Iron in PDB 5obp: Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor

The structure of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor, PDB code: 5obp was solved by S.Keller, C.Kunze, M.Bommer, C.Paetz, R.C.Menezes, A.Svatos, H.Dobbek, T.Schubert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.07 / 1.59
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.565, 73.565, 184.677, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.7

The structure of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor (pdb code 5obp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor, PDB code: 5obp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:17.8 occ:1.00 FE1 A:SF4501 0.0 17.8 1.0 S3 A:SF4501 2.3 18.8 1.0 S2 A:SF4501 2.3 18.2 1.0 S4 A:SF4501 2.3 18.5 1.0 SG A:CYS390 2.3 17.8 1.0 FE4 A:SF4501 2.7 19.4 1.0 FE2 A:SF4501 2.7 18.4 1.0 FE3 A:SF4501 2.8 18.9 1.0 CB A:CYS390 3.3 16.6 1.0 CA A:CYS390 3.8 18.7 1.0 S1 A:SF4501 3.9 19.6 1.0 CD A:PRO391 4.0 20.7 1.0 CD1 A:ILE296 4.1 19.6 1.0 CE A:MET292 4.1 18.1 1.0 N A:PRO391 4.5 17.8 1.0 C A:CYS390 4.6 18.2 1.0 CD2 A:PHE392 4.6 18.5 1.0 SG A:CYS329 4.7 19.2 1.0 SG A:CYS335 4.8 18.6 1.0 SG A:CYS332 4.8 22.0 1.0

Iron binding site 2 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.4 occ:1.00 FE2 A:SF4501 0.0 18.4 1.0 S1 A:SF4501 2.3 19.6 1.0 SG A:CYS329 2.3 19.2 1.0 S3 A:SF4501 2.3 18.8 1.0 S4 A:SF4501 2.3 18.5 1.0 FE3 A:SF4501 2.7 18.9 1.0 FE1 A:SF4501 2.7 17.8 1.0 FE4 A:SF4501 2.7 19.4 1.0 CB A:CYS329 3.3 19.1 1.0 CA A:CYS329 3.6 20.1 1.0 S2 A:SF4501 3.9 18.2 1.0 CB A:ARG291 4.1 21.8 1.0 N A:ARG291 4.2 17.6 1.0 N A:CYS329 4.3 22.9 1.0 CB A:SER290 4.5 19.1 1.0 CD1 A:ILE296 4.6 19.6 1.0 SG A:CYS332 4.8 22.0 1.0 CB A:CYS332 4.8 23.2 1.0 CA A:ARG291 4.8 15.9 1.0 SG A:CYS390 4.8 17.8 1.0 SG A:CYS335 4.8 18.6 1.0 C A:CYS329 4.8 25.0 1.0 O A:CYS329 5.0 21.6 1.0

Iron binding site 3 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.9 occ:1.00 FE3 A:SF4501 0.0 18.9 1.0 S2 A:SF4501 2.3 18.2 1.0 S4 A:SF4501 2.3 18.5 1.0 SG A:CYS335 2.3 18.6 1.0 S1 A:SF4501 2.3 19.6 1.0 FE2 A:SF4501 2.7 18.4 1.0 FE4 A:SF4501 2.7 19.4 1.0 FE1 A:SF4501 2.8 17.8 1.0 CB A:CYS335 3.3 17.8 1.0 N A:CYS335 3.8 20.1 1.0 S3 A:SF4501 3.9 18.8 1.0 CB A:ARG291 4.1 21.8 1.0 CA A:CYS335 4.2 21.1 1.0 CE A:MET292 4.4 18.1 1.0 N A:MET292 4.5 19.7 1.0 CD A:ARG291 4.6 20.4 1.0 N A:LYS334 4.6 24.2 1.0 CG A:ARG291 4.7 18.8 1.0 SG A:CYS332 4.8 22.0 1.0 SG A:CYS329 4.8 19.2 1.0 CB A:MET292 4.9 20.4 1.0 SG A:CYS390 4.9 17.8 1.0 C A:LYS334 5.0 23.4 1.0 N A:LYS333 5.0 26.1 1.0

