Iron in PDB 1bvb: Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea

The structure of Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea, PDB code: 1bvb was solved by T.M.Iverson, D.M.Arciero, B.T.Hsu, M.S.P.Logan, A.B.Hooper, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.200, 68.200, 168.833, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Iron atom in the Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea (pdb code 1bvb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea, PDB code: 1bvb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe213 b:15.1 occ:1.00 FE A:HEM213 0.0 15.1 1.0 NC A:HEM213 2.0 19.2 1.0 ND A:HEM213 2.0 20.3 1.0 NB A:HEM213 2.0 19.9 1.0 NA A:HEM213 2.0 19.1 1.0 NE2 A:HIS15 2.0 14.4 1.0 ND1 A:HIS102 2.2 22.9 1.0 C1C A:HEM213 3.0 16.6 1.0 C4C A:HEM213 3.0 18.0 1.0 C1A A:HEM213 3.0 21.2 1.0 C4B A:HEM213 3.0 21.4 1.0 CE1 A:HIS15 3.0 13.2 1.0 C4A A:HEM213 3.0 21.3 1.0 C4D A:HEM213 3.0 20.3 1.0 C1D A:HEM213 3.0 17.8 1.0 CE1 A:HIS102 3.0 25.0 1.0 C1B A:HEM213 3.1 17.8 1.0 CD2 A:HIS15 3.1 12.7 1.0 CG A:HIS102 3.3 29.9 1.0 CHC A:HEM213 3.4 20.0 1.0 CHA A:HEM213 3.4 19.5 1.0 CHD A:HEM213 3.4 14.7 1.0 CHB A:HEM213 3.4 20.8 1.0 CB A:HIS102 3.8 29.3 1.0 ND1 A:HIS15 4.2 16.0 1.0 C3C A:HEM213 4.2 19.0 1.0 CG A:HIS15 4.2 18.4 1.0 C2C A:HEM213 4.2 15.0 1.0 NE2 A:HIS102 4.3 27.3 1.0 C2A A:HEM213 4.3 20.4 1.0 C3D A:HEM213 4.3 19.5 1.0 C2D A:HEM213 4.3 19.3 1.0 C3A A:HEM213 4.3 23.1 1.0 C3B A:HEM213 4.3 18.1 1.0 C2B A:HEM213 4.3 17.7 1.0 CD2 A:HIS102 4.4 30.9 1.0

Iron binding site 2 out of 4 in the Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe214 b:13.4 occ:1.00 FE A:HEM214 0.0 13.4 1.0 ND A:HEM214 2.0 15.4 1.0 NC A:HEM214 2.0 8.9 1.0 NA A:HEM214 2.0 7.1 1.0 NB A:HEM214 2.0 10.8 1.0 NE2 A:HIS64 2.4 10.7 1.0 C1A A:HEM214 3.0 13.0 1.0 C1C A:HEM214 3.0 10.4 1.0 C4D A:HEM214 3.0 16.3 1.0 C4C A:HEM214 3.0 13.7 1.0 C1D A:HEM214 3.1 14.4 1.0 C4B A:HEM214 3.1 11.9 1.0 C4A A:HEM214 3.1 9.9 1.0 C1B A:HEM214 3.1 11.0 1.0 CE1 A:HIS64 3.2 15.5 1.0 CHA A:HEM214 3.4 11.4 1.0 CHC A:HEM214 3.4 8.9 1.0 CHD A:HEM214 3.4 12.8 1.0 CHB A:HEM214 3.5 11.3 1.0 CD2 A:HIS64 3.6 9.3 1.0 CD A:PRO155 4.1 17.6 1.0 CD2 A:PHE156 4.1 14.1 1.0 CE2 A:PHE156 4.2 9.4 1.0 C3C A:HEM214 4.3 8.6 1.0 C2D A:HEM214 4.3 16.1 1.0 C3D A:HEM214 4.3 15.4 1.0 C2C A:HEM214 4.3 12.8 1.0 C2A A:HEM214 4.3 10.5 1.0 C3B A:HEM214 4.3 9.5 1.0 C2B A:HEM214 4.3 6.1 1.0 C3A A:HEM214 4.4 9.8 1.0 ND1 A:HIS64 4.4 10.3 1.0 CG A:HIS64 4.7 9.9 1.0 CG A:PRO155 4.7 12.4 1.0 CMD A:HEM216 4.7 12.4 1.0

