Iron in PDB 1yhu: Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.

The structure of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits., PDB code: 1yhu was solved by J.F.Flores, C.R.Fisher, S.L.Carney, B.N.Green, J.K.Freytag, S.W.Schaeffer, W.E.Royer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	195.840, 195.840, 308.820, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 27.1

The structure of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. (pdb code 1yhu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits., PDB code: 1yhu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe160 b:55.7 occ:1.00 FE A:HEM160 0.0 55.7 1.0 NA A:HEM160 1.9 55.7 1.0 O1 A:OXY161 2.0 65.1 1.0 NB A:HEM160 2.0 55.7 1.0 NC A:HEM160 2.0 55.7 1.0 ND A:HEM160 2.0 55.7 1.0 NE2 A:HIS96 2.0 96.3 1.0 O2 A:OXY161 2.8 65.1 1.0 C1A A:HEM160 3.0 55.7 1.0 CE1 A:HIS96 3.0 96.3 1.0 C4A A:HEM160 3.0 55.7 1.0 C4B A:HEM160 3.0 55.7 1.0 C1B A:HEM160 3.0 55.7 1.0 C4D A:HEM160 3.1 55.7 1.0 C1C A:HEM160 3.1 55.7 1.0 C1D A:HEM160 3.1 55.7 1.0 C4C A:HEM160 3.1 55.7 1.0 CD2 A:HIS96 3.1 96.3 1.0 CHA A:HEM160 3.4 55.7 1.0 CHB A:HEM160 3.4 55.7 1.0 CHC A:HEM160 3.4 55.7 1.0 CHD A:HEM160 3.5 55.7 1.0 ND1 A:HIS96 4.2 96.3 1.0 C2A A:HEM160 4.2 55.7 1.0 C3A A:HEM160 4.2 55.7 1.0 CG A:HIS96 4.2 96.3 1.0 C3B A:HEM160 4.3 55.7 1.0 C2B A:HEM160 4.3 55.7 1.0 C3D A:HEM160 4.3 55.7 1.0 C2D A:HEM160 4.3 55.7 1.0 C2C A:HEM160 4.3 55.7 1.0 C3C A:HEM160 4.3 55.7 1.0

Iron binding site 2 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe160 b:27.8 occ:1.00 FE B:HEM160 0.0 27.8 1.0 O1 B:OXY161 1.9 73.4 1.0 NA B:HEM160 2.0 27.8 1.0 ND B:HEM160 2.0 27.8 1.0 NB B:HEM160 2.0 27.8 1.0 NC B:HEM160 2.0 27.8 1.0 NE2 B:HIS96 2.0 43.0 1.0 O2 B:OXY161 2.7 73.4 1.0 CE1 B:HIS96 2.9 43.0 1.0 C4D B:HEM160 3.0 27.8 1.0 C1A B:HEM160 3.0 27.8 1.0 C4A B:HEM160 3.0 27.8 1.0 C1D B:HEM160 3.0 27.8 1.0 C1B B:HEM160 3.0 27.8 1.0 C1C B:HEM160 3.0 27.8 1.0 C4C B:HEM160 3.0 27.8 1.0 C4B B:HEM160 3.1 27.8 1.0 CD2 B:HIS96 3.2 43.0 1.0 CHA B:HEM160 3.4 27.8 1.0 CHB B:HEM160 3.4 27.8 1.0 CHD B:HEM160 3.4 27.8 1.0 CHC B:HEM160 3.4 27.8 1.0 ND1 B:HIS96 4.1 43.0 1.0 C2A B:HEM160 4.2 27.8 1.0 C3D B:HEM160 4.2 27.8 1.0 CG B:HIS96 4.2 43.0 1.0 C2C B:HEM160 4.2 27.8 1.0 C3A B:HEM160 4.2 27.8 1.0 C2D B:HEM160 4.3 27.8 1.0 C3C B:HEM160 4.3 27.8 1.0 C2B B:HEM160 4.3 27.8 1.0 C3B B:HEM160 4.3 27.8 1.0

