Iron in PDB 1duw: Structure of Nonaheme Cytochrome C

The structure of Structure of Nonaheme Cytochrome C, PDB code: 1duw was solved by S.Umhau, G.Fritz, K.Diederichs, J.Breed, P.M.Kroneck, W.Welte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.89
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.400, 55.400, 236.800, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.5

The binding sites of Iron atom in the Structure of Nonaheme Cytochrome C (pdb code 1duw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Structure of Nonaheme Cytochrome C, PDB code: 1duw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe293 b:28.4 occ:1.00 FE A:HEM293 0.0 28.4 1.0 NA A:HEM293 2.0 22.6 1.0 NB A:HEM293 2.0 19.2 1.0 NC A:HEM293 2.0 23.8 1.0 ND A:HEM293 2.0 23.9 1.0 NE2 A:HIS52 2.2 27.0 1.0 NE2 A:HIS63 2.2 25.4 1.0 C4A A:HEM293 3.0 22.0 1.0 C1B A:HEM293 3.0 18.6 1.0 C1C A:HEM293 3.0 23.7 1.0 C4D A:HEM293 3.0 24.0 1.0 C1D A:HEM293 3.0 23.9 1.0 C1A A:HEM293 3.0 21.9 1.0 C4C A:HEM293 3.0 21.5 1.0 C4B A:HEM293 3.0 21.2 1.0 CD2 A:HIS63 3.1 25.9 1.0 CD2 A:HIS52 3.1 27.0 1.0 CE1 A:HIS52 3.2 29.7 1.0 CE1 A:HIS63 3.2 26.2 1.0 CHB A:HEM293 3.4 22.5 1.0 CHC A:HEM293 3.4 24.4 1.0 CHA A:HEM293 3.5 24.2 1.0 CHD A:HEM293 3.5 25.1 1.0 C3A A:HEM293 4.2 23.3 1.0 C3D A:HEM293 4.2 26.7 1.0 C2A A:HEM293 4.2 23.8 1.0 C2B A:HEM293 4.2 18.1 1.0 C2C A:HEM293 4.2 24.4 1.0 C2D A:HEM293 4.2 25.9 1.0 ND1 A:HIS52 4.2 29.1 1.0 C3C A:HEM293 4.3 24.9 1.0 C3B A:HEM293 4.3 18.9 1.0 CG A:HIS52 4.3 27.4 1.0 ND1 A:HIS63 4.3 24.8 1.0 CG A:HIS63 4.3 24.2 1.0 CG2 A:THR53 4.9 18.0 1.0

Iron binding site 2 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe294 b:22.9 occ:1.00 FE A:HEM294 0.0 22.9 1.0 ND A:HEM294 2.0 18.9 1.0 NC A:HEM294 2.0 23.6 1.0 NA A:HEM294 2.0 23.5 1.0 NB A:HEM294 2.0 22.3 1.0 NE2 A:HIS81 2.2 22.7 1.0 NE2 A:HIS131 2.2 18.6 1.0 C1D A:HEM294 3.0 19.7 1.0 C4D A:HEM294 3.0 20.2 1.0 C1C A:HEM294 3.0 23.1 1.0 C1B A:HEM294 3.0 22.8 1.0 C4A A:HEM294 3.0 24.8 1.0 C4C A:HEM294 3.0 22.6 1.0 C1A A:HEM294 3.0 23.5 1.0 C4B A:HEM294 3.1 21.3 1.0 CE1 A:HIS81 3.1 23.1 1.0 CD2 A:HIS131 3.2 19.7 1.0 CE1 A:HIS131 3.2 16.3 1.0 CD2 A:HIS81 3.2 22.1 1.0 CHD A:HEM294 3.4 19.8 1.0 CHB A:HEM294 3.5 23.5 1.0 CHA A:HEM294 3.5 24.0 1.0 CHC A:HEM294 3.5 21.3 1.0 C2D A:HEM294 4.2 19.9 1.0 C3D A:HEM294 4.2 20.4 1.0 ND1 A:HIS81 4.2 25.8 1.0 C2C A:HEM294 4.2 24.7 1.0 C3C A:HEM294 4.2 22.5 1.0 C2A A:HEM294 4.2 22.5 1.0 C2B A:HEM294 4.3 22.1 1.0 C3A A:HEM294 4.3 24.6 1.0 C3B A:HEM294 4.3 20.5 1.0 CG A:HIS81 4.3 24.2 1.0 ND1 A:HIS131 4.3 18.0 1.0 CG A:HIS131 4.3 18.6 1.0

