.7 49.5 1.0 C A:GLY570 4.8 37.5 1.0 SG A:CYS423 4.8 40.1 1.0 SG A:CYS571 4.9 25.3 1.0 N A:GLY574 4.9 30.5 1.0 N A:CYS571 4.9 30.9 1.0 N A:ALA566 4.9 39.9 1.0 CA A:ALA566 5.0 41.5 1.0

Iron binding site 5 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:31.0 occ:1.00 FE3 A:SF4702 0.0 31.0 1.0 SG A:CYS368 2.3 36.4 1.0 S4 A:SF4702 2.3 37.7 1.0 S2 A:SF4702 2.3 24.5 1.0 S1 A:SF4702 2.3 26.3 1.0 FE2 A:SF4702 2.7 38.4 1.0 FE1 A:SF4702 2.7 34.0 1.0 FE4 A:SF4702 2.7 24.4 1.0 CB A:CYS368 3.2 31.2 1.0 CA A:CYS368 3.8 28.0 1.0 S3 A:SF4702 3.9 24.5 1.0 CB A:ALA566 4.1 39.3 1.0 N A:ALA566 4.3 39.9 1.0 CD A:PRO369 4.5 28.3 1.0 C2 A:402701 4.5 29.7 1.0 C A:CYS368 4.7 34.2 1.0 SG A:CYS567 4.7 38.8 1.0 SG A:CYS571 4.8 25.3 1.0 CA A:ALA566 4.8 41.5 1.0 OG A:SER370 4.8 33.0 1.0 N A:PRO369 4.8 31.8 1.0 SG A:CYS423 4.8 40.1 1.0 N A:CYS567 4.9 42.8 1.0 N A:CYS368 5.0 34.3 1.0

Iron binding site 6 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:24.4 occ:1.00 FE4 A:SF4702 0.0 24.4 1.0 SG A:CYS571 2.3 25.3 1.0 S3 A:SF4702 2.3 24.5 1.0 S1 A:SF4702 2.3 26.3 1.0 S2 A:SF4702 2.3 24.5 1.0 FE1 A:SF4702 2.7 34.0 1.0 FE2 A:SF4702 2.7 38.4 1.0 FE3 A:SF4702 2.7 31.0 1.0 CB A:CYS571 3.3 25.3 1.0 CA A:CYS571 3.4 28.1 1.0 C3 A:402701 3.8 23.8 1.0 N A:CYS571 3.8 30.9 1.0 S4 A:SF4702 3.9 37.7 1.0 C2 A:402701 4.0 29.7 1.0 FE1 A:402701 4.0 27.0 1.0 S2 A:402701 4.1 34.8 1.0 O3 A:402701 4.2 28.1 1.0 C A:GLY570 4.5 37.5 1.0 SG A:CYS423 4.6 40.1 1.0 C A:CYS571 4.7 26.4 1.0 O A:GLY570 4.7 31.9 1.0 SG A:CYS368 4.8 36.4 1.0 CG A:PRO422 4.9 25.1 1.0 SG A:CYS567 4.9 38.8 1.0 SD A:MET565 4.9 41.5 1.0 O A:CYS571 4.9 34.0 1.0 C4 A:402701 5.0 24.3 1.0 C1 A:402701 5.0 42.2 1.0

Iron binding site 7 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:61.4 occ:1.00 FE1 A:SF4703 0.0 61.4 1.0 SG A:CYS228 2.3 60.5 1.0 S4 A:SF4703 2.3 72.0 1.0 S2 A:SF4703 2.3 70.1 1.0 S3 A:SF4703 2.3 60.9 1.0 FE3 A:SF4703 2.7 56.5 1.0 FE4 A:SF4703 2.7 69.2 1.0 FE2 A:SF4703 2.7 76.3 1.0 CB A:CYS228 3.0 70.9 1.0 N A:CYS228 3.8 74.7 1.0 S1 A:SF4703 3.9 65.0 1.0 CA A:CYS228 4.1 63.3 1.0 ND1 A:HIS245 4.1 82.9 1.0 CD1 A:ILE267 4.5 47.6 1.0 SG A:CYS222 4.6 76.8 1.0 N A:GLY226 4.7 93.2 1.0 CB A:HIS245 4.8 72.8 1.0 CG A:HIS245 4.8 69.0 1.0 N A:ALA227 4.9 88.2 1.0 SG A:CYS262 4.9 59.9 1.0 CB A:CYS225 4.9 94.5 1.0 CE1 A:HIS245 4.9 97.7 1.0 CD1 A:ILE218 5.0 52.8 1.0 SG A:CYS225 5.0 122.4 1.0

