Iron in PDB 1v4x: Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0

The structure of Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0, PDB code: 1v4x was solved by T.Yokoyama, K.T.Chong, Y.Miyazaki, T.Nakatsukasa, S.Unzai, G.Miyazaki, H.Morimoto, R.H.T.Jeremy, S.Y.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.979, 60.537, 80.640, 90.00, 95.12, 90.00
R / Rfree (%)	20.4 / 25

The binding sites of Iron atom in the Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0 (pdb code 1v4x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0, PDB code: 1v4x:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0


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 Bluefin Tuna Hemoglobin Deoxy Form at PH5.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe144 b:14.9 occ:1.00 FE A:HEM144 0.0 14.9 1.0 NC A:HEM144 2.1 11.3 1.0 NA A:HEM144 2.1 15.8 1.0 NB A:HEM144 2.1 12.8 1.0 ND A:HEM144 2.1 15.0 1.0 NE2 A:HIS89 2.2 8.7 1.0 C4C A:HEM144 3.0 13.4 1.0 CE1 A:HIS89 3.1 10.8 1.0 C1C A:HEM144 3.1 12.6 1.0 C1A A:HEM144 3.1 18.7 1.0 C4B A:HEM144 3.1 12.9 1.0 C4A A:HEM144 3.1 14.8 1.0 C1D A:HEM144 3.1 18.2 1.0 C1B A:HEM144 3.1 13.1 1.0 C4D A:HEM144 3.1 19.2 1.0 CD2 A:HIS89 3.3 9.3 1.0 CHD A:HEM144 3.4 17.4 1.0 CHA A:HEM144 3.5 18.3 1.0 CHB A:HEM144 3.5 12.4 1.0 CHC A:HEM144 3.5 9.7 1.0 NE2 A:HIS60 4.1 32.8 1.0 ND1 A:HIS89 4.2 14.3 1.0 C3C A:HEM144 4.3 14.3 1.0 CE1 A:HIS60 4.3 30.1 1.0 C2C A:HEM144 4.3 14.7 1.0 C2A A:HEM144 4.3 18.4 1.0 C3B A:HEM144 4.3 14.1 1.0 C3A A:HEM144 4.3 14.2 1.0 C2B A:HEM144 4.4 14.1 1.0 C3D A:HEM144 4.4 20.7 1.0 CG A:HIS89 4.4 13.3 1.0 CG2 A:VAL64 4.4 16.1 1.0 C2D A:HEM144 4.4 18.9 1.0 CE A:MET93 4.6 14.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0


