Iron in PDB 1j3y: Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed)

The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed), PDB code: 1j3y was solved by S.Adachi, S.-Y.Park, J.R.H.Tame, Y.Shiro, N.Shibayama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.61 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.494, 94.012, 100.111, 90.00, 101.65, 90.00
R / Rfree (%)	16.2 / 20.5

The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed) also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Iron atom in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed) (pdb code 1j3y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed), PDB code: 1j3y:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:9.6 occ:1.00 FE A:HEM142 0.0 9.6 1.0 NC A:HEM142 2.1 9.0 1.0 ND A:HEM142 2.1 8.3 1.0 NA A:HEM142 2.1 8.9 1.0 NB A:HEM142 2.1 7.2 1.0 NE2 A:HIS87 2.1 9.0 1.0 CE1 A:HIS87 3.0 9.4 1.0 C1C A:HEM142 3.1 8.7 1.0 C4C A:HEM142 3.1 9.7 1.0 C4B A:HEM142 3.1 8.3 1.0 C1D A:HEM142 3.1 9.4 1.0 C1A A:HEM142 3.1 10.8 1.0 C4D A:HEM142 3.1 9.8 1.0 C4A A:HEM142 3.1 9.7 1.0 C1B A:HEM142 3.2 8.9 1.0 CD2 A:HIS87 3.2 7.4 1.0 CHC A:HEM142 3.4 9.9 1.0 CHD A:HEM142 3.5 9.3 1.0 CHA A:HEM142 3.5 9.6 1.0 CHB A:HEM142 3.5 9.9 1.0 C A:CMO3143 3.6 17.1 1.0 O A:CMO3143 4.0 17.3 1.0 ND1 A:HIS87 4.2 9.4 1.0 C2C A:HEM142 4.3 9.5 1.0 C3C A:HEM142 4.3 8.7 1.0 CG A:HIS87 4.3 7.8 1.0 C3B A:HEM142 4.3 8.5 1.0 C2A A:HEM142 4.3 11.8 1.0 C2D A:HEM142 4.3 10.9 1.0 C3D A:HEM142 4.4 9.7 1.0 C3A A:HEM142 4.4 10.7 1.0 C2B A:HEM142 4.4 8.7 1.0 NE2 A:HIS58 4.5 11.4 1.0 CD1 A:LEU91 4.7 10.5 1.0

Iron binding site 2 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:8.6 occ:1.00 FE C:HEM142 0.0 8.6 1.0 NC C:HEM142 2.1 8.0 1.0 NB C:HEM142 2.1 6.4 1.0 ND C:HEM142 2.1 7.9 1.0 NA C:HEM142 2.1 8.7 1.0 NE2 C:HIS87 2.2 8.9 1.0 C1C C:HEM142 3.1 7.6 1.0 C1D C:HEM142 3.1 8.9 1.0 C4B C:HEM142 3.1 7.1 1.0 C4D C:HEM142 3.1 8.2 1.0 C1A C:HEM142 3.1 9.6 1.0 C1B C:HEM142 3.1 7.5 1.0 CE1 C:HIS87 3.1 10.1 1.0 C4C C:HEM142 3.1 9.3 1.0 C4A C:HEM142 3.1 7.2 1.0 CD2 C:HIS87 3.3 9.5 1.0 CHC C:HEM142 3.4 7.3 1.0 CHA C:HEM142 3.5 9.4 1.0 CHD C:HEM142 3.5 8.2 1.0 CHB C:HEM142 3.5 6.6 1.0 C C:CMO4143 3.8 17.8 1.0 O C:CMO4143 4.0 17.0 1.0 ND1 C:HIS87 4.3 9.8 1.0 C3B C:HEM142 4.3 8.3 1.0 C2D C:HEM142 4.3 8.8 1.0 C2B C:HEM142 4.3 6.4 1.0 C3D C:HEM142 4.3 10.5 1.0 C2C C:HEM142 4.3 7.3 1.0 C3C C:HEM142 4.3 7.3 1.0 C2A C:HEM142 4.3 10.3 1.0 C3A C:HEM142 4.3 10.2 1.0 CG C:HIS87 4.4 9.1 1.0 NE2 C:HIS58 4.5 13.4 1.0 CD1 C:LEU91 4.6 10.8 1.0

