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

Protein crystallography data

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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 1j3y

Go back to Nickel Binding Sites List in 1j3y
Nickel 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 Nickel with other atoms in the Ni 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
B:Ni147

b:7.2
occ:1.00
NI B:HNI147 0.0 7.2 1.0
ND B:HNI147 1.9 7.0 1.0
NB B:HNI147 2.0 7.0 1.0
NA B:HNI147 2.0 6.0 1.0
NC B:HNI147 2.0 6.0 1.0
NE2 B:HIS92 2.1 7.3 1.0
CE1 B:HIS92 3.0 6.6 1.0
C1D B:HNI147 3.0 6.9 1.0
C1A B:HNI147 3.0 7.6 1.0
C4D B:HNI147 3.1 7.2 1.0
C1C B:HNI147 3.1 6.1 1.0
C4A B:HNI147 3.1 5.9 1.0
C4B B:HNI147 3.1 5.8 1.0
C1B B:HNI147 3.1 6.3 1.0
C4C B:HNI147 3.1 7.8 1.0
CD2 B:HIS92 3.1 8.3 1.0
CHA B:HNI147 3.4 6.8 1.0
CHC B:HNI147 3.4 6.4 1.0
CHD B:HNI147 3.5 7.4 1.0
CHB B:HNI147 3.5 7.2 1.0
CG2 B:VAL67 4.0 9.2 1.0
ND1 B:HIS92 4.2 6.4 1.0
NE2 B:HIS63 4.2 10.4 1.0
CG B:HIS92 4.3 6.2 1.0
C2D B:HNI147 4.3 7.5 1.0
C3D B:HNI147 4.3 7.7 1.0
C2A B:HNI147 4.3 6.2 1.0
C3A B:HNI147 4.3 6.6 1.0
C2B B:HNI147 4.3 6.0 1.0
C2C B:HNI147 4.3 6.5 1.0
C3B B:HNI147 4.3 6.8 1.0
C3C B:HNI147 4.3 7.9 1.0
CE1 B:HIS63 4.9 11.7 1.0
CE1 B:PHE103 5.0 11.5 1.0
CD1 B:LEU96 5.0 8.7 1.0

Nickel binding site 2 out of 4 in 1j3y

Go back to Nickel Binding Sites List in 1j3y
Nickel 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 Nickel with other atoms in the Ni 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
D:Ni147

b:10.5
occ:1.00
NI D:HNI147 0.0 10.5 1.0
ND D:HNI147 2.0 10.8 1.0
NB D:HNI147 2.0 10.2 1.0
NA D:HNI147 2.0 10.8 1.0
NC D:HNI147 2.0 11.6 1.0
NE2 D:HIS92 2.1 9.2 1.0
C1A D:HNI147 3.0 12.8 1.0
C4D D:HNI147 3.0 12.3 1.0
C4A D:HNI147 3.1 12.0 1.0
C1D D:HNI147 3.1 11.9 1.0
C1C D:HNI147 3.1 13.6 1.0
C4C D:HNI147 3.1 10.9 1.0
CE1 D:HIS92 3.1 8.3 1.0
C4B D:HNI147 3.1 10.4 1.0
C1B D:HNI147 3.1 10.5 1.0
CD2 D:HIS92 3.2 9.0 1.0
CHA D:HNI147 3.4 12.8 1.0
CHD D:HNI147 3.4 9.6 1.0
CHB D:HNI147 3.5 9.4 1.0
CHC D:HNI147 3.5 10.5 1.0
CG2 D:VAL67 4.0 10.5 1.0
NE2 D:HIS63 4.1 14.0 1.0
ND1 D:HIS92 4.2 9.8 1.0
C2A D:HNI147 4.3 13.9 1.0
C3A D:HNI147 4.3 12.7 1.0
CG D:HIS92 4.3 9.0 1.0
C3D D:HNI147 4.3 14.0 1.0
C2D D:HNI147 4.3 12.8 1.0
C2C D:HNI147 4.3 13.1 1.0
C2B D:HNI147 4.3 10.8 1.0
C3C D:HNI147 4.3 11.0 1.0
C3B D:HNI147 4.3 12.1 1.0
CE1 D:HIS63 4.5 15.1 1.0

