Iron in PDB 3h4n: Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens

The structure of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens, PDB code: 3h4n was solved by P.R.Pokkuluri, M.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.04 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	27.400, 55.900, 94.800, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.3

The binding sites of Iron atom in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens (pdb code 3h4n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens, PDB code: 3h4n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe72 b:4.3 occ:1.00 FE A:HEM72 0.0 4.3 1.0 NC A:HEM72 2.0 4.8 1.0 ND A:HEM72 2.0 4.5 1.0 NB A:HEM72 2.0 4.5 1.0 NA A:HEM72 2.0 4.0 1.0 NE2 A:HIS31 2.1 6.3 1.0 NE2 A:HIS17 2.1 7.0 1.0 CE1 A:HIS31 3.0 3.6 1.0 C4C A:HEM72 3.0 4.5 1.0 C1D A:HEM72 3.0 4.5 1.0 C1C A:HEM72 3.0 4.9 1.0 C4D A:HEM72 3.0 4.3 1.0 CD2 A:HIS17 3.0 3.8 1.0 C4A A:HEM72 3.0 4.2 1.0 C1B A:HEM72 3.1 4.0 1.0 CE1 A:HIS17 3.1 2.8 1.0 C4B A:HEM72 3.1 4.3 1.0 CD2 A:HIS31 3.1 2.8 1.0 C1A A:HEM72 3.1 4.7 1.0 CHD A:HEM72 3.4 4.7 1.0 CHB A:HEM72 3.4 4.1 1.0 CHC A:HEM72 3.4 4.4 1.0 CHA A:HEM72 3.4 4.4 1.0 ND1 A:HIS31 4.1 6.0 1.0 ND1 A:HIS17 4.2 5.8 1.0 CG A:HIS31 4.2 4.8 1.0 CG A:HIS17 4.2 4.4 1.0 C2C A:HEM72 4.2 4.4 1.0 C3C A:HEM72 4.2 4.6 1.0 C2D A:HEM72 4.3 5.7 1.0 C3D A:HEM72 4.3 5.2 1.0 C2A A:HEM72 4.3 5.5 1.0 C3A A:HEM72 4.3 5.0 1.0 C3B A:HEM72 4.3 5.1 1.0 C2B A:HEM72 4.3 4.6 1.0 CE2 A:PHE15 4.9 6.9 1.0

Iron binding site 2 out of 6 in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe73 b:5.0 occ:1.00 FE A:HEM73 0.0 5.0 1.0 NC A:HEM73 2.0 4.9 1.0 NB A:HEM73 2.0 4.8 1.0 NE2 A:HIS55 2.0 4.5 1.0 ND A:HEM73 2.0 4.5 1.0 NE2 A:HIS20 2.0 5.2 1.0 NA A:HEM73 2.0 5.4 1.0 CE1 A:HIS55 3.0 5.3 1.0 CD2 A:HIS20 3.0 5.1 1.0 C1C A:HEM73 3.0 5.3 1.0 C4B A:HEM73 3.0 4.7 1.0 CE1 A:HIS20 3.0 5.5 1.0 CD2 A:HIS55 3.0 4.5 1.0 C1B A:HEM73 3.0 5.2 1.0 C4D A:HEM73 3.0 5.5 1.0 C4C A:HEM73 3.1 5.8 1.0 C1A A:HEM73 3.1 5.9 1.0 C1D A:HEM73 3.1 5.1 1.0 C4A A:HEM73 3.1 5.8 1.0 CHC A:HEM73 3.4 4.8 1.0 CHA A:HEM73 3.4 6.0 1.0 CHD A:HEM73 3.4 5.2 1.0 CHB A:HEM73 3.4 5.1 1.0 ND1 A:HIS55 4.1 5.8 1.0 ND1 A:HIS20 4.1 6.5 1.0 CG A:HIS20 4.2 6.3 1.0 CG A:HIS55 4.2 5.1 1.0 C3B A:HEM73 4.2 5.4 1.0 C2C A:HEM73 4.3 5.3 1.0 C2B A:HEM73 4.3 5.7 1.0 C3D A:HEM73 4.3 5.7 1.0 C2D A:HEM73 4.3 6.6 1.0 C3A A:HEM73 4.3 6.8 1.0 C3C A:HEM73 4.3 5.3 1.0 C2A A:HEM73 4.3 7.2 1.0

