Iron in PDB 4tpu: Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans

The structure of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans, PDB code: 4tpu was solved by A.K.Kumar, H.P.Yennawar, N.H.Yennawar, J.G.Ferry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.36
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	93.181, 93.181, 93.181, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.9

The structure of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans also contains other interesting chemical elements:

Bromine	(Br)	7 atoms
Sodium	(Na)	4 atoms

The binding sites of Iron atom in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans (pdb code 4tpu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans, PDB code: 4tpu:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


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 Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:41.7 occ:1.00 FE1 A:SF4302 0.0 41.7 1.0 S4 A:SF4302 2.1 37.2 1.0 S3 A:SF4302 2.2 48.3 1.0 S2 A:SF4302 2.2 43.2 1.0 SG A:CYS67 2.3 42.0 1.0 HB2 A:CYS67 2.8 43.9 1.0 FE4 A:SF4302 2.9 40.7 1.0 FE3 A:SF4302 3.0 42.4 1.0 FE2 A:SF4302 3.0 38.2 1.0 CB A:CYS67 3.0 36.6 1.0 HA A:PRO68 3.1 38.8 1.0 HA A:CYS67 3.2 50.9 1.0 HD22 A:LEU86 3.4 52.8 1.0 CA A:CYS67 3.7 42.5 1.0 HE2 A:TYR87 3.7 43.1 1.0 S1 A:SF4302 3.8 42.3 1.0 H A:CYS69 3.8 39.8 1.0 HB3 A:CYS67 3.9 43.9 1.0 HD2 A:PRO51 3.9 51.1 1.0 HD21 A:LEU86 4.0 52.8 1.0 CA A:PRO68 4.1 32.4 1.0 HB3 A:LEU86 4.1 45.0 1.0 CD2 A:LEU86 4.2 44.1 1.0 HA A:CYS50 4.2 42.3 1.0 HD21 A:LEU38 4.3 45.6 1.0 HD2 A:TYR87 4.3 43.9 1.0 N A:CYS69 4.4 33.2 1.0 HD3 A:PRO51 4.5 51.1 1.0 C A:CYS67 4.5 52.8 1.0 CE2 A:TYR87 4.6 36.0 1.0 HB3 A:PRO68 4.6 39.5 1.0 CD A:PRO51 4.6 42.7 1.0 HB2 A:LEU86 4.6 45.0 1.0 N A:PRO68 4.6 42.1 1.0 HD11 A:LEU38 4.7 77.5 1.0 HB3 A:CYS69 4.7 39.7 1.0 HB2 A:CYS50 4.7 42.1 1.0 CB A:LEU86 4.8 37.6 1.0 C A:PRO68 4.8 41.2 1.0 N A:CYS67 4.8 36.5 1.0 HD23 A:LEU86 4.8 52.8 1.0 CD2 A:TYR87 4.9 36.7 1.0 O A:HOH439 4.9 54.5 1.0 CB A:PRO68 4.9 33.0 1.0

Iron binding site 2 out of 5 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


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 Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:38.2 occ:1.00 FE2 A:SF4302 0.0 38.2 1.0 S1 A:SF4302 2.2 42.3 1.0 S3 A:SF4302 2.2 48.3 1.0 S4 A:SF4302 2.2 37.2 1.0 SG A:CYS69 2.2 39.8 1.0 H A:CYS69 2.7 39.8 1.0 FE4 A:SF4302 2.9 40.7 1.0 HB3 A:CYS69 2.9 39.7 1.0 FE3 A:SF4302 2.9 42.4 1.0 HH22 A:ARG53 3.0 43.5 1.0 FE1 A:SF4302 3.0 41.7 1.0 CB A:CYS69 3.1 33.2 1.0 N A:CYS69 3.5 33.2 1.0 HB2 A:CYS82 3.7 48.6 1.0 HB2 A:ARG72 3.7 40.2 1.0 NH2 A:ARG53 3.7 36.3 1.0 S2 A:SF4302 3.8 43.2 1.0 CA A:CYS69 3.9 36.1 1.0 HH21 A:ARG53 3.9 43.5 1.0 HA A:PRO68 3.9 38.8 1.0 HB2 A:CYS69 3.9 39.7 1.0 HA A:CYS67 4.2 50.9 1.0 HB2 A:CYS50 4.3 42.1 1.0 CB A:CYS82 4.5 40.6 1.0 H A:ARG72 4.5 40.3 1.0 C A:PRO68 4.5 41.2 1.0 CB A:ARG72 4.6 33.6 1.0 HH12 A:ARG53 4.6 55.8 1.0 HA A:ARG72 4.6 46.1 1.0 HG3 A:ARG72 4.6 49.2 1.0 SG A:CYS50 4.6 39.5 1.0 HA A:CYS69 4.7 43.2 1.0 CA A:PRO68 4.7 32.4 1.0 H A:TYR83 4.7 57.5 1.0 HB3 A:CYS82 4.8 48.6 1.0 HB3 A:TYR83 4.8 44.1 1.0 C A:CYS69 4.8 40.6 1.0 SG A:CYS82 4.8 48.8 1.0 N A:ARG72 4.8 33.6 1.0 HB2 A:CYS67 4.8 43.9 1.0 CZ A:ARG53 4.9 39.4 1.0 CA A:ARG72 4.9 38.5 1.0 H A:TYR71 5.0 50.8 1.0 H A:CYS84 5.0 60.1 1.0 HB2 A:TYR71 5.0 51.9 1.0