Iron binding site 3 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe160 b:66.8 occ:1.00 FE C:HEM160 0.0 66.8 1.0 NA C:HEM160 2.0 66.8 1.0 NE2 C:HIS99 2.0 69.5 1.0 ND C:HEM160 2.0 66.8 1.0 NC C:HEM160 2.0 66.8 1.0 O1 C:OXY161 2.0 78.8 1.0 NB C:HEM160 2.0 66.8 1.0 CE1 C:HIS99 2.7 69.5 1.0 O2 C:OXY161 2.8 78.8 1.0 C1A C:HEM160 3.0 66.8 1.0 C4A C:HEM160 3.0 66.8 1.0 C4D C:HEM160 3.0 66.8 1.0 C1D C:HEM160 3.0 66.8 1.0 C4C C:HEM160 3.1 66.8 1.0 C1C C:HEM160 3.1 66.8 1.0 C1B C:HEM160 3.1 66.8 1.0 C4B C:HEM160 3.1 66.8 1.0 CD2 C:HIS99 3.1 69.5 1.0 CHA C:HEM160 3.4 66.8 1.0 CHB C:HEM160 3.4 66.8 1.0 CHD C:HEM160 3.4 66.8 1.0 CHC C:HEM160 3.5 66.8 1.0 ND1 C:HIS99 3.9 69.5 1.0 CG C:HIS99 4.1 69.5 1.0 C2A C:HEM160 4.2 66.8 1.0 C3A C:HEM160 4.3 66.8 1.0 C3D C:HEM160 4.3 66.8 1.0 C2D C:HEM160 4.3 66.8 1.0 C2C C:HEM160 4.3 66.8 1.0 C2B C:HEM160 4.3 66.8 1.0 C3C C:HEM160 4.3 66.8 1.0 C3B C:HEM160 4.3 66.8 1.0 CZ C:PHE110 4.8 59.0 1.0 CG2 C:VAL71 4.9 37.1 1.0

Iron binding site 4 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe160 b:59.0 occ:1.00 FE D:HEM160 0.0 59.0 1.0 O1 D:OXY161 1.9 58.1 1.0 ND D:HEM160 2.0 59.0 1.0 NA D:HEM160 2.0 59.0 1.0 NB D:HEM160 2.0 59.0 1.0 NC D:HEM160 2.0 59.0 1.0 NE2 D:HIS98 2.1 58.0 1.0 O2 D:OXY161 2.7 58.1 1.0 CE1 D:HIS98 2.8 58.0 1.0 C4D D:HEM160 3.0 59.0 1.0 C1A D:HEM160 3.0 59.0 1.0 C1D D:HEM160 3.0 59.0 1.0 C4B D:HEM160 3.0 59.0 1.0 C4A D:HEM160 3.0 59.0 1.0 C4C D:HEM160 3.0 59.0 1.0 C1B D:HEM160 3.1 59.0 1.0 C1C D:HEM160 3.1 59.0 1.0 CD2 D:HIS98 3.2 58.0 1.0 CHA D:HEM160 3.4 59.0 1.0 CHD D:HEM160 3.4 59.0 1.0 CHC D:HEM160 3.4 59.0 1.0 CHB D:HEM160 3.4 59.0 1.0 ND1 D:HIS98 4.0 58.0 1.0 CG D:HIS98 4.2 58.0 1.0 C3D D:HEM160 4.2 59.0 1.0 C2D D:HEM160 4.2 59.0 1.0 C3B D:HEM160 4.2 59.0 1.0 C2A D:HEM160 4.2 59.0 1.0 C3A D:HEM160 4.2 59.0 1.0 C3C D:HEM160 4.3 59.0 1.0 C2B D:HEM160 4.3 59.0 1.0 C2C D:HEM160 4.3 59.0 1.0

