Iron in PDB 3d1k: R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State

The structure of R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State, PDB code: 3d1k was solved by L.Vitagliano, A.Vergara, G.Bonomi, A.Merlino, L.Mazzarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.458, 87.664, 55.502, 90.00, 99.16, 90.00
R / Rfree (%)	16.7 / 20.2

The binding sites of Iron atom in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State (pdb code 3d1k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State, PDB code: 3d1k:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:15.7 occ:1.00 FE A:HEM200 0.0 15.7 1.0 C A:CMO199 1.9 16.4 1.0 ND A:HEM200 2.0 16.5 1.0 NC A:HEM200 2.0 15.3 1.0 NA A:HEM200 2.0 15.5 1.0 NB A:HEM200 2.0 15.8 1.0 NE2 A:HIS88 2.0 14.8 1.0 O A:CMO199 3.0 25.0 1.0 CE1 A:HIS88 3.0 16.1 1.0 C1D A:HEM200 3.0 16.6 1.0 C1C A:HEM200 3.0 15.0 1.0 C4C A:HEM200 3.0 15.8 1.0 C4D A:HEM200 3.1 16.5 1.0 C4B A:HEM200 3.1 15.8 1.0 C4A A:HEM200 3.1 16.7 1.0 C1A A:HEM200 3.1 16.3 1.0 C1B A:HEM200 3.1 16.1 1.0 CD2 A:HIS88 3.1 14.5 1.0 CHD A:HEM200 3.4 17.1 1.0 CHC A:HEM200 3.4 14.7 1.0 CHA A:HEM200 3.4 16.9 1.0 CHB A:HEM200 3.5 16.2 1.0 ND1 A:HIS88 4.2 16.4 1.0 C3D A:HEM200 4.2 18.4 1.0 C3C A:HEM200 4.3 15.4 1.0 C2C A:HEM200 4.3 15.1 1.0 C2D A:HEM200 4.3 18.0 1.0 C3A A:HEM200 4.3 17.5 1.0 C2A A:HEM200 4.3 17.9 1.0 C2B A:HEM200 4.3 16.8 1.0 C3B A:HEM200 4.3 15.9 1.0 CG A:HIS88 4.3 14.7 1.0 NE2 A:HIS59 4.3 19.9 1.0 CG2 A:VAL63 4.8 24.8 1.0

Iron binding site 2 out of 2 in the R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of R/T Intermediate Quaternary Structure of An Antarctic Fish Hemoglobin in An Alpha(Co)-Beta(Pentacoordinate) State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:24.5 occ:1.00 FE B:HEM400 0.0 24.5 1.0 NA B:HEM400 2.0 23.6 1.0 NC B:HEM400 2.0 24.6 1.0 ND B:HEM400 2.0 24.4 1.0 NB B:HEM400 2.0 25.0 1.0 NE2 B:HIS92 2.1 22.2 1.0 O B:HOH399 2.7 26.5 0.6 C4C B:HEM400 3.0 22.8 1.0 C1C B:HEM400 3.0 24.6 1.0 C1A B:HEM400 3.0 25.4 1.0 C4A B:HEM400 3.0 26.3 1.0 C1D B:HEM400 3.0 24.9 1.0 CE1 B:HIS92 3.1 22.3 1.0 C4B B:HEM400 3.1 26.5 1.0 C4D B:HEM400 3.1 24.3 1.0 C1B B:HEM400 3.1 26.4 1.0 CD2 B:HIS92 3.2 22.5 1.0 CHC B:HEM400 3.4 25.1 1.0 CHD B:HEM400 3.4 25.3 1.0 CHA B:HEM400 3.4 25.1 1.0 CHB B:HEM400 3.5 26.2 1.0 ND1 B:HIS92 4.2 22.4 1.0 C3C B:HEM400 4.2 23.7 1.0 C2A B:HEM400 4.2 28.4 1.0 C2C B:HEM400 4.3 24.1 1.0 C3A B:HEM400 4.3 26.9 1.0 C3D B:HEM400 4.3 25.4 1.0 CG2 B:VAL67 4.3 30.9 1.0 C2D B:HEM400 4.3 27.0 1.0 C3B B:HEM400 4.3 26.4 1.0 CG B:HIS92 4.3 20.9 1.0 C2B B:HEM400 4.3 25.8 1.0 NE2 B:HIS63 4.4 28.2 1.0

L.Vitagliano, A.Vergara, G.Bonomi, A.Merlino, C.Verde, G.Di Prisco, B.D.Howes, G.Smulevich, L.Mazzarella. Spectroscopic and Crystallographic Characterization of A Tetrameric Hemoglobin Oxidation Reveals Structural Features of the Functional Intermediate Relaxed/Tense State. J.Am.Chem.Soc. V. 130 10527 2008.
ISSN: ISSN 0002-7863
PubMed: 18642904
DOI: 10.1021/JA803363P