Iron in PDB 3vm9: Dimeric Horse Myoglobin

The structure of Dimeric Horse Myoglobin, PDB code: 3vm9 was solved by S.Nagao, H.Osuka, T.Yamada, T.Uni, Y.Shomura, K.Imai, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.340, 62.523, 83.354, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 16.8

The binding sites of Iron atom in the Dimeric Horse Myoglobin (pdb code 3vm9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dimeric Horse Myoglobin, PDB code: 3vm9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dimeric Horse Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dimeric Horse Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe154 b:7.8 occ:1.00 FE A:HEM154 0.0 7.8 1.0 ND A:HEM154 2.0 8.4 1.0 NA A:HEM154 2.0 7.9 1.0 NB A:HEM154 2.0 7.8 1.0 NC A:HEM154 2.0 7.7 1.0 NE2 A:HIS93 2.1 8.1 1.0 O A:O155 2.1 8.8 1.0 CE1 A:HIS93 3.0 9.1 1.0 C4C A:HEM154 3.0 7.7 1.0 C4A A:HEM154 3.0 7.7 1.0 C1D A:HEM154 3.0 8.2 1.0 C4D A:HEM154 3.0 8.3 1.0 C1C A:HEM154 3.0 7.4 1.0 C1A A:HEM154 3.1 7.9 1.0 C4B A:HEM154 3.1 7.3 1.0 C1B A:HEM154 3.1 7.2 1.0 CD2 A:HIS93 3.1 8.3 1.0 CHD A:HEM154 3.4 8.3 1.0 CHB A:HEM154 3.4 7.5 1.0 CHA A:HEM154 3.4 8.8 1.0 CHC A:HEM154 3.4 7.9 1.0 ND1 A:HIS93 4.2 9.2 1.0 NE2 B:HIS64 4.2 10.0 1.0 C3C A:HEM154 4.3 7.9 1.0 CG A:HIS93 4.3 8.6 1.0 C3D A:HEM154 4.3 8.9 1.0 C3A A:HEM154 4.3 8.4 1.0 C2C A:HEM154 4.3 7.4 1.0 C2D A:HEM154 4.3 8.5 1.0 C2A A:HEM154 4.3 7.8 1.0 C2B A:HEM154 4.3 6.9 1.0 C3B A:HEM154 4.3 7.5 1.0 CG2 B:VAL68 4.7 8.5 1.0 CE1 B:HIS64 4.8 11.6 1.0 CD2 A:HIS97 5.0 10.3 1.0

Iron binding site 2 out of 2 in the Dimeric Horse Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dimeric Horse Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe154 b:8.0 occ:1.00 FE B:HEM154 0.0 8.0 1.0 NB B:HEM154 2.0 8.0 1.0 ND B:HEM154 2.0 8.5 1.0 NA B:HEM154 2.0 9.0 1.0 NE2 B:HIS93 2.0 8.1 1.0 NC B:HEM154 2.0 7.7 1.0 O B:O155 2.1 9.0 1.0 CE1 B:HIS93 3.0 9.7 1.0 C1D B:HEM154 3.0 8.5 1.0 C4D B:HEM154 3.0 9.2 1.0 C4A B:HEM154 3.0 8.8 1.0 C1A B:HEM154 3.0 9.5 1.0 C1C B:HEM154 3.0 7.6 1.0 C4C B:HEM154 3.0 7.8 1.0 C4B B:HEM154 3.0 7.5 1.0 C1B B:HEM154 3.1 7.9 1.0 CD2 B:HIS93 3.1 8.0 1.0 CHD B:HEM154 3.4 8.8 1.0 CHC B:HEM154 3.4 7.9 1.0 CHA B:HEM154 3.4 9.2 1.0 CHB B:HEM154 3.4 8.4 1.0 ND1 B:HIS93 4.2 9.8 1.0 CG B:HIS93 4.3 8.2 1.0 NE2 A:HIS64 4.3 9.5 1.0 C2A B:HEM154 4.3 9.8 1.0 C2D B:HEM154 4.3 9.5 1.0 C3C B:HEM154 4.3 8.1 1.0 C3B B:HEM154 4.3 7.5 1.0 C3A B:HEM154 4.3 9.3 1.0 C3D B:HEM154 4.3 10.0 1.0 C2C B:HEM154 4.3 7.8 1.0 C2B B:HEM154 4.3 8.0 1.0 CG2 A:VAL68 4.7 9.5 1.0 CE1 A:HIS64 4.8 11.2 1.0 CD2 B:HIS97 5.0 11.5 1.0 CZ A:PHE43 5.0 10.7 1.0

S.Nagao, H.Osuka, T.Yamada, T.Uni, Y.Shomura, K.Imai, Y.Higuchi, S.Hirota. Structural and Oxygen Binding Properties of Dimeric Horse Myoglobin Dalton Trans V. 41 11378 2012.
ISSN: ISSN 1477-9226
PubMed: 22885714
DOI: 10.1039/C2DT30893B