Iron binding site 3 out of 5 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


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 Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:42.4 occ:1.00 FE3 A:SF4302 0.0 42.4 1.0 S2 A:SF4302 2.2 43.2 1.0 S4 A:SF4302 2.2 37.2 1.0 S1 A:SF4302 2.2 42.3 1.0 SG A:CYS50 2.3 39.5 1.0 HD2 A:PRO51 2.8 51.1 1.0 SG A:CYS84 2.9 47.0 1.0 FE4 A:SF4302 2.9 40.7 1.0 FE2 A:SF4302 2.9 38.2 1.0 FE1 A:SF4302 3.0 41.7 1.0 HB2 A:CYS50 3.1 42.1 1.0 CB A:CYS50 3.2 35.2 1.0 HA A:CYS50 3.3 42.3 1.0 HH22 A:ARG53 3.6 43.5 1.0 HH21 A:ARG53 3.6 43.5 1.0 CD A:PRO51 3.8 42.7 1.0 S3 A:SF4302 3.8 48.3 1.0 CA A:CYS50 3.8 35.4 1.0 HB2 A:CYS84 3.8 54.2 1.0 NH2 A:ARG53 3.8 36.3 1.0 H A:CYS84 3.9 60.1 1.0 CB A:CYS84 4.1 45.2 1.0 HB3 A:CYS50 4.1 42.1 1.0 HG2 A:PRO51 4.2 56.2 1.0 HD3 A:PRO51 4.2 51.1 1.0 H A:CYS52 4.2 50.9 1.0 HB2 A:CYS67 4.3 43.9 1.0 N A:PRO51 4.4 50.0 1.0 C A:CYS50 4.4 37.0 1.0 CG A:PRO51 4.5 46.9 1.0 SG A:CYS52 4.5 60.1 1.0 HB3 A:TYR83 4.6 44.1 1.0 N A:CYS84 4.6 50.2 1.0 HB3 A:CYS69 4.7 39.7 1.0 HB3 A:CYS84 4.7 54.2 1.0 HD2 A:TYR83 4.7 50.5 1.0 HG3 A:ARG53 4.8 51.4 1.0 SG A:CYS69 4.8 39.8 1.0 CZ A:ARG53 4.8 39.4 1.0 HG3 A:PRO51 4.9 56.2 1.0 SG A:CYS67 5.0 42.0 1.0 HD2 A:ARG53 5.0 58.1 1.0

Iron binding site 4 out of 5 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


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 Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:40.7 occ:1.00 FE4 A:SF4302 0.0 40.7 1.0 S1 A:SF4302 2.2 42.3 1.0 S2 A:SF4302 2.2 43.2 1.0 S3 A:SF4302 2.2 48.3 1.0 SG A:CYS82 2.3 48.8 1.0 HB2 A:CYS82 2.7 48.6 1.0 FE2 A:SF4302 2.9 38.2 1.0 FE3 A:SF4302 2.9 42.4 1.0 FE1 A:SF4302 2.9 41.7 1.0 CB A:CYS82 3.0 40.6 1.0 HB3 A:LEU86 3.2 45.0 1.0 H A:CYS84 3.2 60.1 1.0 HB2 A:CYS84 3.3 54.2 1.0 HB3 A:CYS82 3.5 48.6 1.0 H A:LEU86 3.5 60.9 1.0 HD2 A:TYR87 3.6 43.9 1.0 S4 A:SF4302 3.7 37.2 1.0 HB2 A:LEU86 3.9 45.0 1.0 CB A:LEU86 4.0 37.6 1.0 N A:CYS84 4.0 50.2 1.0 CB A:CYS84 4.1 45.2 1.0 SG A:CYS84 4.2 47.0 1.0 H A:TYR83 4.2 57.5 1.0 H A:TYR87 4.2 44.9 1.0 N A:LEU86 4.3 50.8 1.0 CA A:CYS82 4.3 46.1 1.0 HG3 A:ARG72 4.3 49.2 1.0 N A:TYR83 4.4 48.0 1.0 HD22 A:LEU86 4.4 52.8 1.0 H A:ALA85 4.4 62.1 1.0 C A:CYS82 4.4 45.0 1.0 CD2 A:TYR87 4.5 36.7 1.0 CA A:CYS84 4.6 40.9 1.0 HE2 A:TYR87 4.6 43.1 1.0 HB3 A:TYR83 4.7 44.1 1.0 CA A:LEU86 4.7 37.8 1.0 N A:ALA85 4.7 51.8 1.0 HB3 A:CYS84 4.9 54.2 1.0 HA A:CYS82 4.9 55.2 1.0 HH22 A:ARG53 4.9 43.5 1.0 HB2 A:ARG72 4.9 40.2 1.0 SG A:CYS69 4.9 39.8 1.0 N A:TYR87 4.9 37.5 1.0 HD2 A:PRO51 4.9 51.1 1.0 HD21 A:LEU86 5.0 52.8 1.0 HB2 A:TYR87 5.0 60.0 1.0 CD2 A:LEU86 5.0 44.1 1.0 SG A:CYS67 5.0 42.0 1.0 H A:CYS69 5.0 39.8 1.0

