Iron in PDB 1j41: Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed)

The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed), PDB code: 1j41 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)	20.00 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.542, 94.565, 99.449, 90.00, 101.84, 90.00
R / Rfree (%)	16.4 / 19.5

The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) 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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed) (pdb code 1j41). 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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed), PDB code: 1j41:
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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) 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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe147 b:7.2 occ:1.00 FE B:HEM147 0.0 7.2 1.0 NC B:HEM147 2.1 7.1 1.0 NA B:HEM147 2.1 6.5 1.0 NE2 B:HIS92 2.1 7.0 1.0 ND B:HEM147 2.1 7.6 1.0 NB B:HEM147 2.1 8.0 1.0 CE1 B:HIS92 3.0 8.4 1.0 C1D B:HEM147 3.1 7.0 1.0 C1C B:HEM147 3.1 7.4 1.0 C4C B:HEM147 3.1 5.7 1.0 C1A B:HEM147 3.1 6.7 1.0 C4B B:HEM147 3.1 7.3 1.0 C4D B:HEM147 3.1 6.6 1.0 C4A B:HEM147 3.1 7.2 1.0 C1B B:HEM147 3.1 7.9 1.0 CD2 B:HIS92 3.1 7.5 1.0 CHD B:HEM147 3.4 7.8 1.0 CHC B:HEM147 3.4 8.5 1.0 CHA B:HEM147 3.5 6.9 1.0 CHB B:HEM147 3.5 7.6 1.0 ND1 B:HIS92 4.2 7.0 1.0 CG B:HIS92 4.3 6.8 1.0 CG2 B:VAL67 4.3 15.2 1.0 C3C B:HEM147 4.3 8.0 1.0 C2C B:HEM147 4.3 8.0 1.0 NE2 B:HIS63 4.3 10.7 1.0 C3B B:HEM147 4.3 8.3 1.0 C2D B:HEM147 4.3 7.6 1.0 C2A B:HEM147 4.3 6.9 1.0 C2B B:HEM147 4.3 7.9 1.0 C3A B:HEM147 4.3 8.4 1.0 C3D B:HEM147 4.3 7.8 1.0 O B:CMO3148 4.4 53.6 1.0 C B:CMO3148 4.5 53.7 1.0 CD1 B:LEU96 4.9 9.5 1.0

Iron binding site 2 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) 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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe147 b:10.7 occ:1.00 FE D:HEM147 0.0 10.7 1.0 NE2 D:HIS92 2.0 11.0 1.0 NC D:HEM147 2.1 10.1 1.0 NA D:HEM147 2.1 10.0 1.0 ND D:HEM147 2.1 11.0 1.0 NB D:HEM147 2.1 10.4 1.0 CE1 D:HIS92 2.9 10.8 1.0 C4C D:HEM147 3.1 10.2 1.0 CD2 D:HIS92 3.1 10.1 1.0 C1C D:HEM147 3.1 10.2 1.0 C1D D:HEM147 3.1 11.7 1.0 C1A D:HEM147 3.1 11.3 1.0 C1B D:HEM147 3.1 10.6 1.0 C4A D:HEM147 3.1 11.6 1.0 C4D D:HEM147 3.1 11.6 1.0 C4B D:HEM147 3.1 9.3 1.0 CHD D:HEM147 3.4 10.7 1.0 CHB D:HEM147 3.5 11.0 1.0 CHA D:HEM147 3.5 11.2 1.0 CHC D:HEM147 3.5 9.6 1.0 ND1 D:HIS92 4.0 10.2 1.0 CG D:HIS92 4.2 10.0 1.0 O D:CMO4148 4.2 34.8 1.0 C2C D:HEM147 4.3 9.1 1.0 C3C D:HEM147 4.3 11.0 1.0 C2B D:HEM147 4.3 10.9 1.0 C2A D:HEM147 4.3 14.2 1.0 C3A D:HEM147 4.3 13.1 1.0 C3B D:HEM147 4.3 9.9 1.0 C2D D:HEM147 4.3 12.5 1.0 C D:CMO4148 4.3 35.4 1.0 C3D D:HEM147 4.3 11.4 1.0 NE2 D:HIS63 4.5 11.8 1.0 CG2 D:VAL67 4.6 12.5 1.0

