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Iron in PDB 1cku: Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution

Protein crystallography data

The structure of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution, PDB code: 1cku was solved by E.Parisini, F.Capozzi, P.Lubini, V.Lamzin, C.Luchinat, G.M.Sheldrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.067, 51.389, 92.390, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 17.8

Iron Binding Sites:

The binding sites of Iron atom in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution (pdb code 1cku). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution, PDB code: 1cku:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1cku

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Iron binding site 1 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe87

b:5.0
occ:1.00
 FE1 A:SF487 0.0 5.0 1.0
S2 A:SF487 2.2 4.7 1.0
SG A:CYS43 2.3 5.4 1.0
S4 A:SF487 2.3 5.1 1.0
S3 A:SF487 2.3 4.8 1.0
FE3 A:SF487 2.7 4.8 1.0
FE4 A:SF487 2.7 4.9 1.0
FE2 A:SF487 2.7 5.0 1.0
CB A:CYS43 3.2 4.7 1.0
CA A:CYS43 3.6 4.3 1.0
S1 A:SF487 3.9 5.3 1.0
N A:CYS43 4.3 4.3 1.0
CG1 A:ILE71 4.5 6.0 1.0
N A:CYS77 4.6 4.9 1.0
CA A:TRP76 4.6 5.2 1.0
C A:TRP76 4.7 5.1 1.0
CD1 A:ILE71 4.7 6.9 1.0
CB A:CYS46 4.8 4.8 1.0
SG A:CYS46 4.8 5.0 1.0
N A:TRP76 4.8 5.2 1.0
CE1 A:TYR19 4.8 5.6 1.0
SG A:CYS63 4.8 5.4 1.0
SG A:CYS77 4.9 5.0 1.0
C A:CYS43 4.9 4.7 1.0
CB A:ILE71 4.9 5.3 1.0
C A:GLY75 4.9 4.6 1.0
CD1 A:TYR19 4.9 5.3 1.0
O A:GLY75 4.9 5.6 1.0

Iron binding site 2 out of 8 in 1cku

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Iron binding site 2 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe87

b:5.0
occ:1.00
 FE2 A:SF487 0.0 5.0 1.0
S1 A:SF487 2.2 5.3 1.0
S4 A:SF487 2.3 5.1 1.0
S3 A:SF487 2.3 4.8 1.0
SG A:CYS46 2.3 5.0 1.0
FE3 A:SF487 2.7 4.8 1.0
FE4 A:SF487 2.7 4.9 1.0
FE1 A:SF487 2.7 5.0 1.0
CB A:CYS46 3.1 4.8 1.0
S2 A:SF487 3.9 4.7 1.0
CB A:PHE48 4.1 4.8 1.0
CD2 A:PHE48 4.3 6.3 1.0
CA A:TRP80 4.4 4.3 1.0
CD1 A:TRP80 4.6 4.6 1.0
CA A:CYS46 4.6 4.8 1.0
SG A:CYS63 4.6 5.4 1.0
CA A:CYS43 4.7 4.3 1.0
CG A:PHE48 4.7 5.2 1.0
N A:PHE48 4.7 4.6 1.0
SG A:CYS77 4.7 5.0 1.0
SG A:CYS43 4.8 5.4 1.0
N A:TRP80 4.8 5.3 1.0
CA A:PHE48 4.9 4.3 1.0
N A:MET49 4.9 4.8 1.0
CB A:TRP80 4.9 5.3 1.0
CB A:CYS43 5.0 4.7 1.0

Iron binding site 3 out of 8 in 1cku

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Iron binding site 3 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe87

b:4.8
occ:1.00
 FE3 A:SF487 0.0 4.8 1.0
S4 A:SF487 2.2 5.1 1.0
SG A:CYS63 2.3 5.4 1.0
S1 A:SF487 2.3 5.3 1.0
S2 A:SF487 2.3 4.7 1.0
FE2 A:SF487 2.7 5.0 1.0
FE1 A:SF487 2.7 5.0 1.0
FE4 A:SF487 2.8 4.9 1.0
CB A:CYS63 3.3 5.4 1.0
S3 A:SF487 3.9 4.8 1.0
CB A:PHE48 4.2 4.8 1.0
CA A:CYS63 4.5 5.3 1.0
SG A:CYS77 4.6 5.0 1.0
CG1 A:ILE71 4.6 6.0 1.0
SG A:CYS43 4.7 5.4 1.0
CD1 A:PHE66 4.7 6.0 1.0
CE1 A:PHE66 4.7 7.0 1.0
SG A:CYS46 4.7 5.0 1.0
CG2 A:ILE71 4.9 7.9 1.0
C A:PHE48 5.0 4.8 1.0
CB A:LEU65 5.0 5.7 1.0

Iron binding site 4 out of 8 in 1cku

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Iron binding site 4 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe87

b:4.9
occ:1.00
 FE4 A:SF487 0.0 4.9 1.0
SG A:CYS77 2.3 5.0 1.0
S3 A:SF487 2.3 4.8 1.0
S1 A:SF487 2.3 5.3 1.0
S2 A:SF487 2.3 4.7 1.0
FE1 A:SF487 2.7 5.0 1.0
FE2 A:SF487 2.7 5.0 1.0
FE3 A:SF487 2.8 4.8 1.0
CB A:CYS77 3.2 5.2 1.0
N A:CYS77 3.6 4.9 1.0
CA A:CYS77 3.9 4.5 1.0
S4 A:SF487 3.9 5.1 1.0
O A:CYS77 4.3 4.5 1.0
C A:CYS77 4.3 4.3 1.0
C A:TRP76 4.4 5.1 1.0
N A:TRP80 4.6 5.3 1.0
SG A:CYS63 4.7 5.4 1.0
SG A:CYS43 4.8 5.4 1.0
CB A:SER79 4.8 6.5 1.0
SG A:CYS46 4.8 5.0 1.0
CA A:TRP80 4.9 4.3 1.0
C A:SER79 4.9 5.3 1.0
N A:SER79 4.9 5.1 1.0

