Nickel in PDB 1j40: Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)

The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed), PDB code: 1j40 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 (°)	64.708, 94.860, 99.730, 90.00, 101.97, 90.00
R / Rfree (%)	16.5 / 19.7

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

Iron

(Fe)

4 atoms

The binding sites of Nickel atom in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) (pdb code 1j40). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed), PDB code: 1j40:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel 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-Co) Hemoglobin (Laser Unphotolysed)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni142 b:9.7 occ:1.00 NI A:HNI142 0.0 9.7 1.0 ND A:HNI142 2.0 9.8 1.0 NB A:HNI142 2.0 9.0 1.0 NA A:HNI142 2.0 9.8 1.0 NC A:HNI142 2.0 9.7 1.0 C1D A:HNI142 3.0 11.0 1.0 C4D A:HNI142 3.0 11.0 1.0 C1A A:HNI142 3.0 11.6 1.0 C4A A:HNI142 3.0 9.5 1.0 C1C A:HNI142 3.1 8.3 1.0 C4C A:HNI142 3.1 9.5 1.0 C4B A:HNI142 3.1 10.1 1.0 C1B A:HNI142 3.1 9.2 1.0 CHD A:HNI142 3.4 9.2 1.0 CHA A:HNI142 3.4 10.7 1.0 CHC A:HNI142 3.4 10.0 1.0 CHB A:HNI142 3.4 8.7 1.0 CE1 A:HIS87 3.5 11.6 1.0 CE1 A:HIS58 3.6 12.4 1.0 NE2 A:HIS87 3.7 11.7 1.0 NE2 A:HIS58 3.9 18.4 1.0 C3D A:HNI142 4.2 11.7 1.0 C2D A:HNI142 4.3 11.2 1.0 C2A A:HNI142 4.3 12.3 1.0 C3A A:HNI142 4.3 11.3 1.0 C2C A:HNI142 4.3 9.6 1.0 C3C A:HNI142 4.3 8.3 1.0 C2B A:HNI142 4.3 10.4 1.0 C3B A:HNI142 4.3 10.2 1.0 CG2 A:VAL62 4.5 9.6 1.0 CD1 A:LEU91 4.5 14.2 1.0 ND1 A:HIS87 4.7 10.6 1.0 ND1 A:HIS58 4.8 16.2 1.0 CD2 A:HIS87 5.0 11.1 1.0

Nickel 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-Co) Hemoglobin (Laser Unphotolysed)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni142 b:8.5 occ:1.00 NI C:HNI142 0.0 8.5 1.0 ND C:HNI142 1.9 9.9 1.0 NB C:HNI142 2.0 8.8 1.0 NA C:HNI142 2.0 9.5 1.0 NC C:HNI142 2.0 7.9 1.0 C1D C:HNI142 3.0 7.6 1.0 C4B C:HNI142 3.0 8.3 1.0 C1C C:HNI142 3.0 8.4 1.0 C4A C:HNI142 3.0 9.9 1.0 C4D C:HNI142 3.0 8.0 1.0 C1A C:HNI142 3.0 11.4 1.0 C4C C:HNI142 3.1 7.4 1.0 C1B C:HNI142 3.1 9.2 1.0 CHC C:HNI142 3.4 8.9 1.0 CHD C:HNI142 3.4 8.3 1.0 CHA C:HNI142 3.4 11.3 1.0 CHB C:HNI142 3.4 9.9 1.0 CE1 C:HIS87 3.5 11.5 1.0 NE2 C:HIS87 3.7 10.8 1.0 NE2 C:HIS58 3.7 14.5 1.0 CE1 C:HIS58 4.1 15.8 1.0 C3A C:HNI142 4.3 11.2 1.0 C3D C:HNI142 4.3 10.4 1.0 C2A C:HNI142 4.3 11.6 1.0 C2D C:HNI142 4.3 8.8 1.0 C2C C:HNI142 4.3 7.7 1.0 C2B C:HNI142 4.3 9.7 1.0 C3B C:HNI142 4.3 9.4 1.0 C3C C:HNI142 4.3 8.3 1.0 CG2 C:VAL62 4.4 9.9 1.0 CD1 C:LEU91 4.5 14.0 1.0 ND1 C:HIS87 4.7 10.5 1.0 CD2 C:HIS58 5.0 13.8 1.0

