Iron in PDB 2d6c: Crystal Structure of Myoglobin Reconstituted with Iron Porphycene

The structure of Crystal Structure of Myoglobin Reconstituted with Iron Porphycene, PDB code: 2d6c was solved by T.Hayashi, D.Murata, M.Makino, H.Sugimoto, T.Matsuo, H.Sato, Y.Shiro, Y.Hisaeda, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.533, 79.902, 54.619, 90.00, 110.88, 90.00
R / Rfree (%)	25.1 / 29.5

The binding sites of Iron atom in the Crystal Structure of Myoglobin Reconstituted with Iron Porphycene (pdb code 2d6c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Myoglobin Reconstituted with Iron Porphycene, PDB code: 2d6c:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Myoglobin Reconstituted with Iron Porphycene


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 Myoglobin Reconstituted with Iron Porphycene within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe154 b:17.9 occ:1.00 FE A:HME154 0.0 17.9 1.0 ND A:HME154 2.1 16.1 1.0 NC A:HME154 2.1 22.3 1.0 NB A:HME154 2.1 23.2 1.0 NA A:HME154 2.2 16.0 1.0 NE2 A:HIS93 2.3 15.8 1.0 N1 A:IMD155 2.3 24.9 1.0 C5 A:IMD155 2.9 31.0 1.0 CD2 A:HIS93 3.0 3.3 1.0 C4D A:HME154 3.0 16.9 1.0 C1D A:HME154 3.1 19.1 1.0 C1A A:HME154 3.1 21.2 1.0 C4B A:HME154 3.1 15.8 1.0 C1C A:HME154 3.1 27.5 1.0 C4C A:HME154 3.2 22.5 1.0 C1B A:HME154 3.2 28.7 1.0 C4A A:HME154 3.3 22.4 1.0 CE1 A:HIS93 3.4 19.0 1.0 C2 A:IMD155 3.5 37.0 1.0 CHD A:HME154 3.5 23.0 1.0 CHC A:HME154 3.6 20.3 1.0 CHB A:HME154 3.7 15.6 1.0 CHA A:HME154 3.7 18.6 1.0 C4 A:IMD155 4.2 40.4 1.0 CG A:HIS93 4.3 10.7 1.0 C3D A:HME154 4.3 24.9 1.0 C2D A:HME154 4.3 19.8 1.0 C3B A:HME154 4.4 24.7 1.0 C2C A:HME154 4.4 26.8 1.0 ND1 A:HIS93 4.4 18.3 1.0 C2B A:HME154 4.4 24.9 1.0 C3C A:HME154 4.4 26.1 1.0 C2A A:HME154 4.4 10.8 1.0 N3 A:IMD155 4.5 43.9 1.0 C3A A:HME154 4.5 13.1 1.0 CG1 A:VAL68 4.8 37.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Myoglobin Reconstituted with Iron Porphycene


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 Myoglobin Reconstituted with Iron Porphycene within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe154 b:19.3 occ:1.00 FE B:HME154 0.0 19.3 1.0 ND B:HME154 2.1 22.6 1.0 NB B:HME154 2.1 27.1 1.0 NC B:HME154 2.2 20.1 1.0 NA B:HME154 2.2 11.8 1.0 NE2 B:HIS93 2.3 24.2 1.0 N1 B:IMD155 2.4 53.5 1.0 C5 B:IMD155 3.0 55.9 1.0 C4D B:HME154 3.1 25.7 1.0 C4B B:HME154 3.1 28.7 1.0 C1A B:HME154 3.1 21.7 1.0 C1C B:HME154 3.1 33.9 1.0 C1D B:HME154 3.1 19.2 1.0 C1B B:HME154 3.2 28.4 1.0 C4C B:HME154 3.2 17.5 1.0 C4A B:HME154 3.2 11.9 1.0 CD2 B:HIS93 3.2 18.8 1.0 CE1 B:HIS93 3.3 17.2 1.0 C2 B:IMD155 3.6 58.3 1.0 CHD B:HME154 3.6 28.1 1.0 CHC B:HME154 3.6 15.3 1.0 CHB B:HME154 3.6 21.7 1.0 CHA B:HME154 3.7 22.8 1.0 C4 B:IMD155 4.2 58.4 1.0 C3D B:HME154 4.3 24.8 1.0 C2D B:HME154 4.3 22.7 1.0 C3B B:HME154 4.3 24.3 1.0 C2B B:HME154 4.4 18.2 1.0 ND1 B:HIS93 4.4 24.6 1.0 CG B:HIS93 4.4 23.7 1.0 C2C B:HME154 4.4 33.0 1.0 C2A B:HME154 4.4 13.6 1.0 C3C B:HME154 4.4 21.6 1.0 C3A B:HME154 4.5 12.3 1.0 N3 B:IMD155 4.5 55.0 1.0

T.Hayashi, D.Murata, M.Makino, H.Sugimoto, T.Matsuo, H.Sato, Y.Shiro, Y.Hisaeda. Crystal Structure and Peroxidase Activity of Myoglobin Reconstituted with Iron Porphycene Inorg.Chem. V. 45 10530 2006.
ISSN: ISSN 0020-1669
PubMed: 17173408
DOI: 10.1021/IC061130X