Iron binding site 3 out of 4 in the Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe215 b:12.0 occ:1.00 FE A:HEM215 0.0 12.0 1.0 NC A:HEM215 2.0 13.1 1.0 ND A:HEM215 2.0 11.9 1.0 NB A:HEM215 2.0 16.1 1.0 NA A:HEM215 2.0 14.9 1.0 NE2 A:HIS92 2.1 9.5 1.0 NE2 A:HIS179 2.2 6.2 1.0 C1C A:HEM215 3.0 14.8 1.0 C4D A:HEM215 3.0 16.1 1.0 C4C A:HEM215 3.0 14.1 1.0 C4B A:HEM215 3.0 19.3 1.0 C1A A:HEM215 3.0 18.6 1.0 C1D A:HEM215 3.1 12.3 1.0 C1B A:HEM215 3.1 17.9 1.0 CE1 A:HIS92 3.1 15.7 1.0 C4A A:HEM215 3.1 15.2 1.0 CD2 A:HIS179 3.2 12.4 1.0 CD2 A:HIS92 3.2 12.8 1.0 CE1 A:HIS179 3.3 11.4 1.0 CHC A:HEM215 3.4 16.8 1.0 CHA A:HEM215 3.4 18.1 1.0 CHD A:HEM215 3.4 10.5 1.0 CHB A:HEM215 3.4 16.5 1.0 ND1 A:HIS92 4.2 13.8 1.0 C3C A:HEM215 4.3 11.1 1.0 C2C A:HEM215 4.3 12.5 1.0 C3D A:HEM215 4.3 13.9 1.0 C2B A:HEM215 4.3 21.1 1.0 C2D A:HEM215 4.3 14.1 1.0 C3B A:HEM215 4.3 17.3 1.0 C2A A:HEM215 4.3 19.9 1.0 CG A:HIS92 4.3 12.9 1.0 C3A A:HEM215 4.3 18.5 1.0 CG A:HIS179 4.4 11.6 1.0 ND1 A:HIS179 4.4 13.0 1.0

Iron binding site 4 out of 4 in the Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Heme-Packing Motifs Revealed By the Crystal Structure of Cytochrome C554 From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe216 b:8.8 occ:1.00 FE A:HEM216 0.0 8.8 1.0 ND A:HEM216 2.0 12.6 1.0 NC A:HEM216 2.0 12.2 1.0 NA A:HEM216 2.0 11.2 1.0 NB A:HEM216 2.0 15.3 1.0 NE2 A:HIS27 2.1 9.4 1.0 NE2 A:HIS138 2.1 7.8 1.0 C1A A:HEM216 3.0 15.4 1.0 C4D A:HEM216 3.0 13.6 1.0 C4C A:HEM216 3.0 11.2 1.0 CE1 A:HIS27 3.0 12.9 1.0 CE1 A:HIS138 3.0 9.7 1.0 C4A A:HEM216 3.0 15.7 1.0 C1D A:HEM216 3.0 12.5 1.0 C1C A:HEM216 3.0 16.1 1.0 C4B A:HEM216 3.1 15.0 1.0 C1B A:HEM216 3.1 15.1 1.0 CD2 A:HIS27 3.1 12.7 1.0 CD2 A:HIS138 3.1 5.6 1.0 CHA A:HEM216 3.4 17.1 1.0 CHD A:HEM216 3.4 11.1 1.0 CHB A:HEM216 3.4 16.1 1.0 CHC A:HEM216 3.4 14.1 1.0 ND1 A:HIS27 4.2 12.2 1.0 ND1 A:HIS138 4.2 11.3 1.0 CG A:HIS27 4.2 16.7 1.0 C3D A:HEM216 4.2 15.3 1.0 CG A:HIS138 4.2 7.0 1.0 C2A A:HEM216 4.3 14.0 1.0 C3C A:HEM216 4.3 12.2 1.0 C2D A:HEM216 4.3 11.8 1.0 C3A A:HEM216 4.3 13.3 1.0 C2C A:HEM216 4.3 14.0 1.0 C2B A:HEM216 4.3 18.9 1.0 C3B A:HEM216 4.3 15.4 1.0

T.M.Iverson, D.M.Arciero, B.T.Hsu, M.S.Logan, A.B.Hooper, D.C.Rees. Heme Packing Motifs Revealed By the Crystal Structure of the Tetra-Heme Cytochrome C554 From Nitrosomonas Europaea. Nat.Struct.Biol. V. 5 1005 1998.
ISSN: ISSN 1072-8368
PubMed: 9808046
DOI: 10.1038/2975