Iron binding site 3 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe295 b:22.3 occ:1.00 FE A:HEM295 0.0 22.3 1.0 NA A:HEM295 2.0 21.7 1.0 NB A:HEM295 2.0 16.3 1.0 ND A:HEM295 2.0 20.0 1.0 NC A:HEM295 2.0 20.7 1.0 NE2 A:HIS115 2.2 23.5 1.0 NE2 A:HIS218 2.2 20.4 1.0 C1A A:HEM295 3.0 25.1 1.0 C1B A:HEM295 3.0 19.4 1.0 C4D A:HEM295 3.0 22.6 1.0 C1C A:HEM295 3.0 22.1 1.0 C4A A:HEM295 3.0 21.7 1.0 C1D A:HEM295 3.0 21.8 1.0 C4C A:HEM295 3.0 21.7 1.0 C4B A:HEM295 3.0 21.8 1.0 CE1 A:HIS115 3.1 24.0 1.0 CD2 A:HIS218 3.1 17.8 1.0 CE1 A:HIS218 3.2 18.6 1.0 CD2 A:HIS115 3.2 21.3 1.0 CHA A:HEM295 3.4 24.8 1.0 CHD A:HEM295 3.4 23.9 1.0 CHB A:HEM295 3.5 20.6 1.0 CHC A:HEM295 3.5 21.4 1.0 ND1 A:HIS115 4.2 23.0 1.0 C2A A:HEM295 4.2 25.0 1.0 C3D A:HEM295 4.2 22.9 1.0 C2B A:HEM295 4.2 20.9 1.0 C3A A:HEM295 4.2 23.1 1.0 C2D A:HEM295 4.3 22.8 1.0 ND1 A:HIS218 4.3 20.9 1.0 C2C A:HEM295 4.3 21.3 1.0 C3C A:HEM295 4.3 19.8 1.0 C3B A:HEM295 4.3 21.4 1.0 CG A:HIS218 4.3 19.7 1.0 CG A:HIS115 4.3 21.3 1.0

Iron binding site 4 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe296 b:28.0 occ:1.00 FE A:HEM296 0.0 28.0 1.0 ND A:HEM296 2.0 23.6 1.0 NA A:HEM296 2.0 31.6 1.0 NC A:HEM296 2.0 27.8 1.0 NB A:HEM296 2.0 31.8 1.0 NE2 A:HIS51 2.2 25.1 1.0 NE2 A:HIS37 2.2 30.9 1.0 C1D A:HEM296 3.0 24.0 1.0 C1A A:HEM296 3.0 30.3 1.0 C4C A:HEM296 3.0 28.4 1.0 C4A A:HEM296 3.0 29.5 1.0 C4D A:HEM296 3.0 26.0 1.0 C4B A:HEM296 3.0 33.4 1.0 C1C A:HEM296 3.0 28.5 1.0 C1B A:HEM296 3.0 29.8 1.0 CD2 A:HIS37 3.1 29.0 1.0 CE1 A:HIS51 3.1 21.6 1.0 CD2 A:HIS51 3.2 25.0 1.0 CE1 A:HIS37 3.2 30.9 1.0 CHD A:HEM296 3.4 26.0 1.0 CHA A:HEM296 3.4 28.7 1.0 CHC A:HEM296 3.5 29.4 1.0 CHB A:HEM296 3.5 26.9 1.0 C3D A:HEM296 4.2 23.1 1.0 C2A A:HEM296 4.2 28.5 1.0 C2D A:HEM296 4.2 24.4 1.0 ND1 A:HIS51 4.2 21.6 1.0 C3A A:HEM296 4.2 28.9 1.0 C3C A:HEM296 4.2 26.9 1.0 C2C A:HEM296 4.2 27.3 1.0 C2B A:HEM296 4.3 33.4 1.0 C3B A:HEM296 4.3 33.7 1.0 CG A:HIS37 4.3 30.2 1.0 CG A:HIS51 4.3 24.9 1.0 ND1 A:HIS37 4.3 31.9 1.0 CB A:ALA10 4.9 30.9 1.0