Nickel binding site 3 out of 4 in 1j3y

Go back to Nickel Binding Sites List in 1j3y
Nickel 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 Nickel with other atoms in the Ni 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
F:Ni147

b:7.7
occ:1.00
NI F:HNI147 0.0 7.7 1.0
ND F:HNI147 2.0 7.8 1.0
NB F:HNI147 2.0 6.6 1.0
NA F:HNI147 2.0 7.2 1.0
NC F:HNI147 2.0 4.8 1.0
NE2 F:HIS92 2.1 6.1 1.0
CE1 F:HIS92 3.0 8.5 1.0
C4D F:HNI147 3.0 7.4 1.0
C1D F:HNI147 3.0 7.6 1.0
C4B F:HNI147 3.1 5.9 1.0
C1C F:HNI147 3.1 5.6 1.0
C4A F:HNI147 3.1 8.1 1.0
C1A F:HNI147 3.1 8.4 1.0
C1B F:HNI147 3.1 7.3 1.0
C4C F:HNI147 3.1 4.8 1.0
CD2 F:HIS92 3.1 6.6 1.0
CHC F:HNI147 3.4 6.5 1.0
CHD F:HNI147 3.4 6.5 1.0
CHA F:HNI147 3.4 7.0 1.0
CHB F:HNI147 3.5 7.8 1.0
CG2 F:VAL67 3.9 8.9 1.0
NE2 F:HIS63 4.1 12.1 1.0
ND1 F:HIS92 4.2 7.9 1.0
CG F:HIS92 4.2 6.6 1.0
C2D F:HNI147 4.3 7.7 1.0
C3D F:HNI147 4.3 8.6 1.0
C3A F:HNI147 4.3 9.1 1.0
C2A F:HNI147 4.3 9.8 1.0
C2B F:HNI147 4.3 6.2 1.0
C2C F:HNI147 4.3 6.3 1.0
C3B F:HNI147 4.3 7.0 1.0
C3C F:HNI147 4.4 6.1 1.0
CE1 F:HIS63 4.6 11.7 1.0

Nickel binding site 4 out of 4 in 1j3y

Go back to Nickel Binding Sites List in 1j3y
Nickel 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 Nickel with other atoms in the Ni 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
H:Ni147

b:9.2
occ:1.00
NI H:HNI147 0.0 9.2 1.0
ND H:HNI147 2.0 10.6 1.0
NB H:HNI147 2.0 8.9 1.0
NA H:HNI147 2.0 10.1 1.0
NC H:HNI147 2.0 7.5 1.0
NE2 H:HIS92 2.1 8.1 1.0
CE1 H:HIS92 3.0 9.0 1.0
C1A H:HNI147 3.0 11.4 1.0
C4D H:HNI147 3.0 10.9 1.0
C1D H:HNI147 3.0 7.9 1.0
C1C H:HNI147 3.1 8.9 1.0
C4B H:HNI147 3.1 9.1 1.0
C4A H:HNI147 3.1 11.0 1.0
C1B H:HNI147 3.1 8.8 1.0
C4C H:HNI147 3.1 7.5 1.0
CD2 H:HIS92 3.2 9.1 1.0
CHA H:HNI147 3.4 11.7 1.0
CHC H:HNI147 3.4 9.9 1.0
CHD H:HNI147 3.4 7.7 1.0
CHB H:HNI147 3.5 9.6 1.0
CG2 H:VAL67 4.0 10.3 1.0
NE2 H:HIS63 4.0 12.2 1.0
ND1 H:HIS92 4.2 11.4 1.0
CG H:HIS92 4.3 9.2 1.0
C2A H:HNI147 4.3 13.1 1.0
C3D H:HNI147 4.3 12.8 1.0
C2D H:HNI147 4.3 10.4 1.0
C3A H:HNI147 4.3 12.2 1.0
C2B H:HNI147 4.3 8.5 1.0
C2C H:HNI147 4.3 8.3 1.0
C3B H:HNI147 4.3 8.5 1.0
C3C H:HNI147 4.3 7.8 1.0
CE1 H:HIS63 4.4 10.7 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 07:55:11 2020
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