Iron binding site 3 out of 6 in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe74 b:5.1 occ:1.00 FE A:HEM74 0.0 5.1 1.0 NB A:HEM74 2.0 4.2 1.0 NC A:HEM74 2.0 4.9 1.0 ND A:HEM74 2.0 5.2 1.0 NA A:HEM74 2.0 5.3 1.0 NE2 A:HIS69 2.0 4.9 1.0 NE2 A:HIS47 2.1 6.7 1.0 CE1 A:HIS69 3.0 5.0 1.0 CE1 A:HIS47 3.0 2.6 1.0 C4B A:HEM74 3.0 4.4 1.0 C1C A:HEM74 3.0 4.5 1.0 C1D A:HEM74 3.0 5.0 1.0 C4D A:HEM74 3.0 4.8 1.0 C1B A:HEM74 3.0 4.7 1.0 C1A A:HEM74 3.0 4.9 1.0 C4C A:HEM74 3.1 4.6 1.0 C4A A:HEM74 3.1 4.9 1.0 CD2 A:HIS69 3.1 5.1 1.0 CD2 A:HIS47 3.1 3.1 1.0 CHC A:HEM74 3.3 4.1 1.0 CHA A:HEM74 3.4 5.2 1.0 CHD A:HEM74 3.4 4.0 1.0 CHB A:HEM74 3.4 5.5 1.0 ND1 A:HIS69 4.1 5.4 1.0 ND1 A:HIS47 4.2 7.4 1.0 CG A:HIS69 4.2 5.6 1.0 CG A:HIS47 4.2 5.4 1.0 C3B A:HEM74 4.2 4.8 1.0 C2C A:HEM74 4.3 5.3 1.0 C2B A:HEM74 4.3 4.8 1.0 C3D A:HEM74 4.3 5.4 1.0 C2D A:HEM74 4.3 5.6 1.0 C3C A:HEM74 4.3 6.0 1.0 C3A A:HEM74 4.3 5.0 1.0 C2A A:HEM74 4.3 5.7 1.0 ND2 A:ASN10 4.8 7.6 1.0

Iron binding site 4 out of 6 in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe72 b:6.4 occ:1.00 FE B:HEM72 0.0 6.4 1.0 NC B:HEM72 2.0 6.4 1.0 NE2 B:HIS31 2.0 7.0 1.0 ND B:HEM72 2.0 6.5 1.0 NB B:HEM72 2.0 5.8 1.0 NE2 B:HIS17 2.0 5.7 1.0 NA B:HEM72 2.0 5.9 1.0 CE1 B:HIS31 3.0 7.2 1.0 CE1 B:HIS17 3.0 7.5 1.0 C4C B:HEM72 3.0 6.4 1.0 C1D B:HEM72 3.0 6.3 1.0 CD2 B:HIS31 3.0 6.0 1.0 C1C B:HEM72 3.0 5.6 1.0 C1B B:HEM72 3.0 5.5 1.0 CD2 B:HIS17 3.0 6.0 1.0 C4B B:HEM72 3.0 6.0 1.0 C4A B:HEM72 3.1 5.8 1.0 C1A B:HEM72 3.1 7.5 1.0 C4D B:HEM72 3.1 7.1 1.0 CHD B:HEM72 3.4 5.7 1.0 CHC B:HEM72 3.4 5.5 1.0 CHB B:HEM72 3.4 5.7 1.0 CHA B:HEM72 3.5 7.5 1.0 ND1 B:HIS31 4.1 7.4 1.0 ND1 B:HIS17 4.1 7.1 1.0 CG B:HIS31 4.1 7.0 1.0 CG B:HIS17 4.2 6.5 1.0 C3C B:HEM72 4.2 6.1 1.0 C2B B:HEM72 4.2 6.0 1.0 C2C B:HEM72 4.2 6.6 1.0 C3B B:HEM72 4.3 6.0 1.0 C2D B:HEM72 4.3 7.5 1.0 C3A B:HEM72 4.3 7.5 1.0 C2A B:HEM72 4.3 9.3 1.0 C3D B:HEM72 4.3 7.5 1.0 CE2 B:PHE15 4.9 8.5 1.0

