Iron in PDB 7ddu: Elephant Seal Myoglobin Esmb

The structure of Elephant Seal Myoglobin Esmb, PDB code: 7ddu was solved by Y.Isogai, H.Imamura, S.Nakae, T.Sumi, K.Takahashi, T.Shirai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.09, 29.35, 75.36, 90, 96.2, 90
R / Rfree (%)	19.9 / 20.5

The binding sites of Iron atom in the Elephant Seal Myoglobin Esmb (pdb code 7ddu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Elephant Seal Myoglobin Esmb, PDB code: 7ddu:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Elephant Seal Myoglobin Esmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Elephant Seal Myoglobin Esmb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:17.3 occ:1.00 FE A:HEM201 0.0 17.3 1.0 NA A:HEM201 1.9 15.1 1.0 ND A:HEM201 2.0 21.4 1.0 NB A:HEM201 2.0 15.2 1.0 NC A:HEM201 2.1 15.1 1.0 NE2 A:HIS93 2.2 17.6 1.0 O A:HOH331 2.2 20.0 1.0 C1A A:HEM201 3.0 22.5 1.0 C4A A:HEM201 3.0 17.3 1.0 C4D A:HEM201 3.0 20.1 1.0 C1D A:HEM201 3.0 15.5 1.0 C4B A:HEM201 3.1 15.1 1.0 C1B A:HEM201 3.1 14.6 1.0 C4C A:HEM201 3.1 12.3 1.0 CE1 A:HIS93 3.1 18.2 1.0 C1C A:HEM201 3.1 13.4 1.0 CD2 A:HIS93 3.2 12.0 1.0 HE1 A:HIS93 3.2 21.9 1.0 CHA A:HEM201 3.4 21.1 1.0 CHB A:HEM201 3.4 17.1 1.0 HD2 A:HIS93 3.4 14.4 1.0 CHD A:HEM201 3.4 16.2 1.0 CHC A:HEM201 3.5 12.5 1.0 HG22 A:VAL68 3.8 20.3 1.0 HE1 A:HIS64 4.1 21.2 1.0 C2A A:HEM201 4.2 19.9 1.0 C3A A:HEM201 4.2 20.1 1.0 C3D A:HEM201 4.2 21.6 1.0 C2D A:HEM201 4.2 21.6 1.0 ND1 A:HIS93 4.2 15.5 1.0 C3B A:HEM201 4.3 14.8 1.0 C2B A:HEM201 4.3 15.8 1.0 CG A:HIS93 4.3 17.9 1.0 C2C A:HEM201 4.3 14.0 1.0 C3C A:HEM201 4.3 15.6 1.0 NE2 A:HIS64 4.3 15.3 1.0 HD11 A:LEU89 4.5 35.5 1.0 CE1 A:HIS64 4.6 17.6 1.0 HZ A:PHE43 4.6 26.1 1.0 HG13 A:ILE99 4.6 17.2 1.0 CG2 A:VAL68 4.7 16.9 1.0 HE1 A:PHE43 4.7 20.0 1.0 HD2 A:HIS97 4.7 34.1 1.0 HG21 A:VAL68 4.8 20.3 1.0 HG23 A:VAL68 5.0 20.3 1.0

Iron binding site 2 out of 2 in the Elephant Seal Myoglobin Esmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Elephant Seal Myoglobin Esmb within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:13.3 occ:1.00 FE C:HEM201 0.0 13.3 1.0 NC C:HEM201 2.0 9.4 1.0 NB C:HEM201 2.0 11.4 1.0 ND C:HEM201 2.0 14.4 1.0 NA C:HEM201 2.0 13.2 1.0 NE2 C:HIS93 2.1 13.7 1.0 O C:HOH324 2.2 18.2 1.0 C4C C:HEM201 3.0 10.8 1.0 C1D C:HEM201 3.0 15.0 1.0 C1C C:HEM201 3.0 9.8 1.0 C4B C:HEM201 3.0 11.7 1.0 C1B C:HEM201 3.0 17.1 1.0 C4A C:HEM201 3.1 12.3 1.0 C4D C:HEM201 3.1 16.0 1.0 C1A C:HEM201 3.1 12.7 1.0 CD2 C:HIS93 3.1 12.9 1.0 CE1 C:HIS93 3.1 13.1 1.0 HD2 C:HIS93 3.2 15.5 1.0 HE1 C:HIS93 3.3 15.8 1.0 CHD C:HEM201 3.3 9.7 1.0 CHC C:HEM201 3.4 13.8 1.0 CHB C:HEM201 3.4 13.6 1.0 CHA C:HEM201 3.5 17.5 1.0 HG22 C:VAL68 3.8 18.7 1.0 ND1 C:HIS93 4.2 16.4 1.0 C3C C:HEM201 4.2 10.5 1.0 CG C:HIS93 4.2 11.5 1.0 C2D C:HEM201 4.2 15.1 1.0 C2C C:HEM201 4.2 14.2 1.0 C2B C:HEM201 4.3 12.4 1.0 C3D C:HEM201 4.3 13.7 1.0 C3B C:HEM201 4.3 12.7 1.0 NE2 C:HIS64 4.3 13.7 1.0 C3A C:HEM201 4.3 13.6 1.0 C2A C:HEM201 4.3 9.7 1.0 HE1 C:HIS64 4.4 26.0 1.0 HZ C:PHE43 4.5 16.1 1.0 HD11 C:LEU89 4.5 20.5 1.0 HG13 C:ILE99 4.6 14.1 1.0 CG2 C:VAL68 4.6 15.6 1.0 HG21 C:VAL68 4.6 18.7 1.0 CE1 C:HIS64 4.7 21.6 1.0 HD2 C:HIS97 4.8 33.7 1.0 HE1 C:PHE43 4.8 20.1 1.0 HG23 C:VAL68 5.0 18.7 1.0 HD1 C:HIS93 5.0 19.7 1.0

Y.Isogai, H.Imamura, S.Nakae, T.Sumi, K.I.Takahashi, T.Shirai. Common and Unique Strategies of Myoglobin Evolution For Deep-Sea Adaptation of Diving Mammals. Iscience V. 24 02920 2021.
ISSN: ESSN 2589-0042
PubMed: 34430810
DOI: 10.1016/J.ISCI.2021.102920