Iron binding site 8 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:76.3 occ:1.00 FE2 A:SF4703 0.0 76.3 1.0 SG A:CYS225 2.3 122.4 1.0 S3 A:SF4703 2.3 60.9 1.0 S1 A:SF4703 2.3 65.0 1.0 S4 A:SF4703 2.3 72.0 1.0 CB A:CYS225 2.7 94.5 1.0 FE4 A:SF4703 2.7 69.2 1.0 FE3 A:SF4703 2.7 56.5 1.0 FE1 A:SF4703 2.7 61.4 1.0 N A:CYS225 3.2 101.7 1.0 CA A:CYS225 3.5 97.4 1.0 S2 A:SF4703 3.9 70.1 1.0 N A:GLY226 4.1 93.2 1.0 CD A:PRO263 4.2 62.8 1.0 C A:CYS225 4.3 101.4 1.0 C A:GLY224 4.4 85.7 1.0 N A:GLY224 4.5 78.3 1.0 SG A:CYS262 4.6 59.9 1.0 N A:ALA227 4.6 88.2 1.0 SG A:CYS222 4.7 76.8 1.0 SG A:CYS228 4.8 60.5 1.0 CA A:GLY224 4.8 79.3 1.0 ND1 A:HIS245 4.9 82.9 1.0 CG1 A:ILE223 4.9 74.3 1.0 N A:CYS228 5.0 74.7 1.0 CG A:PRO263 5.0 62.0 1.0

Iron binding site 9 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:56.5 occ:1.00 FE3 A:SF4703 0.0 56.5 1.0 SG A:CYS262 2.3 59.9 1.0 S2 A:SF4703 2.3 70.1 1.0 S4 A:SF4703 2.3 72.0 1.0 S1 A:SF4703 2.3 65.0 1.0 FE1 A:SF4703 2.7 61.4 1.0 FE2 A:SF4703 2.7 76.3 1.0 FE4 A:SF4703 2.7 69.2 1.0 CB A:CYS262 3.2 63.2 1.0 CB A:ALA266 3.8 81.7 1.0 CA A:CYS262 3.8 65.5 1.0 S3 A:SF4703 3.9 60.9 1.0 CD A:PRO263 4.2 62.8 1.0 CG1 A:ILE267 4.3 52.3 1.0 CD1 A:ILE267 4.4 47.6 1.0 SG A:CYS225 4.5 122.4 1.0 C A:CYS262 4.6 64.4 1.0 N A:PRO263 4.7 75.1 1.0 SG A:CYS228 4.8 60.5 1.0 CA A:ALA266 4.9 79.4 1.0 SG A:CYS222 4.9 76.8 1.0 CB A:CYS228 4.9 70.9 1.0 N A:CYS262 4.9 61.9 1.0

Iron binding site 10 out of 28 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii in Hinact State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:69.2 occ:1.00 FE4 A:SF4703 0.0 69.2 1.0 SG A:CYS222 2.3 76.8 1.0 S3 A:SF4703 2.3 60.9 1.0 S1 A:SF4703 2.3 65.0 1.0 S2 A:SF4703 2.3 70.1 1.0 FE2 A:SF4703 2.7 76.3 1.0 FE1 A:SF4703 2.7 61.4 1.0 FE3 A:SF4703 2.7 56.5 1.0 CB A:CYS222 3.2 59.5 1.0 CA A:CYS222 3.6 79.5 1.0 N A:ILE223 3.9 69.4 1.0 S4 A:SF4703 3.9 72.0 1.0 N A:GLY224 4.0 78.3 1.0 C A:CYS222 4.1 76.7 1.0 ND1 A:HIS245 4.2 82.9 1.0 CB A:ALA266 4.3 81.7 1.0 N A:CYS225 4.5 101.7 1.0 CG2 A:ILE218 4.5 57.4 1.0 SG A:CYS225 4.6 122.4 1.0 CA A:GLY224 4.6 79.3 1.0 SG A:CYS228 4.7 60.5 1.0 SG A:CYS262 4.8 59.9 1.0 N A:CYS222 4.8 67.7 1.0 CB A:HIS245 5.0 72.8 1.0 C A:ILE223 5.0 85.4 1.0

J.Duan, F.Arrigoni, A.Rutz, E.Hofmann, C.Greco, T.Happe. Direct Binding of Cysteine-367 Thiolate to the Active Site of the [Fefe]-Hydrogenase From Clostridium Beijerinckii in the O2-Stable State Biochemistry 2026.
ISSN: ISSN 0006-2960
DOI: 10.1021/ACS.BIOCHEM.6C00395