Iron binding site 5 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe160 b:37.1 occ:1.00 FE E:HEM160 0.0 37.1 1.0 O1 E:OXY161 2.0 65.1 1.0 NC E:HEM160 2.0 37.1 1.0 NA E:HEM160 2.0 37.1 1.0 NB E:HEM160 2.0 37.1 1.0 NE2 E:HIS96 2.0 49.8 1.0 ND E:HEM160 2.0 37.1 1.0 O2 E:OXY161 2.8 65.1 1.0 CE1 E:HIS96 3.0 49.8 1.0 C1C E:HEM160 3.0 37.1 1.0 C4B E:HEM160 3.0 37.1 1.0 C1A E:HEM160 3.0 37.1 1.0 C4C E:HEM160 3.0 37.1 1.0 C4A E:HEM160 3.0 37.1 1.0 C4D E:HEM160 3.1 37.1 1.0 CD2 E:HIS96 3.1 49.8 1.0 C1D E:HEM160 3.1 37.1 1.0 C1B E:HEM160 3.1 37.1 1.0 CHC E:HEM160 3.4 37.1 1.0 CHA E:HEM160 3.4 37.1 1.0 CHD E:HEM160 3.4 37.1 1.0 CHB E:HEM160 3.5 37.1 1.0 ND1 E:HIS96 4.1 49.8 1.0 CG E:HIS96 4.2 49.8 1.0 C2A E:HEM160 4.2 37.1 1.0 C3A E:HEM160 4.2 37.1 1.0 C2C E:HEM160 4.3 37.1 1.0 C3B E:HEM160 4.3 37.1 1.0 C2B E:HEM160 4.3 37.1 1.0 C3C E:HEM160 4.3 37.1 1.0 C3D E:HEM160 4.3 37.1 1.0 C2D E:HEM160 4.3 37.1 1.0

Iron binding site 6 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe160 b:19.2 occ:1.00 FE F:HEM160 0.0 19.2 1.0 O1 F:OXY161 1.9 73.4 1.0 ND F:HEM160 1.9 19.2 1.0 NC F:HEM160 2.0 19.2 1.0 NA F:HEM160 2.0 19.2 1.0 NE2 F:HIS96 2.0 46.6 1.0 NB F:HEM160 2.0 19.2 1.0 O2 F:OXY161 2.7 73.4 1.0 CE1 F:HIS96 2.9 46.6 1.0 C4D F:HEM160 3.0 19.2 1.0 C1D F:HEM160 3.0 19.2 1.0 C1A F:HEM160 3.0 19.2 1.0 C4C F:HEM160 3.0 19.2 1.0 C1C F:HEM160 3.0 19.2 1.0 C4A F:HEM160 3.0 19.2 1.0 C1B F:HEM160 3.1 19.2 1.0 C4B F:HEM160 3.1 19.2 1.0 CD2 F:HIS96 3.1 46.6 1.0 CHA F:HEM160 3.4 19.2 1.0 CHD F:HEM160 3.4 19.2 1.0 CHC F:HEM160 3.4 19.2 1.0 CHB F:HEM160 3.4 19.2 1.0 ND1 F:HIS96 4.0 46.6 1.0 CG F:HIS96 4.2 46.6 1.0 C3D F:HEM160 4.2 19.2 1.0 C2D F:HEM160 4.2 19.2 1.0 C2A F:HEM160 4.2 19.2 1.0 C2C F:HEM160 4.2 19.2 1.0 C3C F:HEM160 4.3 19.2 1.0 C3A F:HEM160 4.3 19.2 1.0 C2B F:HEM160 4.3 19.2 1.0 C3B F:HEM160 4.3 19.2 1.0