Iron binding site 5 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe297 b:22.4 occ:1.00 FE A:HEM297 0.0 22.4 1.0 NB A:HEM297 2.0 19.7 1.0 NA A:HEM297 2.0 22.0 1.0 NC A:HEM297 2.0 22.1 1.0 ND A:HEM297 2.0 21.6 1.0 NE2 A:HIS40 2.2 19.4 1.0 NE2 A:HIS101 2.2 22.6 1.0 C1D A:HEM297 3.0 23.4 1.0 C1B A:HEM297 3.0 22.0 1.0 C4D A:HEM297 3.0 22.6 1.0 C4A A:HEM297 3.0 22.0 1.0 C1A A:HEM297 3.0 19.4 1.0 C4B A:HEM297 3.0 20.8 1.0 C1C A:HEM297 3.0 21.2 1.0 C4C A:HEM297 3.0 23.4 1.0 CD2 A:HIS40 3.1 22.7 1.0 CE1 A:HIS101 3.1 21.9 1.0 CE1 A:HIS40 3.1 20.9 1.0 CD2 A:HIS101 3.2 24.1 1.0 CHB A:HEM297 3.4 20.2 1.0 CHD A:HEM297 3.4 20.9 1.0 CHA A:HEM297 3.5 22.2 1.0 CHC A:HEM297 3.5 20.9 1.0 C3D A:HEM297 4.2 26.4 1.0 C2D A:HEM297 4.2 24.7 1.0 C2A A:HEM297 4.2 19.9 1.0 ND1 A:HIS40 4.2 23.2 1.0 C2B A:HEM297 4.2 24.8 1.0 C3A A:HEM297 4.2 21.9 1.0 C3B A:HEM297 4.2 21.5 1.0 CG A:HIS40 4.2 23.5 1.0 C2C A:HEM297 4.3 22.4 1.0 ND1 A:HIS101 4.3 22.2 1.0 C3C A:HEM297 4.3 24.9 1.0 CG A:HIS101 4.3 24.9 1.0 CE1 A:PHE35 4.7 23.0 1.0 CD1 A:LEU213 5.0 19.4 1.0

