Iron in PDB 3mkb: Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution

The structure of Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution, PDB code: 3mkb was solved by P.Ramesh, S.S.Sundaresan, P.Sathya Moorthy, M.Balasubramanian, M.N.Ponnuswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.89 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.259, 61.099, 72.207, 90.00, 96.49, 90.00
R / Rfree (%)	19.9 / 26.8

The binding sites of Iron atom in the Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution (pdb code 3mkb). 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 Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution, PDB code: 3mkb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe141 b:38.6 occ:1.00 FE A:HEM141 0.0 38.6 1.0 NB A:HEM141 2.0 36.1 1.0 ND A:HEM141 2.0 36.5 1.0 NA A:HEM141 2.1 36.9 1.0 NE2 A:HIS87 2.2 45.0 1.0 NC A:HEM141 2.2 30.7 1.0 NE2 A:HIS58 2.4 32.4 1.0 CE1 A:HIS87 2.8 48.6 1.0 C1B A:HEM141 3.0 36.3 1.0 C1D A:HEM141 3.0 34.1 1.0 C4B A:HEM141 3.0 34.9 1.0 C4A A:HEM141 3.1 39.1 1.0 C4D A:HEM141 3.1 38.0 1.0 C1A A:HEM141 3.1 37.7 1.0 C1C A:HEM141 3.2 32.8 1.0 C4C A:HEM141 3.2 30.2 1.0 CE1 A:HIS58 3.3 37.0 1.0 CHB A:HEM141 3.4 37.7 1.0 CD2 A:HIS87 3.4 43.7 1.0 CHD A:HEM141 3.4 32.8 1.0 CHC A:HEM141 3.5 33.5 1.0 CD2 A:HIS58 3.5 33.9 1.0 CHA A:HEM141 3.5 37.6 1.0 ND1 A:HIS87 4.1 46.6 1.0 C2B A:HEM141 4.2 35.9 1.0 C3B A:HEM141 4.2 35.9 1.0 C2D A:HEM141 4.2 33.6 1.0 C3D A:HEM141 4.3 36.5 1.0 C2A A:HEM141 4.3 39.9 1.0 C3A A:HEM141 4.4 40.6 1.0 CG A:HIS87 4.4 41.9 1.0 C2C A:HEM141 4.4 30.1 1.0 C3C A:HEM141 4.4 28.2 1.0 ND1 A:HIS58 4.4 33.6 1.0 CG A:HIS58 4.6 33.3 1.0 CG2 A:VAL62 4.6 30.2 1.0 CD1 A:LEU91 4.8 32.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe137 b:40.2 occ:1.00 FE B:HEM137 0.0 40.2 1.0 NC B:HEM137 1.9 38.7 1.0 NA B:HEM137 2.0 38.0 1.0 ND B:HEM137 2.1 39.3 1.0 NB B:HEM137 2.1 35.8 1.0 NE2 B:HIS82 2.2 34.8 1.0 O B:HOH347 2.2 54.5 1.0 C1C B:HEM137 2.9 38.4 1.0 C4C B:HEM137 3.0 39.5 1.0 C1A B:HEM137 3.0 38.5 1.0 C4B B:HEM137 3.0 35.1 1.0 C4D B:HEM137 3.0 33.5 1.0 C4A B:HEM137 3.1 37.7 1.0 C1D B:HEM137 3.1 35.1 1.0 CD2 B:HIS82 3.1 36.1 1.0 C1B B:HEM137 3.2 36.3 1.0 CE1 B:HIS82 3.2 30.9 1.0 CHC B:HEM137 3.3 36.3 1.0 CHA B:HEM137 3.4 35.5 1.0 CHD B:HEM137 3.4 36.7 1.0 CHB B:HEM137 3.5 36.3 1.0 NE2 B:HIS53 4.0 55.0 1.0 CE1 B:HIS53 4.1 55.8 1.0 C2C B:HEM137 4.1 36.5 1.0 C3C B:HEM137 4.2 39.2 1.0 C2A B:HEM137 4.2 37.7 1.0 C3A B:HEM137 4.3 37.0 1.0 C3D B:HEM137 4.3 37.0 1.0 ND1 B:HIS82 4.3 36.1 1.0 C3B B:HEM137 4.3 36.0 1.0 CG B:HIS82 4.3 37.9 1.0 C2D B:HEM137 4.3 35.6 1.0 C2B B:HEM137 4.4 34.7 1.0 CG2 B:VAL57 4.8 45.6 1.0 CD1 B:ILE131 4.9 30.