Iron in PDB 1wad: Cytochrome C3 with 4 Heme Groups and One Calcium Ion

The structure of Cytochrome C3 with 4 Heme Groups and One Calcium Ion, PDB code: 1wad was solved by P.M.Matias, J.Morais, R.Coelho, M.A.Carrondo, K.Wilson, Z.Dauter, L.Sieker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.800, 50.100, 51.700, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 21.9

The structure of Cytochrome C3 with 4 Heme Groups and One Calcium Ion also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Cytochrome C3 with 4 Heme Groups and One Calcium Ion (pdb code 1wad). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cytochrome C3 with 4 Heme Groups and One Calcium Ion, PDB code: 1wad:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytochrome C3 with 4 Heme Groups and One Calcium Ion


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C3 with 4 Heme Groups and One Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe117 b:11.6 occ:1.00 FE A:HEM117 0.0 11.6 1.0 NC A:HEM117 2.0 9.8 1.0 NE2 A:HIS26 2.0 8.9 1.0 NA A:HEM117 2.0 7.7 1.0 ND A:HEM117 2.0 10.5 1.0 NB A:HEM117 2.0 9.3 1.0 NE2 A:HIS38 2.0 12.5 1.0 CE1 A:HIS38 3.0 12.4 1.0 CE1 A:HIS26 3.0 8.6 1.0 CD2 A:HIS26 3.0 13.3 1.0 C1D A:HEM117 3.0 9.2 1.0 C4C A:HEM117 3.0 10.1 1.0 C4A A:HEM117 3.0 11.0 1.0 C1C A:HEM117 3.0 11.0 1.0 C1A A:HEM117 3.0 12.4 1.0 C1B A:HEM117 3.0 11.4 1.0 C4B A:HEM117 3.1 9.1 1.0 C4D A:HEM117 3.1 10.2 1.0 CD2 A:HIS38 3.1 13.6 1.0 CHD A:HEM117 3.4 10.5 1.0 CHB A:HEM117 3.4 12.9 1.0 CHC A:HEM117 3.4 9.6 1.0 CHA A:HEM117 3.4 13.0 1.0 ND1 A:HIS26 4.1 10.0 1.0 ND1 A:HIS38 4.1 11.2 1.0 CG A:HIS26 4.1 11.4 1.0 CG A:HIS38 4.2 11.9 1.0 C3C A:HEM117 4.2 8.1 1.0 C2C A:HEM117 4.2 11.1 1.0 C3A A:HEM117 4.2 16.4 1.0 C2A A:HEM117 4.2 15.6 1.0 C2D A:HEM117 4.3 13.6 1.0 C3D A:HEM117 4.3 10.8 1.0 C2B A:HEM117 4.3 11.3 1.0 C3B A:HEM117 4.3 12.8 1.0 CE2 A:PHE24 4.7 11.3 1.0 CD A:PRO4 4.8 20.9 1.0 CG A:PRO4 4.9 20.2 1.0

Iron binding site 2 out of 4 in the Cytochrome C3 with 4 Heme Groups and One Calcium Ion


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C3 with 4 Heme Groups and One Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe113 b:14.1 occ:1.00 FE A:HEM113 0.0 14.1 1.0 NE2 A:HIS55 1.9 11.6 1.0 NE2 A:HIS39 2.0 11.6 1.0 ND A:HEM113 2.0 15.2 1.0 NA A:HEM113 2.0 13.2 1.0 NC A:HEM113 2.0 12.8 1.0 NB A:HEM113 2.0 10.0 1.0 CE1 A:HIS55 2.8 15.0 1.0 CE1 A:HIS39 2.8 16.2 1.0 C1D A:HEM113 3.0 16.8 1.0 CD2 A:HIS55 3.0 11.4 1.0 C4A A:HEM113 3.0 15.3 1.0 C1A A:HEM113 3.0 14.2 1.0 C4D A:HEM113 3.0 13.7 1.0 C4C A:HEM113 3.0 15.2 1.0 C1B A:HEM113 3.0 15.0 1.0 C1C A:HEM113 3.0 13.7 1.0 C4B A:HEM113 3.0 11.1 1.0 CD2 A:HIS39 3.1 10.3 1.0 CHD A:HEM113 3.4 19.0 1.0 CHA A:HEM113 3.4 17.5 1.0 CHC A:HEM113 3.4 11.0 1.0 CHB A:HEM113 3.4 15.5 1.0 ND1 A:HIS55 4.0 14.3 1.0 ND1 A:HIS39 4.0 15.7 1.0 CG A:HIS55 4.1 10.9 1.0 CG A:HIS39 4.1 14.9 1.0 C2A A:HEM113 4.2 17.6 1.0 C3D A:HEM113 4.2 13.7 1.0 C2D A:HEM113 4.2 14.5 1.0 C3A A:HEM113 4.3 12.3 1.0 C3C A:HEM113 4.3 14.4 1.0 C2B A:HEM113 4.3 12.3 1.0 C2C A:HEM113 4.3 15.9 1.0 C3B A:HEM113 4.3 10.5 1.0