Iron binding site 6 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe298 b:24.0 occ:1.00 FE A:HEM298 0.0 24.0 1.0 NB A:HEM298 2.0 17.9 1.0 NC A:HEM298 2.0 22.2 1.0 NA A:HEM298 2.0 23.5 1.0 ND A:HEM298 2.0 23.2 1.0 NE2 A:HIS245 2.2 19.6 1.0 NE2 A:HIS230 2.2 23.6 1.0 C1B A:HEM298 3.0 20.9 1.0 C4D A:HEM298 3.0 22.8 1.0 C1D A:HEM298 3.0 24.7 1.0 C4C A:HEM298 3.0 24.7 1.0 C4B A:HEM298 3.0 19.7 1.0 C1C A:HEM298 3.0 22.9 1.0 C4A A:HEM298 3.0 22.0 1.0 C1A A:HEM298 3.0 23.2 1.0 CE1 A:HIS245 3.1 20.2 1.0 CD2 A:HIS230 3.1 22.2 1.0 CD2 A:HIS245 3.2 19.4 1.0 CE1 A:HIS230 3.2 24.3 1.0 CHD A:HEM298 3.4 25.8 1.0 CHB A:HEM298 3.5 22.2 1.0 CHA A:HEM298 3.5 23.5 1.0 CHC A:HEM298 3.5 23.1 1.0 ND1 A:HIS245 4.2 19.7 1.0 C2C A:HEM298 4.2 23.1 1.0 C2D A:HEM298 4.2 24.5 1.0 C3D A:HEM298 4.2 25.4 1.0 C3C A:HEM298 4.2 25.1 1.0 C2B A:HEM298 4.2 22.2 1.0 C3B A:HEM298 4.2 19.8 1.0 C3A A:HEM298 4.3 20.8 1.0 C2A A:HEM298 4.3 20.3 1.0 CG A:HIS245 4.3 19.3 1.0 ND1 A:HIS230 4.3 23.2 1.0 CG A:HIS230 4.3 22.5 1.0 NH1 A:ARG231 4.6 29.1 1.0

Iron binding site 7 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe299 b:25.2 occ:1.00 FE A:HEM299 0.0 25.2 1.0 NA A:HEM299 2.0 24.6 1.0 NC A:HEM299 2.0 29.3 1.0 ND A:HEM299 2.0 18.8 1.0 NB A:HEM299 2.0 27.4 1.0 NE2 A:HIS264 2.2 21.9 1.0 NE2 A:HIS288 2.2 24.2 1.0 C4A A:HEM299 3.0 27.1 1.0 C1A A:HEM299 3.0 24.0 1.0 C4D A:HEM299 3.0 20.5 1.0 C1C A:HEM299 3.0 28.4 1.0 C4B A:HEM299 3.0 28.9 1.0 C1D A:HEM299 3.0 20.1 1.0 C1B A:HEM299 3.0 26.6 1.0 C4C A:HEM299 3.0 27.6 1.0 CE1 A:HIS264 3.1 22.0 1.0 CD2 A:HIS288 3.2 25.5 1.0 CD2 A:HIS264 3.2 22.9 1.0 CE1 A:HIS288 3.2 23.7 1.0 CHC A:HEM299 3.5 27.2 1.0 CHA A:HEM299 3.5 21.6 1.0 CHD A:HEM299 3.5 22.7 1.0 CHB A:HEM299 3.5 28.0 1.0 ND1 A:HIS264 4.2 22.2 1.0 C3D A:HEM299 4.2 22.4 1.0 C2A A:HEM299 4.2 25.2 1.0 C3A A:HEM299 4.3 25.3 1.0 C2D A:HEM299 4.3 18.9 1.0 C2B A:HEM299 4.3 28.7 1.0 C2C A:HEM299 4.3 27.9 1.0 C3C A:HEM299 4.3 30.7 1.0 C3B A:HEM299 4.3 29.2 1.0 CG A:HIS264 4.3 21.9 1.0 ND1 A:HIS288 4.3 23.9 1.0 CG A:HIS288 4.3 23.9 1.0

