Iron in PDB 5ksj: Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate

The structure of Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate, PDB code: 5ksj was solved by M.H.Ahmed, M.K.Safo, Y.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.180, 97.550, 65.030, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 28.7

The binding sites of Iron atom in the Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate (pdb code 5ksj). 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 Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate, PDB code: 5ksj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate


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 Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:41.4 occ:1.00 FE A:HEM201 0.0 41.4 1.0 ND A:HEM201 2.0 44.2 1.0 NB A:HEM201 2.0 41.6 1.0 NC A:HEM201 2.0 41.6 1.0 NA A:HEM201 2.0 45.4 1.0 NE2 A:HIS87 2.1 43.5 1.0 CE1 A:HIS87 3.0 36.1 1.0 C1D A:HEM201 3.1 48.9 1.0 C1B A:HEM201 3.1 43.5 1.0 C4B A:HEM201 3.1 43.5 1.0 C4D A:HEM201 3.1 51.5 1.0 C4A A:HEM201 3.1 38.0 1.0 C1C A:HEM201 3.1 38.4 1.0 C4C A:HEM201 3.1 42.3 1.0 C1A A:HEM201 3.1 47.1 1.0 CD2 A:HIS87 3.2 36.7 1.0 CHD A:HEM201 3.5 45.4 1.0 CHB A:HEM201 3.5 41.7 1.0 CHC A:HEM201 3.5 42.9 1.0 CHA A:HEM201 3.5 46.6 1.0 O A:HOH312 3.7 32.1 1.0 ND1 A:HIS87 4.2 31.3 1.0 C2B A:HEM201 4.3 40.0 1.0 CG A:HIS87 4.3 36.6 1.0 C3B A:HEM201 4.3 42.5 1.0 C2D A:HEM201 4.3 50.1 1.0 C3D A:HEM201 4.3 46.9 1.0 C3A A:HEM201 4.3 42.3 1.0 C2C A:HEM201 4.4 29.7 1.0 CD1 A:LEU91 4.4 34.5 1.0 C3C A:HEM201 4.4 31.9 1.0 C2A A:HEM201 4.4 44.3 1.0 CE1 A:HIS58 4.6 51.2 1.0 NE2 A:HIS58 4.9 42.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate


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 Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:45.7 occ:1.00 FE B:HEM201 0.0 45.7 1.0 ND B:HEM201 2.0 51.0 1.0 NA B:HEM201 2.0 58.9 1.0 NC B:HEM201 2.0 52.7 1.0 NB B:HEM201 2.0 49.5 1.0 NE2 B:HIS92 2.1 49.7 1.0 C4D B:HEM201 3.0 54.9 1.0 C1A B:HEM201 3.1 58.7 1.0 C1D B:HEM201 3.1 46.9 1.0 CE1 B:HIS92 3.1 46.7 1.0 C4B B:HEM201 3.1 44.3 1.0 C4C B:HEM201 3.1 46.0 1.0 C4A B:HEM201 3.1 60.1 1.0 C1B B:HEM201 3.1 48.7 1.0 CD2 B:HIS92 3.1 42.6 1.0 C1C B:HEM201 3.1 48.3 1.0 CHA B:HEM201 3.4 55.7 1.0 CHD B:HEM201 3.5 43.6 1.0 CHC B:HEM201 3.5 44.3 1.0 CHB B:HEM201 3.5 57.0 1.0 ND1 B:HIS92 4.2 43.5 1.0 CG B:HIS92 4.2 41.3 1.0 C3D B:HEM201 4.3 56.4 1.0 C2A B:HEM201 4.3 60.1 1.0 CG2 B:VAL67 4.3 40.0 1.0 C3B B:HEM201 4.3 39.7 1.0 C2D B:HEM201 4.3 52.0 1.0 C3A B:HEM201 4.3 58.1 1.0 C2B B:HEM201 4.3 44.6 1.0 C2C B:HEM201 4.4 44.3 1.0 C3C B:HEM201 4.4 43.5 1.0 NE2 B:HIS63 4.6 60.4 1.0 CE1 B:HIS63 4.8 61.4 1.0 CE1 B:PHE103 5.0 46.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate


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 Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:42.7 occ:1.00 FE C:HEM201 0.0 42.7 1.0 ND C:HEM201 2.0 47.2 1.0 NA C:HEM201 2.0 38.8 1.0 NB C:HEM201 2.0 37.0 1.0 NC C:HEM201 2.0 39.7 1.0 NE2 C:HIS87 2.1 37.6 1.0 CE1 C:HIS87 3.0 42.4 1.0 C4D C:HEM201 3.0 47.2 1.0 C1A C:HEM201 3.0 41.5 1.0 C1C C:HEM201 3.1 39.0 1.0 C4B C:HEM201 3.1 35.6 1.0 C1D C:HEM201 3.1 50.0 1.0 C1B C:HEM201 3.1 30.6 1.0 C4A C:HEM201 3.1 38.1 1.0 C4C C:HEM201 3.1 40.1 1.0 CD2 C:HIS87 3.2 32.7 1.0 O C:HOH328 3.3 29.5 1.0 CHA C:HEM201 3.4 49.6 1.0 CHC C:HEM201 3.5 31.2 1.0 CHB C:HEM201 3.5 35.9 1.0 CHD C:HEM201 3.5 43.5 1.0 ND1 C:HIS87 4.2 37.4 1.0 CG C:HIS87 4.3 29.2 1.0 C2A C:HEM201 4.3 37.3 1.0 C3D C:HEM201 4.3 43.2 1.0 C3B C:HEM201 4.3 31.9 1.0 C2D C:HEM201 4.3 50.0 1.0 C2B C:HEM201 4.3 26.6 1.0 C2C C:HEM201 4.3 37.1 1.0 C3A C:HEM201 4.3 35.1 1.0 C3C C:HEM201 4.4 32.4 1.0 CD1 C:LEU91 4.5 36.0 1.0 CE1 C:HIS58 4.5 45.9 1.0 NE2 C:HIS58 4.8 36.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate


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 Deoxygenated Hemoglobin in Complex with Sphingosine Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:28.6 occ:1.00 FE D:HEM201 0.0 28.6 1.0 NA D:HEM201 2.0 36.0 1.0 ND D:HEM201 2.0 36.0 1.0 NB D:HEM201 2.0 26.5 1.0 NE2 D:HIS92 2.0 25.2 1.0 NC D:HEM201 2.0 25.4 1.0 CE1 D:HIS92 2.9 23.2 1.0 C4D D:HEM201 3.1 35.8 1.0 C1B D:HEM201 3.1 29.6 1.0 C4B D:HEM201 3.1 29.1 1.0 C4A D:HEM201 3.1 35.3 1.0 C1A D:HEM201 3.1 36.5 1.0 C1C D:HEM201 3.1 28.5 1.0 C1D D:HEM201 3.1 29.3 1.0 C4C D:HEM201 3.1 20.8 1.0 CD2 D:HIS92 3.1 24.7 1.0 CHB D:HEM201 3.4 42.2 1.0 CHC D:HEM201 3.4 29.3 1.0 CHA D:HEM201 3.4 37.7 1.0 CHD D:HEM201 3.5 30.3 1.0 ND1 D:HIS92 4.1 20.7 1.0 CG D:HIS92 4.2 20.7 1.0 C3D D:HEM201 4.3 38.7 1.0 C2D D:HEM201 4.3 36.4 1.0 C3B D:HEM201 4.3 32.9 1.0 C2B D:HEM201 4.3 36.3 1.0 C2A D:HEM201 4.3 36.4 1.0 C3A D:HEM201 4.3 36.1 1.0 C2C D:HEM201 4.3 28.7 1.0 C3C D:HEM201 4.3 21.5 1.0 NE2 D:HIS63 4.4 38.9 1.0 CG2 D:VAL67 4.4 27.9 1.0

K.Sun, A.D'alessandro, M.H.Ahmed, Y.Zhang, A.Song, T.P.Ko, T.Nemkov, J.A.Reisz, H.Wu, M.Adebiyi, Z.Peng, J.Gong, H.Liu, A.Huang, Y.E.Wen, A.Q.Wen, V.Berka, M.V.Bogdanov, O.Abdulmalik, L.Han, A.L.Tsai, M.Idowu, H.S.Juneja, R.E.Kellems, W.Dowhan, K.C.Hansen, M.K.Safo, Y.Xia. Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease. Sci Rep V. 7 15281 2017.
ISSN: ESSN 2045-2322
PubMed: 29127281
DOI: 10.1038/S41598-017-13667-8