Iron binding site 5 out of 5 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


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 Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:24.4 occ:1.00 SG A:CYS145 2.1 32.4 1.0 SG A:CYS161 2.2 35.5 1.0 SG A:CYS142 2.3 30.6 1.0 SG A:CYS158 2.3 36.3 1.0 H A:CYS161 2.8 44.8 1.0 H A:CYS145 2.9 45.7 1.0 HB3 A:CYS161 3.0 35.4 1.0 HB3 A:CYS158 3.1 31.0 1.0 CB A:CYS158 3.1 25.9 1.0 HB3 A:CYS142 3.1 42.7 1.0 CB A:CYS142 3.2 35.7 1.0 CB A:CYS161 3.2 29.6 1.0 HB2 A:CYS158 3.2 31.0 1.0 HB2 A:CYS142 3.3 42.7 1.0 HB A:ILE160 3.3 40.8 1.0 HB3 A:CYS145 3.4 43.6 1.0 CB A:CYS145 3.4 36.4 1.0 HB A:VAL144 3.4 44.8 1.0 N A:CYS161 3.5 37.4 1.0 N A:CYS145 3.7 38.2 1.0 CA A:CYS161 3.9 26.6 1.0 HB3 A:TYR147 3.9 33.8 1.0 HB2 A:TYR147 4.0 33.8 1.0 HB2 A:CYS161 4.0 35.4 1.0 CA A:CYS145 4.1 28.1 1.0 HB3 A:ALA163 4.1 34.6 1.0 H A:TYR147 4.1 33.0 1.0 HB2 A:CYS145 4.2 43.6 1.0 H A:ALA163 4.2 46.2 1.0 H A:LYS162 4.2 45.7 1.0 CB A:ILE160 4.3 34.0 1.0 CB A:VAL144 4.4 37.4 1.0 H A:ILE160 4.4 45.3 1.0 CB A:TYR147 4.4 28.2 1.0 C A:CYS161 4.6 35.9 1.0 CA A:CYS158 4.6 32.1 1.0 H A:GLY146 4.6 37.0 1.0 H A:VAL144 4.6 44.5 1.0 C A:ILE160 4.6 46.8 1.0 N A:LYS162 4.6 38.2 1.0 CA A:CYS142 4.6 29.4 1.0 HB2 A:ALA163 4.6 34.6 1.0 HG22 A:ILE160 4.6 36.0 1.0 HG12 A:VAL144 4.7 33.5 1.0 HA A:CYS161 4.7 31.9 1.0 C A:CYS145 4.7 29.2 1.0 C A:VAL144 4.8 38.6 1.0 CB A:ALA163 4.8 28.9 1.0 HG11 A:VAL144 4.9 33.5 1.0 N A:GLY146 4.9 30.9 1.0 CA A:ILE160 4.9 41.2 1.0 HG21 A:ILE160 4.9 36.0 1.0 CG2 A:ILE160 4.9 30.1 1.0 N A:TYR147 4.9 27.6 1.0 HZ A:PHE168 4.9 53.5 1.0 HA A:CYS158 4.9 38.4 1.0 HA A:CYS145 4.9 33.7 1.0 CG1 A:VAL144 4.9 28.0 1.0 HG12 A:ILE160 4.9 35.2 1.0 N A:ALA163 4.9 38.6 1.0 HA A:CYS142 5.0 35.2 1.0 N A:ILE160 5.0 37.8 1.0

A.K.Kumar, R.S.Kumar, N.H.Yennawar, H.P.Yennawar, J.G.Ferry. Structural and Biochemical Characterization of A Ferredoxin:Thioredoxin Reductase-Like Enzyme From Methanosarcina Acetivorans. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25915695
DOI: 10.1021/ACS.BIOCHEM.5B00137