Iron binding site 3 out of 4 in the Cytochrome C3 with 4 Heme Groups and One Calcium Ion


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C3 with 4 Heme Groups and One Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe114 b:11.4 occ:1.00 FE A:HEM114 0.0 11.4 1.0 NB A:HEM114 2.0 10.2 1.0 NA A:HEM114 2.0 10.5 1.0 NC A:HEM114 2.0 9.8 1.0 ND A:HEM114 2.0 11.3 1.0 NE2 A:HIS29 2.0 9.7 1.0 NE2 A:HIS87 2.0 13.8 1.0 CD2 A:HIS29 3.0 9.9 1.0 CE1 A:HIS87 3.0 15.4 1.0 C4B A:HEM114 3.0 11.2 1.0 CE1 A:HIS29 3.0 11.3 1.0 C1C A:HEM114 3.0 9.5 1.0 C4D A:HEM114 3.0 10.6 1.0 C1B A:HEM114 3.0 10.9 1.0 C1A A:HEM114 3.1 10.1 1.0 C4A A:HEM114 3.1 10.5 1.0 C1D A:HEM114 3.1 12.5 1.0 C4C A:HEM114 3.1 11.1 1.0 CD2 A:HIS87 3.1 14.1 1.0 CHB A:HEM114 3.4 8.2 1.0 CHA A:HEM114 3.4 12.3 1.0 CHC A:HEM114 3.4 10.2 1.0 CHD A:HEM114 3.4 12.6 1.0 CG A:HIS29 4.1 9.7 1.0 ND1 A:HIS29 4.1 11.4 1.0 ND1 A:HIS87 4.1 11.1 1.0 CG A:HIS87 4.2 11.0 1.0 C2B A:HEM114 4.2 10.7 1.0 C3B A:HEM114 4.3 8.5 1.0 C2A A:HEM114 4.3 9.2 1.0 C3D A:HEM114 4.3 13.6 1.0 C2C A:HEM114 4.3 12.1 1.0 C3C A:HEM114 4.3 11.4 1.0 C3A A:HEM114 4.3 9.9 1.0 C2D A:HEM114 4.3 12.6 1.0

Iron binding site 4 out of 4 in the Cytochrome C3 with 4 Heme Groups and One Calcium Ion


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C3 with 4 Heme Groups and One Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe115 b:10.9 occ:1.00 FE A:HEM115 0.0 10.9 1.0 NE2 A:HIS110 2.0 10.8 1.0 ND A:HEM115 2.0 8.2 1.0 NA A:HEM115 2.0 9.3 1.0 NC A:HEM115 2.0 8.5 1.0 NB A:HEM115 2.0 8.3 1.0 NE2 A:HIS73 2.1 8.7 1.0 CE1 A:HIS110 3.0 9.7 1.0 CD2 A:HIS110 3.0 11.7 1.0 C1C A:HEM115 3.0 8.8 1.0 C4D A:HEM115 3.0 5.5 1.0 C4A A:HEM115 3.0 10.2 1.0 C1A A:HEM115 3.0 9.2 1.0 C1B A:HEM115 3.0 12.0 1.0 C1D A:HEM115 3.0 8.6 1.0 CE1 A:HIS73 3.1 14.2 1.0 CD2 A:HIS73 3.1 10.0 1.0 C4C A:HEM115 3.1 8.9 1.0 C4B A:HEM115 3.1 10.0 1.0 CHB A:HEM115 3.4 8.5 1.0 CHA A:HEM115 3.4 8.4 1.0 CHC A:HEM115 3.4 10.6 1.0 CHD A:HEM115 3.4 8.7 1.0 ND1 A:HIS110 4.1 11.5 1.0 CG A:HIS110 4.1 12.2 1.0 ND1 A:HIS73 4.2 11.7 1.0 CG A:HIS73 4.2 9.5 1.0 C3D A:HEM115 4.2 7.6 1.0 C2C A:HEM115 4.2 8.4 1.0 C2A A:HEM115 4.3 9.9 1.0 C3A A:HEM115 4.3 12.5 1.0 C2D A:HEM115 4.3 8.7 1.0 C3C A:HEM115 4.3 6.9 1.0 C2B A:HEM115 4.3 12.8 1.0 C3B A:HEM115 4.3 11.6 1.0 CG1 A:VAL72 4.9 6.0 1.0 CD1 A:LEU20 5.0 20.6 1.0

P.M.Matias, J.Morais, R.Coelho, M.A.Carrondo, K.Wilson, Z.Dauter, L.Sieker. Cytochrome C3 From Desulfovibrio Gigas: Crystal Structure at 1.8 A Resolution and Evidence For A Specific Calcium-Binding Site. Protein Sci. V. 5 1342 1996.
ISSN: ISSN 0961-8368
PubMed: 8819167