Iron in PDB 5e29: Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide

The structure of Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide, PDB code: 5e29 was solved by M.K.Safo, T.M.Deshpande, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.878, 98.419, 65.444, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.3

The structure of Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Iron atom in the Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide (pdb code 5e29). 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 An Allosteric Effector and Nitric Oxide, PDB code: 5e29:
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 An Allosteric Effector and Nitric Oxide


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 An Allosteric Effector and Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:17.5 occ:1.00 FE A:HEM202 0.0 17.5 1.0 N A:NO201 1.6 17.0 1.0 NA A:HEM202 2.0 18.6 1.0 NB A:HEM202 2.0 18.3 1.0 ND A:HEM202 2.0 21.4 1.0 NC A:HEM202 2.0 16.2 1.0 O A:NO201 2.6 19.7 1.0 C1A A:HEM202 3.0 19.6 1.0 C1B A:HEM202 3.1 18.5 1.0 C4A A:HEM202 3.1 17.4 1.0 C4B A:HEM202 3.1 16.1 1.0 C1C A:HEM202 3.1 16.9 1.0 C4D A:HEM202 3.1 16.1 1.0 C4C A:HEM202 3.1 14.2 1.0 C1D A:HEM202 3.1 18.9 1.0 NE2 A:HIS87 3.4 24.4 1.0 CHA A:HEM202 3.4 18.7 1.0 CHB A:HEM202 3.4 17.9 1.0 CHC A:HEM202 3.4 18.1 1.0 CHD A:HEM202 3.5 16.0 1.0 CE1 A:HIS87 3.9 19.4 1.0 NE2 A:HIS58 4.1 25.1 1.0 C2A A:HEM202 4.3 11.8 1.0 C2B A:HEM202 4.3 17.2 1.0 C3A A:HEM202 4.3 17.8 1.0 C3B A:HEM202 4.3 21.1 1.0 C2C A:HEM202 4.3 12.3 1.0 C3D A:HEM202 4.3 20.1 1.0 C3C A:HEM202 4.3 11.3 1.0 C2D A:HEM202 4.3 22.1 1.0 CD1 A:LEU91 4.6 14.9 1.0 CD2 A:HIS87 4.6 20.6 1.0 CG2 A:VAL62 4.7 23.3 1.0 CE1 A:HIS58 4.8 25.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide


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 An Allosteric Effector and Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:24.1 occ:1.00 FE B:HEM201 0.0 24.1 1.0 ND B:HEM201 2.0 25.6 1.0 NB B:HEM201 2.0 26.5 1.0 NE2 B:HIS92 2.0 27.5 1.0 NA B:HEM201 2.0 28.0 1.0 NC B:HEM201 2.0 25.8 1.0 CE1 B:HIS92 3.0 26.9 1.0 C1D B:HEM201 3.1 25.9 1.0 C4D B:HEM201 3.1 28.3 1.0 C1A B:HEM201 3.1 25.6 1.0 C1B B:HEM201 3.1 26.8 1.0 C4B B:HEM201 3.1 23.3 1.0 C4A B:HEM201 3.1 24.3 1.0 C4C B:HEM201 3.1 18.7 1.0 C1C B:HEM201 3.1 24.7 1.0 CD2 B:HIS92 3.1 24.5 1.0 CHA B:HEM201 3.4 28.0 1.0 CHD B:HEM201 3.4 25.6 1.0 CHB B:HEM201 3.5 27.5 1.0 CHC B:HEM201 3.5 22.1 1.0 ND1 B:HIS92 4.2 25.8 1.0 CG2 B:VAL67 4.2 19.4 1.0 CG B:HIS92 4.2 27.6 1.0 C3D B:HEM201 4.3 32.0 1.0 C2D B:HEM201 4.3 25.0 1.0 C2B B:HEM201 4.3 22.3 1.0 C3B B:HEM201 4.3 21.2 1.0 C2A B:HEM201 4.3 24.3 1.0 C3A B:HEM201 4.3 27.8 1.0 C2C B:HEM201 4.3 20.8 1.0 C3C B:HEM201 4.4 24.6 1.0 NE2 B:HIS63 4.5 34.6 1.0 CD1 B:LEU96 4.8 22.7 1.0 CE1 B:HIS63 4.9 33.2 1.0 CG1 B:VAL67 5.0 20.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide


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 An Allosteric Effector and Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:19.3 occ:1.00 FE C:HEM202 0.0 19.3 1.0 N C:NO201 1.7 17.7 1.0 NB C:HEM202 2.0 18.6 1.0 ND C:HEM202 2.0 14.2 1.0 NC C:HEM202 2.0 13.9 1.0 NA C:HEM202 2.0 19.0 1.0 O C:NO201 2.6 19.7 1.0 C4B C:HEM202 3.0 16.8 1.0 C1C C:HEM202 3.0 18.9 1.0 C1A C:HEM202 3.0 16.9 1.0 C4D C:HEM202 3.1 20.3 1.0 C1D C:HEM202 3.1 12.9 1.0 C1B C:HEM202 3.1 14.1 1.0 C4C C:HEM202 3.1 12.2 1.0 C4A C:HEM202 3.1 16.4 1.0 CHC C:HEM202 3.4 15.4 1.0 CHA C:HEM202 3.4 16.2 1.0 CHD C:HEM202 3.4 13.5 1.0 NE2 C:HIS87 3.4 27.3 1.0 CHB C:HEM202 3.5 17.0 1.0 CE1 C:HIS87 3.9 18.7 1.0 NE2 C:HIS58 4.2 25.6 1.0 C3B C:HEM202 4.3 15.3 1.0 C2B C:HEM202 4.3 14.2 1.0 C2A C:HEM202 4.3 22.7 1.0 C2C C:HEM202 4.3 14.4 1.0 C3A C:HEM202 4.3 15.1 1.0 C2D C:HEM202 4.3 16.1 1.0 C3D C:HEM202 4.3 16.0 1.0 C3C C:HEM202 4.3 14.2 1.0 CD1 C:LEU91 4.6 14.0 1.0 CD2 C:HIS87 4.7 19.7 1.0 CG2 C:VAL62 4.8 23.2 1.0 CE1 C:HIS58 5.0 28.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with An Allosteric Effector and Nitric Oxide


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 An Allosteric Effector and Nitric Oxide within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:15.9 occ:1.00 FE D:HEM201 0.0 15.9 1.0 ND D:HEM201 2.0 13.2 1.0 NB D:HEM201 2.0 12.5 1.0 NC D:HEM201 2.0 20.5 1.0 NA D:HEM201 2.1 14.3 1.0 NE2 D:HIS92 2.1 16.8 1.0 C4D D:HEM201 3.0 17.0 1.0 CE1 D:HIS92 3.0 15.9 1.0 C1D D:HEM201 3.1 15.7 1.0 C4B D:HEM201 3.1 18.3 1.0 C4C D:HEM201 3.1 10.7 1.0 C1C D:HEM201 3.1 17.2 1.0 C1A D:HEM201 3.1 12.8 1.0 C1B D:HEM201 3.1 18.7 1.0 C4A D:HEM201 3.2 13.4 1.0 CD2 D:HIS92 3.2 9.2 1.0 CHA D:HEM201 3.4 11.5 1.0 CHD D:HEM201 3.5 15.6 1.0 CHC D:HEM201 3.5 17.4 1.0 CHB D:HEM201 3.5 16.4 1.0 ND1 D:HIS92 4.2 13.8 1.0 NE2 D:HIS63 4.2 12.2 1.0 C3D D:HEM201 4.2 11.3 1.0 C2D D:HEM201 4.3 14.6 1.0 C2C D:HEM201 4.3 19.2 1.0 C3C D:HEM201 4.3 15.1 1.0 C3B D:HEM201 4.3 17.2 1.0 CG D:HIS92 4.3 19.4 1.0 CG2 D:VAL67 4.3 18.9 1.0 C2B D:HEM201 4.4 15.9 1.0 C2A D:HEM201 4.4 15.1 1.0 C3A D:HEM201 4.4 16.8 1.0 CE1 D:HIS63 5.0 18.0 1.0

G.G.Xu, T.M.Deshpande, M.S.Ghatge, A.Y.Mehta, A.S.Omar, M.H.Ahmed, J.Venitz, O.Abdulmalik, Y.Zhang, M.K.Safo. Design, Synthesis, and Investigation of Novel Nitric Oxide (No)-Releasing Prodrugs As Drug Candidates For the Treatment of Ischemic Disorders: Insights Into No-Releasing Prodrug Biotransformation and Hemoglobin-No Biochemistry. Biochemistry V. 54 7178 2015.
ISSN: ISSN 0006-2960
PubMed: 26582149
DOI: 10.1021/ACS.BIOCHEM.5B01074