Iron binding site 4 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.4 occ:1.00 FE4 A:SF4501 0.0 19.4 1.0 S2 A:SF4501 2.3 18.2 1.0 S3 A:SF4501 2.3 18.8 1.0 SG A:CYS332 2.3 22.0 1.0 S1 A:SF4501 2.3 19.6 1.0 FE1 A:SF4501 2.7 17.8 1.0 FE2 A:SF4501 2.7 18.4 1.0 FE3 A:SF4501 2.7 18.9 1.0 CB A:CYS332 3.2 23.2 1.0 S4 A:SF4501 3.9 18.5 1.0 N A:LYS334 4.0 24.2 1.0 N A:LYS333 4.0 26.1 1.0 CD A:PRO391 4.1 20.7 1.0 CA A:CYS332 4.4 25.6 1.0 C A:CYS332 4.5 27.6 1.0 CB A:LYS334 4.5 26.4 1.0 N A:CYS335 4.7 20.1 1.0 SG A:CYS390 4.7 17.8 1.0 SG A:CYS335 4.7 18.6 1.0 CA A:LYS333 4.8 26.9 1.0 CA A:LYS334 4.8 24.0 1.0 C A:LYS333 4.8 27.0 1.0 CG A:PRO391 4.8 25.9 1.0 SG A:CYS329 4.9 19.2 1.0 CE2 A:PHE412 4.9 29.0 1.0 CA A:CYS329 4.9 20.1 1.0

Iron binding site 5 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.1 occ:1.00 FE1 A:SF4502 0.0 19.1 1.0 S3 A:SF4502 2.3 18.8 1.0 SG A:CYS383 2.3 17.1 1.0 S2 A:SF4502 2.3 19.9 1.0 S4 A:SF4502 2.3 17.6 1.0 FE3 A:SF4502 2.7 18.8 1.0 FE2 A:SF4502 2.7 18.0 1.0 FE4 A:SF4502 2.7 19.1 1.0 CB A:CYS383 3.1 32.3 1.0 S1 A:SF4502 3.9 19.1 1.0 N A:GLY384 4.0 16.5 1.0 CD A:PRO340 4.0 17.1 1.0 N A:VAL385 4.1 17.1 1.0 CA A:CYS383 4.4 20.8 1.0 CB A:VAL385 4.5 16.0 1.0 SG A:CYS386 4.6 16.8 1.0 CD2 A:TYR375 4.7 18.6 1.0 C A:CYS383 4.7 23.8 1.0 SG A:CYS339 4.7 19.0 1.0 N A:CYS386 4.7 15.0 1.0 SG A:CYS372 4.7 18.0 1.0 CA A:GLY384 4.8 14.8 1.0 CA A:VAL385 4.9 14.1 1.0 C A:GLY384 4.9 16.5 1.0 CG A:PRO340 4.9 19.1 1.0

Iron binding site 6 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.0 occ:1.00 FE2 A:SF4502 0.0 18.0 1.0 S3 A:SF4502 2.3 18.8 1.0 S4 A:SF4502 2.3 17.6 1.0 SG A:CYS386 2.3 16.8 1.0 S1 A:SF4502 2.3 19.1 1.0 FE3 A:SF4502 2.7 18.8 1.0 FE1 A:SF4502 2.7 19.1 1.0 FE4 A:SF4502 2.7 19.1 1.0 CB A:CYS386 3.3 16.2 1.0 N A:CYS386 3.8 15.0 1.0 S2 A:SF4502 3.9 19.9 1.0 C41 A:9QQ503 4.0 22.4 1.0 CA A:CYS386 4.2 17.1 1.0 N45 A:9QQ503 4.2 25.3 1.0 CD1 A:ILE344 4.4 19.3 1.0 N A:VAL385 4.7 17.1 1.0 SG A:CYS383 4.7 17.1 1.0 SG A:CYS372 4.7 18.0 1.0 SG A:CYS339 4.8 19.0 1.0 N A:GLY384 4.9 16.5 1.0 C8 A:9QQ503 4.9 18.5 1.0 C A:GLY384 5.0 16.5 1.0 CA A:GLY384 5.0 14.8 1.0

Iron binding site 7 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.8 occ:1.00 FE3 A:SF4502 0.0 18.8 1.0 S4 A:SF4502 2.3 17.6 1.0 SG A:CYS372 2.3 18.0 1.0 S1 A:SF4502 2.3 19.1 1.0 S2 A:SF4502 2.3 19.9 1.0 FE4 A:SF4502 2.7 19.1 1.0 FE1 A:SF4502 2.7 19.1 1.0 FE2 A:SF4502 2.7 18.0 1.0 CB A:CYS372 3.3 19.9 1.0 CA A:CYS372 3.8 21.3 1.0 S3 A:SF4502 3.8 18.8 1.0 C41 A:9QQ503 4.3 22.4 1.0 NE1 A:TRP376 4.4 19.1 1.0 C A:CYS372 4.5 19.3 1.0 O A:CYS372 4.5 19.4 1.0 SG A:CYS339 4.7 19.0 1.0 SG A:CYS383 4.7 17.1 1.0 CB A:CYS383 4.7 32.3 1.0 C8 A:9QQ503 4.8 18.5 1.0 OG A:SER341 4.8 26.2 1.0 SG A:CYS386 4.8 16.8 1.0