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 Bluefin Tuna Hemoglobin Deoxy Form at PH5.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe347 b:9.8 occ:1.00 FE B:HEM347 0.0 9.8 1.0 NA B:HEM347 2.1 10.1 1.0 NC B:HEM347 2.1 9.8 1.0 ND B:HEM347 2.1 10.1 1.0 NB B:HEM347 2.1 9.5 1.0 NE2 B:HIS292 2.2 10.2 1.0 C4A B:HEM347 3.1 11.1 1.0 C1D B:HEM347 3.1 9.5 1.0 C4D B:HEM347 3.1 10.9 1.0 C1C B:HEM347 3.1 9.7 1.0 C1A B:HEM347 3.1 14.0 1.0 C4B B:HEM347 3.1 10.3 1.0 CE1 B:HIS292 3.1 9.6 1.0 C4C B:HEM347 3.1 10.5 1.0 C1B B:HEM347 3.1 7.8 1.0 CD2 B:HIS292 3.2 5.9 1.0 CHA B:HEM347 3.5 9.3 1.0 CHC B:HEM347 3.5 7.5 1.0 CHB B:HEM347 3.5 10.6 1.0 CHD B:HEM347 3.5 9.7 1.0 CG2 B:VAL267 4.1 9.8 1.0 ND1 B:HIS292 4.3 9.6 1.0 NE2 B:HIS263 4.3 12.1 1.0 C3B B:HEM347 4.3 7.4 1.0 C2D B:HEM347 4.3 7.8 1.0 C3A B:HEM347 4.3 11.4 1.0 C2A B:HEM347 4.3 14.0 1.0 C2C B:HEM347 4.3 10.5 1.0 C3D B:HEM347 4.3 9.3 1.0 C3C B:HEM347 4.4 9.6 1.0 CG B:HIS292 4.4 8.3 1.0 C2B B:HEM347 4.4 8.7 1.0 CE1 B:HIS263 4.8 10.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe544 b:11.8 occ:1.00 FE C:HEM544 0.0 11.8 1.0 NB C:HEM544 2.0 6.6 1.0 ND C:HEM544 2.0 10.9 1.0 NC C:HEM544 2.1 9.8 1.0 NA C:HEM544 2.1 11.8 1.0 NE2 C:HIS489 2.2 12.6 1.0 C4D C:HEM544 3.0 14.1 1.0 C1B C:HEM544 3.1 10.5 1.0 C1D C:HEM544 3.1 12.7 1.0 CE1 C:HIS489 3.1 10.2 1.0 C4B C:HEM544 3.1 9.6 1.0 C4C C:HEM544 3.1 8.7 1.0 C1A C:HEM544 3.1 15.1 1.0 C1C C:HEM544 3.1 8.9 1.0 C4A C:HEM544 3.2 11.7 1.0 CD2 C:HIS489 3.2 13.6 1.0 CHA C:HEM544 3.4 12.9 1.0 CHD C:HEM544 3.4 9.7 1.0 CHB C:HEM544 3.5 9.2 1.0 CHC C:HEM544 3.5 6.7 1.0 ND1 C:HIS489 4.2 10.4 1.0 C3D C:HEM544 4.2 15.6 1.0 C3B C:HEM544 4.3 7.3 1.0 C2B C:HEM544 4.3 6.3 1.0 C2D C:HEM544 4.3 12.3 1.0 CG C:HIS489 4.3 12.5 1.0 C3C C:HEM544 4.3 7.5 1.0 CG2 C:VAL464 4.3 16.2 1.0 C2A C:HEM544 4.4 16.0 1.0 C2C C:HEM544 4.4 8.9 1.0 C3A C:HEM544 4.4 13.6 1.0 CE C:MET493 4.5 11.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Bluefin Tuna Hemoglobin Deoxy Form at PH5.0 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe747 b:15.8 occ:1.00 FE D:HEM747 0.0 15.8 1.0 NA D:HEM747 2.1 15.1 1.0 NB D:HEM747 2.1 14.2 1.0 NC D:HEM747 2.1 15.3 1.0 NE2 D:HIS692 2.1 17.1 1.0 ND D:HEM747 2.2 15.9 1.0 CE1 D:HIS692 3.0 14.7 1.0 C1B D:HEM747 3.1 16.3 1.0 C4A D:HEM747 3.1 15.0 1.0 C4B D:HEM747 3.1 13.8 1.0 C1A D:HEM747 3.1 16.6 1.0 C1C D:HEM747 3.1 14.4 1.0 C4D D:HEM747 3.1 19.7 1.0 C1D D:HEM747 3.2 16.4 1.0 C4C D:HEM747 3.2 14.2 1.0 CD2 D:HIS692 3.3 16.2 1.0 CHB D:HEM747 3.4 17.9 1.0 CHC D:HEM747 3.5 13.7 1.0 CHA D:HEM747 3.5 14.8 1.0 CHD D:HEM747 3.5 16.5 1.0 CG2 D:VAL667 3.8 15.4 1.0 ND1 D:HIS692 4.2 12.4 1.0 NE2 D:HIS663 4.2 15.1 1.0 C3B D:HEM747 4.3 12.6 1.0 C2B D:HEM747 4.3 12.7 1.0 C3A D:HEM747 4.3 14.8 1.0 CG D:HIS692 4.3 14.8 1.0 C2A D:HEM747 4.3 15.9 1.0 C2C D:HEM747 4.4 12.8 1.0 C3C D:HEM747 4.4 14.9 1.0 C3D D:HEM747 4.4 21.0 1.0 C2D D:HEM747 4.4 20.3 1.0 CE1 D:HIS663 4.5 19.6 1.0

T.Yokoyama, K.T.Chong, G.Miyazaki, H.Morimoto, D.T.Shih, S.Unzai, J.R.Tame, S.Y.Park. Novel Mechanisms of pH Sensitivity in Tuna Hemoglobin: A Structural Explanation of the Root Effect J.Biol.Chem. V. 279 28632 2004.
ISSN: ISSN 0021-9258
PubMed: 15117955
DOI: 10.1074/JBC.M401740200