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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)

Protein crystallography data

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

Nickel Binding Sites:

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 1j40

Go back to Nickel Binding Sites List in 1j40
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 1j40

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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 1j40

Go back to Nickel Binding Sites List in 1j40
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 1j40

Go back to Nickel Binding Sites List in 1j40
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

Reference:

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
Page generated: Fri Sep 25 07:55:26 2020
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