Iron in PDB 3gkv: X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin

The structure of X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin, PDB code: 3gkv was solved by A.Merlino, L.Vitagliano, F.Sica, A.Vergara, L.Mazzarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.25 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.880, 87.647, 55.339, 90.00, 100.17, 90.00
R / Rfree (%)	18.4 / 21.1

The binding sites of Iron atom in the X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin (pdb code 3gkv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin, PDB code: 3gkv:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:12.4 occ:1.00 FE A:HEM200 0.0 12.4 1.0 O A:HOH1291 1.7 13.5 0.5 C A:CMO199 1.8 13.6 0.5 ND A:HEM200 2.0 13.5 1.0 NA A:HEM200 2.0 13.4 1.0 NC A:HEM200 2.0 12.9 1.0 NB A:HEM200 2.0 12.9 1.0 NE2 A:HIS88 2.1 12.8 1.0 O A:CMO199 3.0 14.8 0.5 CE1 A:HIS88 3.0 12.2 1.0 C1D A:HEM200 3.0 13.8 1.0 C1A A:HEM200 3.0 14.1 1.0 C4D A:HEM200 3.1 14.0 1.0 C4A A:HEM200 3.1 13.1 1.0 C4B A:HEM200 3.1 12.9 1.0 C1C A:HEM200 3.1 13.0 1.0 C4C A:HEM200 3.1 13.3 1.0 C1B A:HEM200 3.1 12.3 1.0 CD2 A:HIS88 3.2 11.7 1.0 CHD A:HEM200 3.4 13.6 1.0 CHA A:HEM200 3.4 14.0 1.0 CHC A:HEM200 3.5 12.7 1.0 CHB A:HEM200 3.5 12.7 1.0 O A:HOH1290 4.1 26.5 0.5 ND1 A:HIS88 4.2 12.4 1.0 CG A:HIS88 4.3 12.3 1.0 C3D A:HEM200 4.3 14.6 1.0 NE2 A:HIS59 4.3 19.0 1.0 C2A A:HEM200 4.3 15.1 1.0 C2D A:HEM200 4.3 14.4 1.0 C3A A:HEM200 4.3 14.1 1.0 C2C A:HEM200 4.3 13.5 1.0 C2B A:HEM200 4.3 12.6 1.0 C3B A:HEM200 4.4 12.8 1.0 C3C A:HEM200 4.4 13.0 1.0 CG2 A:VAL63 4.7 14.7 1.0

Iron binding site 2 out of 2 in the X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of An Intermediate Along the Oxidation Pathway of Trematomus Bernacchii Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:19.7 occ:1.00 FE B:HEM400 0.0 19.7 1.0 C B:CMO399 1.9 20.0 0.5 NA B:HEM400 1.9 20.8 1.0 NC B:HEM400 2.0 19.7 1.0 ND B:HEM400 2.0 21.0 1.0 NE2 B:HIS92 2.0 19.8 1.0 NB B:HEM400 2.1 19.2 1.0 C1A B:HEM400 3.0 22.3 1.0 O B:CMO399 3.0 20.5 0.5 CE1 B:HIS92 3.0 19.6 1.0 C4C B:HEM400 3.0 20.1 1.0 C4A B:HEM400 3.1 21.0 1.0 C4D B:HEM400 3.1 22.3 1.0 C1C B:HEM400 3.1 19.2 1.0 C4B B:HEM400 3.1 18.8 1.0 C1D B:HEM400 3.1 21.3 1.0 CD2 B:HIS92 3.1 19.1 1.0 C1B B:HEM400 3.1 18.9 1.0 CHA B:HEM400 3.4 22.2 1.0 CHC B:HEM400 3.4 18.8 1.0 CHD B:HEM400 3.4 20.7 1.0 CE1 B:HIS63 3.5 18.7 0.5 CHB B:HEM400 3.5 19.9 1.0 NE2 B:HIS63 3.8 18.9 0.5 ND1 B:HIS92 4.2 19.0 1.0 CG B:HIS92 4.2 19.0 1.0 C2A B:HEM400 4.2 23.1 1.0 C3C B:HEM400 4.3 20.1 1.0 C3A B:HEM400 4.3 22.1 1.0 C2C B:HEM400 4.3 19.4 1.0 C2D B:HEM400 4.3 22.4 1.0 C3D B:HEM400 4.3 23.5 1.0 C3B B:HEM400 4.3 18.6 1.0 C2B B:HEM400 4.4 18.7 1.0 CG2 B:VAL67 4.5 15.7 1.0 ND1 B:HIS63 4.7 18.5 0.5

A.Merlino, L.Vitagliano, B.D.Howes, C.Verde, G.Di Prisco, G.Smulevich, F.Sica, A.Vergara. Combined Crystallographic and Spectroscopic Analysis of Trematomus Bernacchii Hemoglobin Highlights Analogies and Differences in the Peculiar Oxidation Pathway of Antarctic Fish Hemoglobins Biopolymers V. 91 1117 2009.
ISSN: ISSN 0006-3525
PubMed: 19373928
DOI: 10.1002/BIP.21206