Iron binding site 7 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe160 b:48.4 occ:1.00 FE G:HEM160 0.0 48.4 1.0 O1 G:OXY161 1.9 78.8 1.0 ND G:HEM160 2.0 48.4 1.0 NA G:HEM160 2.0 48.4 1.0 NE2 G:HIS99 2.0 50.7 1.0 NC G:HEM160 2.0 48.4 1.0 NB G:HEM160 2.0 48.4 1.0 CE1 G:HIS99 2.8 50.7 1.0 O2 G:OXY161 2.8 78.8 1.0 C1A G:HEM160 3.0 48.4 1.0 C4D G:HEM160 3.0 48.4 1.0 C1D G:HEM160 3.0 48.4 1.0 C4A G:HEM160 3.0 48.4 1.0 C4C G:HEM160 3.0 48.4 1.0 C1C G:HEM160 3.0 48.4 1.0 C1B G:HEM160 3.1 48.4 1.0 C4B G:HEM160 3.1 48.4 1.0 CD2 G:HIS99 3.2 50.7 1.0 CHA G:HEM160 3.4 48.4 1.0 CHD G:HEM160 3.4 48.4 1.0 CHB G:HEM160 3.4 48.4 1.0 CHC G:HEM160 3.4 48.4 1.0 ND1 G:HIS99 4.0 50.7 1.0 CG G:HIS99 4.2 50.7 1.0 C2A G:HEM160 4.2 48.4 1.0 C3D G:HEM160 4.2 48.4 1.0 C2D G:HEM160 4.2 48.4 1.0 C3A G:HEM160 4.3 48.4 1.0 C2C G:HEM160 4.3 48.4 1.0 C3C G:HEM160 4.3 48.4 1.0 C2B G:HEM160 4.3 48.4 1.0 C3B G:HEM160 4.3 48.4 1.0 CZ G:PHE110 4.9 37.3 1.0 CG2 G:VAL71 4.9 22.4 1.0

Iron binding site 8 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe160 b:42.9 occ:1.00 FE H:HEM160 0.0 42.9 1.0 O1 H:OXY161 1.9 58.1 1.0 NA H:HEM160 2.0 42.9 1.0 NB H:HEM160 2.0 42.9 1.0 ND H:HEM160 2.0 42.9 1.0 NC H:HEM160 2.0 42.9 1.0 NE2 H:HIS98 2.0 39.5 1.0 O2 H:OXY161 2.7 58.1 1.0 CE1 H:HIS98 2.7 39.5 1.0 C4B H:HEM160 3.0 42.9 1.0 C1A H:HEM160 3.0 42.9 1.0 C4D H:HEM160 3.0 42.9 1.0 C4A H:HEM160 3.0 42.9 1.0 C4C H:HEM160 3.0 42.9 1.0 C1D H:HEM160 3.0 42.9 1.0 C1B H:HEM160 3.0 42.9 1.0 C1C H:HEM160 3.0 42.9 1.0 CD2 H:HIS98 3.2 39.5 1.0 CHA H:HEM160 3.4 42.9 1.0 CHC H:HEM160 3.4 42.9 1.0 CHD H:HEM160 3.4 42.9 1.0 CHB H:HEM160 3.4 42.9 1.0 ND1 H:HIS98 3.9 39.5 1.0 CG H:HIS98 4.2 39.5 1.0 C3B H:HEM160 4.2 42.9 1.0 C3A H:HEM160 4.3 42.9 1.0 C2D H:HEM160 4.3 42.9 1.0 C2A H:HEM160 4.3 42.9 1.0 C3D H:HEM160 4.3 42.9 1.0 C3C H:HEM160 4.3 42.9 1.0 C2B H:HEM160 4.3 42.9 1.0 C2C H:HEM160 4.3 42.9 1.0