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe141 b:42.5 occ:1.00 FE C:HEM141 0.0 42.5 1.0 ND C:HEM141 2.0 43.2 1.0 NB C:HEM141 2.1 41.7 1.0 NA C:HEM141 2.1 39.2 1.0 NC C:HEM141 2.2 40.2 1.0 NE2 C:HIS87 2.2 46.9 1.0 NE2 C:HIS58 2.3 34.2 1.0 CE1 C:HIS87 2.9 47.6 1.0 C4D C:HEM141 3.0 43.9 1.0 C1B C:HEM141 3.1 40.9 1.0 C1A C:HEM141 3.1 40.8 1.0 C1D C:HEM141 3.1 43.0 1.0 C4A C:HEM141 3.1 39.9 1.0 C4C C:HEM141 3.1 39.1 1.0 CE1 C:HIS58 3.1 35.6 1.0 C4B C:HEM141 3.1 40.7 1.0 C1C C:HEM141 3.2 40.0 1.0 CD2 C:HIS87 3.3 45.3 1.0 CD2 C:HIS58 3.4 31.1 1.0 CHA C:HEM141 3.4 41.4 1.0 CHB C:HEM141 3.4 39.2 1.0 CHD C:HEM141 3.4 40.6 1.0 CHC C:HEM141 3.6 39.1 1.0 ND1 C:HIS87 4.1 48.0 1.0 C3D C:HEM141 4.2 45.2 1.0 C2B C:HEM141 4.3 38.5 1.0 C2D C:HEM141 4.3 42.7 1.0 C2A C:HEM141 4.3 39.1 1.0 ND1 C:HIS58 4.3 34.7 1.0 C3A C:HEM141 4.3 38.5 1.0 C3B C:HEM141 4.3 39.1 1.0 CG C:HIS87 4.4 43.1 1.0 C3C C:HEM141 4.4 37.7 1.0 C2C C:HEM141 4.4 40.2 1.0 CG C:HIS58 4.5 32.1 1.0 CG2 C:VAL62 4.5 31.1 1.0 CD1 C:LEU91 4.8 39.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Determination of Shortfin Mako (Isurus Oxyrinchus) Hemoglobin at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe137 b:36.9 occ:1.00 FE D:HEM137 0.0 36.9 1.0 NA D:HEM137 2.0 31.6 1.0 NC D:HEM137 2.0 34.7 1.0 ND D:HEM137 2.1 33.4 1.0 NB D:HEM137 2.1 32.7 1.0 NE2 D:HIS82 2.1 30.8 1.0 O D:HOH175 2.5 32.2 1.0 CE1 D:HIS82 2.9 26.3 1.0 C4C D:HEM137 3.0 35.0 1.0 C1A D:HEM137 3.0 34.2 1.0 C4A D:HEM137 3.0 33.4 1.0 C1C D:HEM137 3.0 34.1 1.0 C4D D:HEM137 3.1 33.6 1.0 C1D D:HEM137 3.1 33.6 1.0 C1B D:HEM137 3.1 31.2 1.0 C4B D:HEM137 3.1 30.4 1.0 CD2 D:HIS82 3.3 26.8 1.0 CHD D:HEM137 3.4 35.0 1.0 CHA D:HEM137 3.4 31.3 1.0 CHB D:HEM137 3.4 31.3 1.0 CHC D:HEM137 3.4 32.2 1.0 ND1 D:HIS82 4.1 27.3 1.0 NE2 D:HIS53 4.2 38.7 1.0 C3C D:HEM137 4.2 33.5 1.0 C2C D:HEM137 4.2 31.8 1.0 C2A D:HEM137 4.2 32.9 1.0 C3A D:HEM137 4.2 31.4 1.0 CE1 D:HIS53 4.3 40.2 1.0 CG D:HIS82 4.3 30.1 1.0 C3D D:HEM137 4.3 32.0 1.0 C2D D:HEM137 4.3 34.8 1.0 C3B D:HEM137 4.3 31.1 1.0 C2B D:HEM137 4.3 31.4 1.0 CG2 D:VAL57 5.0 35.1 1.0

P.Ramesh, S.S.Sundaresan, P.Sathya Moorthy, M.Balasubramanian, M.N.Ponnuswamy. Structural Studies of Haemoglobin From Pisces Species Shortfin Mako Shark (Isurus Oxyrinchus) at 1.9 Angstrom Resolution J.Synchrotron Radiat. V. 20 843 2013.
ISSN: ISSN 0909-0495
PubMed: 24121325
DOI: 10.1107/S0909049513021572