Iron binding site 3 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) 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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe147 b:10.4 occ:1.00 FE F:HEM147 0.0 10.4 1.0 NE2 F:HIS92 2.0 8.2 1.0 NC F:HEM147 2.1 11.0 1.0 NA F:HEM147 2.1 12.3 1.0 NB F:HEM147 2.1 10.7 1.0 ND F:HEM147 2.1 8.6 1.0 CE1 F:HIS92 2.9 9.7 1.0 C4B F:HEM147 3.0 11.8 1.0 C1A F:HEM147 3.1 10.9 1.0 CD2 F:HIS92 3.1 9.4 1.0 C1C F:HEM147 3.1 9.2 1.0 C4D F:HEM147 3.1 10.4 1.0 C4C F:HEM147 3.1 8.7 1.0 C1D F:HEM147 3.1 8.7 1.0 C1B F:HEM147 3.1 12.7 1.0 C4A F:HEM147 3.1 12.0 1.0 CHA F:HEM147 3.4 11.3 1.0 CHC F:HEM147 3.4 12.4 1.0 CHD F:HEM147 3.5 8.8 1.0 CHB F:HEM147 3.5 11.6 1.0 ND1 F:HIS92 4.1 8.2 1.0 O F:CMO5148 4.2 27.5 1.0 CG F:HIS92 4.2 9.0 1.0 C F:CMO5148 4.2 28.6 1.0 C3B F:HEM147 4.3 13.3 1.0 C2B F:HEM147 4.3 12.1 1.0 C3C F:HEM147 4.3 9.8 1.0 C2A F:HEM147 4.3 13.2 1.0 C2C F:HEM147 4.3 9.7 1.0 C2D F:HEM147 4.3 10.5 1.0 C3A F:HEM147 4.3 12.6 1.0 C3D F:HEM147 4.3 11.2 1.0 NE2 F:HIS63 4.5 12.3 1.0 CG2 F:VAL67 4.5 14.9 1.0

Iron binding site 4 out of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) 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 Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe) Hemoglobin (Laser Photolysed) within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe147 b:9.6 occ:1.00 FE H:HEM147 0.0 9.6 1.0 NE2 H:HIS92 2.0 10.7 1.0 NB H:HEM147 2.1 9.7 1.0 ND H:HEM147 2.1 9.8 1.0 NC H:HEM147 2.1 9.4 1.0 NA H:HEM147 2.1 9.9 1.0 CE1 H:HIS92 2.9 10.5 1.0 CD2 H:HIS92 3.1 11.3 1.0 C4B H:HEM147 3.1 10.1 1.0 C1D H:HEM147 3.1 10.3 1.0 C1B H:HEM147 3.1 9.9 1.0 C4D H:HEM147 3.1 9.1 1.0 C1A H:HEM147 3.1 9.9 1.0 C4C H:HEM147 3.1 8.9 1.0 C4A H:HEM147 3.1 10.9 1.0 C1C H:HEM147 3.1 9.4 1.0 CHD H:HEM147 3.4 10.4 1.0 CHA H:HEM147 3.5 9.6 1.0 CHC H:HEM147 3.5 8.9 1.0 CHB H:HEM147 3.5 10.2 1.0 O H:CMO6149 4.0 26.2 1.0 ND1 H:HIS92 4.1 10.4 1.0 C H:CMO6149 4.1 27.2 1.0 CG H:HIS92 4.2 10.7 1.0 C3B H:HEM147 4.3 10.5 1.0 C2B H:HEM147 4.3 9.6 1.0 C2D H:HEM147 4.3 11.8 1.0 C3A H:HEM147 4.3 11.6 1.0 C2A H:HEM147 4.3 11.7 1.0 C2C H:HEM147 4.3 9.6 1.0 C3D H:HEM147 4.3 10.9 1.0 C3C H:HEM147 4.3 9.1 1.0 NE2 H:HIS63 4.5 10.9 1.0 CG2 H:VAL67 4.5 11.2 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