Iron binding site 9 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe160 b:25.2 occ:1.00 FE I:HEM160 0.0 25.2 1.0 O1 I:OXY161 1.9 65.1 1.0 NA I:HEM160 2.0 25.2 1.0 ND I:HEM160 2.0 25.2 1.0 NC I:HEM160 2.0 25.2 1.0 NB I:HEM160 2.0 25.2 1.0 NE2 I:HIS96 2.0 32.2 1.0 O2 I:OXY161 2.8 65.1 1.0 C1A I:HEM160 3.0 25.2 1.0 CE1 I:HIS96 3.0 32.2 1.0 C4D I:HEM160 3.0 25.2 1.0 C1D I:HEM160 3.0 25.2 1.0 C1C I:HEM160 3.0 25.2 1.0 C4C I:HEM160 3.0 25.2 1.0 C4A I:HEM160 3.0 25.2 1.0 C4B I:HEM160 3.1 25.2 1.0 CD2 I:HIS96 3.1 32.2 1.0 C1B I:HEM160 3.1 25.2 1.0 CHA I:HEM160 3.4 25.2 1.0 CHD I:HEM160 3.4 25.2 1.0 CHC I:HEM160 3.4 25.2 1.0 CHB I:HEM160 3.5 25.2 1.0 ND1 I:HIS96 4.2 32.2 1.0 CG I:HIS96 4.2 32.2 1.0 C2A I:HEM160 4.2 25.2 1.0 C3A I:HEM160 4.2 25.2 1.0 C2D I:HEM160 4.3 25.2 1.0 C3D I:HEM160 4.3 25.2 1.0 C2C I:HEM160 4.3 25.2 1.0 C3C I:HEM160 4.3 25.2 1.0 C2B I:HEM160 4.3 25.2 1.0 C3B I:HEM160 4.3 25.2 1.0

Iron binding site 10 out of 24 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe160 b:27.9 occ:1.00 FE J:HEM160 0.0 27.9 1.0 O1 J:OXY161 1.9 73.4 1.0 ND J:HEM160 2.0 27.9 1.0 NC J:HEM160 2.0 27.9 1.0 NA J:HEM160 2.0 27.9 1.0 NB J:HEM160 2.0 27.9 1.0 NE2 J:HIS96 2.0 42.5 1.0 O2 J:OXY161 2.7 73.4 1.0 CE1 J:HIS96 2.9 42.5 1.0 C1C J:HEM160 3.0 27.9 1.0 C4D J:HEM160 3.0 27.9 1.0 C1D J:HEM160 3.0 27.9 1.0 C1A J:HEM160 3.0 27.9 1.0 C4C J:HEM160 3.0 27.9 1.0 C4A J:HEM160 3.0 27.9 1.0 C1B J:HEM160 3.0 27.9 1.0 C4B J:HEM160 3.1 27.9 1.0 CD2 J:HIS96 3.2 42.5 1.0 CHA J:HEM160 3.4 27.9 1.0 CHD J:HEM160 3.4 27.9 1.0 CHC J:HEM160 3.4 27.9 1.0 CHB J:HEM160 3.4 27.9 1.0 ND1 J:HIS96 4.1 42.5 1.0 CG J:HIS96 4.2 42.5 1.0 C2C J:HEM160 4.2 27.9 1.0 C3D J:HEM160 4.2 27.9 1.0 C2A J:HEM160 4.2 27.9 1.0 C2D J:HEM160 4.2 27.9 1.0 C3A J:HEM160 4.3 27.9 1.0 C3C J:HEM160 4.3 27.9 1.0 C2B J:HEM160 4.3 27.9 1.0 C3B J:HEM160 4.3 27.9 1.0

J.F.Flores, C.R.Fisher, S.L.Carney, B.N.Green, J.K.Freytag, S.W.Schaeffer, W.E.Royer Jr. Sulfide Binding Is Mediated By Zinc Ions Discovered in the Crystal Structure of A Hydrothermal Vent Tubeworm Hemoglobin. Proc.Natl.Acad.Sci.Usa V. 102 2713 2005.
ISSN: ISSN 0027-8424
PubMed: 15710902
DOI: 10.1073/PNAS.0407455102