Nickel 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-Co) Hemoglobin (Laser Unphotolysed)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni142 b:9.8 occ:1.00 NI E:HNI142 0.0 9.8 1.0 ND E:HNI142 1.9 10.5 1.0 NB E:HNI142 2.0 10.6 1.0 NA E:HNI142 2.0 9.6 1.0 NC E:HNI142 2.0 9.3 1.0 C1D E:HNI142 3.0 9.3 1.0 C4A E:HNI142 3.0 9.8 1.0 C1C E:HNI142 3.0 11.0 1.0 C4D E:HNI142 3.0 10.4 1.0 C4C E:HNI142 3.0 8.6 1.0 C1A E:HNI142 3.0 12.8 1.0 C4B E:HNI142 3.1 9.7 1.0 C1B E:HNI142 3.1 9.1 1.0 CHD E:HNI142 3.4 9.7 1.0 CHC E:HNI142 3.4 10.1 1.0 CHA E:HNI142 3.4 10.4 1.0 CHB E:HNI142 3.4 10.3 1.0 CE1 E:HIS87 3.5 10.6 1.0 NE2 E:HIS87 3.7 11.8 1.0 NE2 E:HIS58 3.8 16.8 1.0 CE1 E:HIS58 4.2 17.8 1.0 C2D E:HNI142 4.2 11.5 1.0 C3D E:HNI142 4.2 11.2 1.0 C2A E:HNI142 4.3 13.3 1.0 C2C E:HNI142 4.3 10.3 1.0 C3A E:HNI142 4.3 12.2 1.0 C2B E:HNI142 4.3 10.0 1.0 C3B E:HNI142 4.3 9.9 1.0 C3C E:HNI142 4.3 10.6 1.0 CD1 E:LEU91 4.3 12.8 1.0 CG2 E:VAL62 4.5 13.2 1.0 ND1 E:HIS87 4.7 11.4 1.0 CD2 E:HIS87 5.0 10.3 1.0

Nickel 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-Co) Hemoglobin (Laser Unphotolysed)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni142 b:8.8 occ:1.00 NI G:HNI142 0.0 8.8 1.0 ND G:HNI142 1.9 10.0 1.0 NA G:HNI142 2.0 7.6 1.0 NB G:HNI142 2.0 8.7 1.0 NC G:HNI142 2.0 8.4 1.0 C1D G:HNI142 3.0 9.6 1.0 C4A G:HNI142 3.0 7.8 1.0 C4C G:HNI142 3.0 8.7 1.0 C1A G:HNI142 3.0 8.1 1.0 C1C G:HNI142 3.0 8.7 1.0 C4D G:HNI142 3.0 10.1 1.0 C1B G:HNI142 3.0 8.2 1.0 C4B G:HNI142 3.1 7.8 1.0 CHD G:HNI142 3.4 9.1 1.0 CE1 G:HIS87 3.4 9.2 1.0 CHB G:HNI142 3.4 8.3 1.0 CHA G:HNI142 3.4 10.1 1.0 CHC G:HNI142 3.4 9.0 1.0 NE2 G:HIS87 3.6 10.1 1.0 CE1 G:HIS58 3.6 9.1 1.0 NE2 G:HIS58 4.0 13.8 1.0 C3A G:HNI142 4.2 9.1 1.0 C2D G:HNI142 4.2 10.1 1.0 C2A G:HNI142 4.3 9.4 1.0 C3D G:HNI142 4.3 10.6 1.0 C2C G:HNI142 4.3 7.2 1.0 C2B G:HNI142 4.3 8.6 1.0 C3C G:HNI142 4.3 7.8 1.0 C3B G:HNI142 4.3 8.8 1.0 CD1 G:LEU91 4.4 12.1 1.0 CG2 G:VAL62 4.4 9.8 1.0 ND1 G:HIS87 4.6 10.8 1.0 ND1 G:HIS58 4.8 14.6 1.0 CD2 G:HIS87 4.9 9.9 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