Iron binding site 5 out of 6 in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe73 b:6.4 occ:1.00 FE B:HEM73 0.0 6.4 1.0 NB B:HEM73 2.0 6.0 1.0 NC B:HEM73 2.0 4.8 1.0 ND B:HEM73 2.0 7.0 1.0 NE2 B:HIS20 2.0 6.8 1.0 NA B:HEM73 2.1 6.7 1.0 NE2 B:HIS55 2.1 6.6 1.0 CE1 B:HIS55 2.9 6.9 1.0 CD2 B:HIS20 3.0 7.0 1.0 C4B B:HEM73 3.0 6.1 1.0 C1C B:HEM73 3.0 5.0 1.0 C1B B:HEM73 3.0 6.0 1.0 C4D B:HEM73 3.0 7.4 1.0 CE1 B:HIS20 3.1 7.3 1.0 C1D B:HEM73 3.1 6.3 1.0 C4C B:HEM73 3.1 6.0 1.0 C1A B:HEM73 3.1 8.2 1.0 C4A B:HEM73 3.1 6.7 1.0 CD2 B:HIS55 3.1 8.8 1.0 CHC B:HEM73 3.4 5.7 1.0 CHA B:HEM73 3.4 7.6 1.0 CHD B:HEM73 3.4 6.2 1.0 CHB B:HEM73 3.4 6.7 1.0 ND1 B:HIS55 4.1 7.0 1.0 ND1 B:HIS20 4.1 7.8 1.0 CG B:HIS20 4.2 7.7 1.0 CG B:HIS55 4.2 6.4 1.0 C3B B:HEM73 4.2 7.7 1.0 C2B B:HEM73 4.2 7.2 1.0 C2C B:HEM73 4.2 5.6 1.0 C3D B:HEM73 4.3 8.6 1.0 C3C B:HEM73 4.3 6.5 1.0 C2D B:HEM73 4.3 7.8 1.0 C2A B:HEM73 4.3 9.7 1.0 C3A B:HEM73 4.3 7.9 1.0

Iron binding site 6 out of 6 in the Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe74 b:6.0 occ:1.00 FE B:HEM74 0.0 6.0 1.0 NB B:HEM74 2.0 5.9 1.0 NA B:HEM74 2.0 5.9 1.0 NC B:HEM74 2.0 5.9 1.0 NE2 B:HIS69 2.0 5.7 1.0 ND B:HEM74 2.0 6.0 1.0 NE2 B:HIS47 2.0 6.2 1.0 CE1 B:HIS69 3.0 5.5 1.0 CE1 B:HIS47 3.0 5.6 1.0 C4B B:HEM74 3.0 6.1 1.0 C4A B:HEM74 3.0 5.9 1.0 C1C B:HEM74 3.0 5.7 1.0 C1B B:HEM74 3.0 6.1 1.0 C1A B:HEM74 3.0 6.0 1.0 C4C B:HEM74 3.0 6.1 1.0 C1D B:HEM74 3.1 6.3 1.0 C4D B:HEM74 3.1 5.5 1.0 CD2 B:HIS69 3.1 6.9 1.0 CD2 B:HIS47 3.1 6.8 1.0 CHC B:HEM74 3.4 5.9 1.0 CHB B:HEM74 3.4 7.0 1.0 CHD B:HEM74 3.4 6.3 1.0 CHA B:HEM74 3.4 5.4 1.0 ND1 B:HIS69 4.1 5.7 1.0 ND1 B:HIS47 4.1 6.0 1.0 CG B:HIS69 4.2 6.8 1.0 CG B:HIS47 4.2 6.3 1.0 C3B B:HEM74 4.2 6.2 1.0 C3A B:HEM74 4.2 6.1 1.0 C2B B:HEM74 4.2 6.7 1.0 C2A B:HEM74 4.2 6.3 1.0 C2C B:HEM74 4.3 6.4 1.0 C3C B:HEM74 4.3 6.3 1.0 C3D B:HEM74 4.3 6.2 1.0 C2D B:HEM74 4.3 5.5 1.0 ND2 B:ASN10 4.8 7.6 1.0

P.R.Pokkuluri, Y.Y.Londer, X.Yang, N.E.Duke, J.Erickson, V.Orshonsky, G.Johnson, M.Schiffer. Structural Characterization of A Family of Cytochromes C(7) Involved in Fe(III) Respiration By Geobacter Sulfurreducens. Biochim.Biophys.Acta V.1797 222 2010.
ISSN: ISSN 0006-3002
PubMed: 19857457
DOI: 10.1016/J.BBABIO.2009.10.007