Iron binding site 8 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:23.1 occ:1.00 FE A:HEM300 0.0 23.1 1.0 NC A:HEM300 2.0 18.4 1.0 NA A:HEM300 2.0 23.8 1.0 NB A:HEM300 2.0 23.5 1.0 ND A:HEM300 2.0 19.7 1.0 NE2 A:HIS229 2.2 22.7 1.0 NE2 A:HIS197 2.2 20.1 1.0 C4C A:HEM300 3.0 19.1 1.0 C1C A:HEM300 3.0 17.5 1.0 C1A A:HEM300 3.0 22.6 1.0 C1D A:HEM300 3.0 22.1 1.0 C4A A:HEM300 3.0 20.7 1.0 C1B A:HEM300 3.0 23.5 1.0 CD2 A:HIS229 3.0 22.7 1.0 C4D A:HEM300 3.0 21.0 1.0 C4B A:HEM300 3.1 20.0 1.0 CE1 A:HIS197 3.1 21.5 1.0 CE1 A:HIS229 3.1 21.5 1.0 CD2 A:HIS197 3.2 21.5 1.0 CHD A:HEM300 3.4 20.9 1.0 CHC A:HEM300 3.4 17.9 1.0 CHB A:HEM300 3.5 20.6 1.0 CHA A:HEM300 3.5 22.5 1.0 CG A:HIS229 4.2 20.9 1.0 ND1 A:HIS229 4.2 20.1 1.0 C2C A:HEM300 4.2 18.9 1.0 C3C A:HEM300 4.2 18.2 1.0 C2A A:HEM300 4.2 19.8 1.0 C3A A:HEM300 4.2 20.4 1.0 ND1 A:HIS197 4.3 21.1 1.0 C2D A:HEM300 4.3 20.7 1.0 C3D A:HEM300 4.3 20.7 1.0 C2B A:HEM300 4.3 22.9 1.0 C3B A:HEM300 4.3 21.6 1.0 CG A:HIS197 4.3 21.6 1.0 CD A:PRO178 5.0 26.4 1.0 CG A:PRO178 5.0 28.1 1.0

Iron binding site 9 out of 9 in the Structure of Nonaheme Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Nonaheme Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.9 occ:1.00 FE A:HEM301 0.0 22.9 1.0 ND A:HEM301 2.0 19.0 1.0 NC A:HEM301 2.0 22.4 1.0 NA A:HEM301 2.0 23.1 1.0 NB A:HEM301 2.0 20.4 1.0 NE2 A:HIS271 2.2 16.2 1.0 NE2 A:HIS200 2.2 18.5 1.0 CD2 A:HIS200 3.0 18.4 1.0 C1D A:HEM301 3.0 21.8 1.0 C1A A:HEM301 3.0 24.3 1.0 C1C A:HEM301 3.0 21.3 1.0 C4B A:HEM301 3.0 21.0 1.0 C4D A:HEM301 3.0 20.9 1.0 C1B A:HEM301 3.0 20.6 1.0 C4C A:HEM301 3.0 22.5 1.0 C4A A:HEM301 3.0 21.3 1.0 CD2 A:HIS271 3.1 17.0 1.0 CE1 A:HIS271 3.1 16.3 1.0 CE1 A:HIS200 3.3 16.4 1.0 CHA A:HEM301 3.4 23.6 1.0 CHD A:HEM301 3.5 24.6 1.0 CHC A:HEM301 3.5 20.5 1.0 CHB A:HEM301 3.5 21.0 1.0 CG A:HIS200 4.2 18.6 1.0 CG A:HIS271 4.2 15.0 1.0 ND1 A:HIS271 4.2 16.2 1.0 C3D A:HEM301 4.2 20.7 1.0 C2D A:HEM301 4.2 22.5 1.0 C2A A:HEM301 4.2 23.6 1.0 C2C A:HEM301 4.2 21.1 1.0 C3B A:HEM301 4.2 19.5 1.0 C2B A:HEM301 4.3 21.4 1.0 C3A A:HEM301 4.3 20.5 1.0 C3C A:HEM301 4.3 21.9 1.0 ND1 A:HIS200 4.3 16.7 1.0 CE1 A:PHE195 4.7 20.1 1.0

S.Umhau, G.Fritz, K.Diederichs, J.Breed, W.Welte, P.M.Kroneck. Three-Dimensional Structure of the Nonaheme Cytochrome C From Desulfovibrio Desulfuricans Essex in the Fe(III) State at 1.89 A Resolution. Biochemistry V. 40 1308 2001.
ISSN: ISSN 0006-2960
PubMed: 11170457
DOI: 10.1021/BI001479A