Iron binding site 3 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe142 b:8.1 occ:1.00 FE E:HEM142 0.0 8.1 1.0 NC E:HEM142 2.1 6.4 1.0 ND E:HEM142 2.1 8.2 1.0 NA E:HEM142 2.1 7.8 1.0 NB E:HEM142 2.1 7.4 1.0 NE2 E:HIS87 2.2 8.7 1.0 CE1 E:HIS87 3.0 10.1 1.0 C1C E:HEM142 3.1 6.7 1.0 C4B E:HEM142 3.1 7.0 1.0 C4D E:HEM142 3.1 6.5 1.0 C4C E:HEM142 3.1 8.2 1.0 C1A E:HEM142 3.1 9.1 1.0 C4A E:HEM142 3.1 7.9 1.0 C1D E:HEM142 3.1 7.0 1.0 C1B E:HEM142 3.1 6.9 1.0 CD2 E:HIS87 3.2 8.7 1.0 CHC E:HEM142 3.4 7.7 1.0 CHA E:HEM142 3.5 7.1 1.0 CHD E:HEM142 3.5 7.6 1.0 CHB E:HEM142 3.5 6.7 1.0 C E:CMO5143 3.7 16.7 1.0 O E:CMO5143 3.9 16.4 1.0 ND1 E:HIS87 4.2 8.9 1.0 C2C E:HEM142 4.3 8.2 1.0 C3C E:HEM142 4.3 8.6 1.0 C3B E:HEM142 4.3 7.2 1.0 C2A E:HEM142 4.3 9.9 1.0 C3D E:HEM142 4.3 7.9 1.0 C2B E:HEM142 4.3 7.5 1.0 CG E:HIS87 4.3 8.9 1.0 C3A E:HEM142 4.3 9.1 1.0 C2D E:HEM142 4.4 7.4 1.0 NE2 E:HIS58 4.5 10.8 1.0 CD1 E:LEU91 4.7 9.7 1.0

Iron binding site 4 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Hemoglobin; Crystal Structure of Alpha(Fe)-Beta(Ni) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe142 b:7.0 occ:1.00 FE G:HEM142 0.0 7.0 1.0 NB G:HEM142 2.0 6.6 1.0 NC G:HEM142 2.1 5.4 1.0 ND G:HEM142 2.1 6.0 1.0 NA G:HEM142 2.1 6.5 1.0 NE2 G:HIS87 2.1 6.5 1.0 CE1 G:HIS87 3.0 7.8 1.0 C4B G:HEM142 3.0 7.6 1.0 C1C G:HEM142 3.1 7.3 1.0 C1B G:HEM142 3.1 8.4 1.0 C4D G:HEM142 3.1 6.9 1.0 C4C G:HEM142 3.1 7.2 1.0 C1D G:HEM142 3.1 5.8 1.0 C1A G:HEM142 3.1 7.0 1.0 C4A G:HEM142 3.1 6.9 1.0 CD2 G:HIS87 3.2 6.8 1.0 CHC G:HEM142 3.4 7.6 1.0 CHA G:HEM142 3.5 7.7 1.0 CHB G:HEM142 3.5 6.8 1.0 CHD G:HEM142 3.5 5.7 1.0 C G:CMO6143 3.8 20.6 1.0 O G:CMO6143 4.1 20.6 1.0 ND1 G:HIS87 4.2 6.8 1.0 C3B G:HEM142 4.3 8.4 1.0 C2B G:HEM142 4.3 5.4 1.0 C2C G:HEM142 4.3 6.6 1.0 C3C G:HEM142 4.3 7.5 1.0 CG G:HIS87 4.3 6.3 1.0 C2D G:HEM142 4.3 7.4 1.0 C3A G:HEM142 4.3 6.7 1.0 C2A G:HEM142 4.3 6.9 1.0 C3D G:HEM142 4.3 8.0 1.0 NE2 G:HIS58 4.5 14.3 1.0 CD1 G:LEU91 4.7 8.4 1.0

S.Adachi, S.-Y.Park, J.R.H.Tame, Y.Shiro, N.Shibayama. Direct Observation of Photolysis-Induced Tertiary Structural Changes in Hemoglobin Proc.Natl.Acad.Sci.Usa V. 100 7039 2003.
ISSN: ISSN 0027-8424
PubMed: 12773618
DOI: 10.1073/PNAS.1230629100