Iron binding site 8 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.1 occ:1.00 FE4 A:SF4502 0.0 19.1 1.0 S3 A:SF4502 2.3 18.8 1.0 SG A:CYS339 2.3 19.0 1.0 S2 A:SF4502 2.3 19.9 1.0 S1 A:SF4502 2.3 19.1 1.0 FE3 A:SF4502 2.7 18.8 1.0 FE1 A:SF4502 2.7 19.1 1.0 FE2 A:SF4502 2.7 18.0 1.0 CB A:CYS339 3.3 22.1 1.0 CA A:CYS339 3.9 18.2 1.0 S4 A:SF4502 3.9 17.6 1.0 OG A:SER341 4.0 26.2 1.0 CD A:PRO340 4.1 17.1 1.0 C A:CYS339 4.4 23.8 1.0 N A:PRO340 4.4 21.3 1.0 CB A:ALA343 4.5 22.1 1.0 CD1 A:ILE344 4.5 19.3 1.0 CG1 A:ILE344 4.7 19.1 1.0 SG A:CYS372 4.7 18.0 1.0 N A:SER341 4.8 21.5 1.0 SG A:CYS383 4.8 17.1 1.0 SG A:CYS386 4.8 16.8 1.0 N A:ALA343 5.0 22.7 1.0

Iron binding site 9 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:26.3 occ:1.00 FE1 B:SF4501 0.0 26.3 1.0 S3 B:SF4501 2.3 28.1 1.0 S4 B:SF4501 2.3 26.0 1.0 S2 B:SF4501 2.3 25.7 1.0 SG B:CYS390 2.3 25.1 1.0 FE2 B:SF4501 2.7 27.0 1.0 FE4 B:SF4501 2.7 28.9 1.0 FE3 B:SF4501 2.8 26.0 1.0 CB B:CYS390 3.3 23.6 1.0 CA B:CYS390 3.8 22.8 1.0 S1 B:SF4501 3.9 28.6 1.0 CD B:PRO391 4.0 28.7 1.0 CE B:MET292 4.1 20.0 1.0 CD1 B:ILE296 4.1 24.8 1.0 N B:PRO391 4.6 25.0 1.0 CD2 B:PHE392 4.6 28.6 1.0 C B:CYS390 4.6 27.0 1.0 SG B:CYS329 4.7 27.6 1.0 SG B:CYS335 4.8 28.1 1.0 SG B:CYS332 4.9 34.1 1.0

Iron binding site 10 out of 16 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:27.0 occ:1.00 FE2 B:SF4501 0.0 27.0 1.0 S1 B:SF4501 2.3 28.6 1.0 S3 B:SF4501 2.3 28.1 1.0 S4 B:SF4501 2.3 26.0 1.0 SG B:CYS329 2.3 27.6 1.0 FE1 B:SF4501 2.7 26.3 1.0 FE3 B:SF4501 2.7 26.0 1.0 FE4 B:SF4501 2.8 28.9 1.0 CB B:CYS329 3.4 30.2 1.0 CA B:CYS329 3.7 32.2 1.0 S2 B:SF4501 3.9 25.7 1.0 CB B:ARG291 4.1 30.3 1.0 N B:ARG291 4.2 25.9 1.0 N B:CYS329 4.4 34.5 1.0 CB B:SER290 4.5 26.9 1.0 CD1 B:ILE296 4.6 24.8 1.0 CB B:CYS332 4.6 37.6 1.0 SG B:CYS390 4.8 25.1 1.0 SG B:CYS332 4.8 34.1 1.0 CA B:ARG291 4.8 26.1 1.0 SG B:CYS335 4.8 28.1 1.0 C B:CYS329 4.9 38.7 1.0 CD1 B:PHE328 5.0 36.6 1.0

S.Keller, C.Kunze, M.Bommer, C.Paetz, R.C.Menezes, A.Svatos, H.Dobbek, T.Schubert. Selective Utilization of Benzimidazolyl-Norcobamides As Cofactors By the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum Multivorans. J. Bacteriol. V. 200 2018.
ISSN: ESSN 1098-5530
PubMed: 29378885
DOI: 10.1128/JB.00584-17