Iron binding site 5 out of 8 in 1cku

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Iron binding site 5 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:4.6
occ:1.00
 FE1 B:SF487 0.0 4.6 1.0
S2 B:SF487 2.2 4.7 1.0
SG B:CYS43 2.3 5.0 1.0
S4 B:SF487 2.3 4.6 1.0
S3 B:SF487 2.3 5.1 1.0
FE4 B:SF487 2.7 4.9 1.0
FE3 B:SF487 2.7 4.7 1.0
FE2 B:SF487 2.7 4.8 1.0
CB B:CYS43 3.2 4.0 1.0
CA B:CYS43 3.6 4.7 1.0
S1 B:SF487 3.9 4.8 1.0
N B:CYS43 4.3 5.0 1.0
CG1 B:ILE71 4.4 4.7 1.0
N B:CYS77 4.5 4.5 1.0
CA B:TRP76 4.6 4.6 1.0
CD1 B:ILE71 4.7 5.5 1.0
C B:TRP76 4.7 4.7 1.0
N B:TRP76 4.7 4.6 1.0
SG B:CYS46 4.8 4.8 1.0
CB B:CYS46 4.8 5.3 1.0
SG B:CYS77 4.8 5.0 1.0
C B:CYS43 4.9 5.0 1.0
SG B:CYS63 4.9 5.7 1.0
CB B:ILE71 4.9 4.8 1.0
CE1 B:TYR19 4.9 5.6 1.0
C B:GLY75 4.9 4.8 1.0

Iron binding site 6 out of 8 in 1cku

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Iron binding site 6 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:4.8
occ:1.00
 FE2 B:SF487 0.0 4.8 1.0
S1 B:SF487 2.2 4.8 1.0
SG B:CYS46 2.3 4.8 1.0
S3 B:SF487 2.3 5.1 1.0
S4 B:SF487 2.3 4.6 1.0
FE4 B:SF487 2.7 4.9 1.0
FE3 B:SF487 2.7 4.7 1.0
FE1 B:SF487 2.7 4.6 1.0
CB B:CYS46 3.1 5.3 1.0
S2 B:SF487 3.9 4.7 1.0
CB B:PHE48 4.2 5.4 1.0
CA B:TRP80 4.3 4.9 1.0
CD2 B:PHE48 4.5 6.4 1.0
CA B:CYS46 4.6 5.1 1.0
CA B:CYS43 4.6 4.7 1.0
N B:TRP80 4.7 5.2 1.0
CD1 B:TRP80 4.7 4.7 1.0
N B:PHE48 4.7 4.8 1.0
SG B:CYS63 4.7 5.7 1.0
SG B:CYS77 4.7 5.0 1.0
SG B:CYS43 4.8 5.0 1.0
N B:MET49 4.8 5.0 1.0
CA B:PHE48 4.8 4.9 1.0
O B:SER79 4.9 6.5 1.0
CG B:PHE48 4.9 5.8 1.0
C B:SER79 4.9 5.0 1.0
CB B:CYS43 4.9 4.0 1.0
CB B:TRP80 5.0 5.5 1.0
C B:PHE48 5.0 4.5 1.0

Iron binding site 7 out of 8 in 1cku

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Iron binding site 7 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:4.7
occ:1.00
 FE3 B:SF487 0.0 4.7 1.0
S4 B:SF487 2.3 4.6 1.0
SG B:CYS63 2.3 5.7 1.0
S2 B:SF487 2.3 4.7 1.0
S1 B:SF487 2.3 4.8 1.0
FE1 B:SF487 2.7 4.6 1.0
FE2 B:SF487 2.7 4.8 1.0
FE4 B:SF487 2.7 4.9 1.0
CB B:CYS63 3.3 4.9 1.0
S3 B:SF487 3.9 5.1 1.0
CB B:PHE48 4.3 5.4 1.0
CA B:CYS63 4.5 4.7 1.0
SG B:CYS77 4.6 5.0 1.0
CG1 B:ILE71 4.6 4.7 1.0
CD2 B:PHE66 4.7 5.8 1.0
SG B:CYS43 4.7 5.0 1.0
SG B:CYS46 4.8 4.8 1.0
CE2 B:PHE66 4.8 7.9 1.0
C B:PHE48 4.8 4.5 1.0
O B:PHE48 4.9 5.5 1.0
CD1 B:LEU65 5.0 6.6 1.0
N B:MET49 5.0 5.0 1.0
CG2 B:ILE71 5.0 6.3 1.0
CG B:LEU65 5.0 6.8 1.0

Iron binding site 8 out of 8 in 1cku

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Iron binding site 8 out of 8 in the Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ab Initio Solution and Refinement of Two High Potential Iron Protein Structures at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:4.9
occ:1.00
 FE4 B:SF487 0.0 4.9 1.0
SG B:CYS77 2.3 5.0 1.0
S3 B:SF487 2.3 5.1 1.0
S1 B:SF487 2.3 4.8 1.0
S2 B:SF487 2.3 4.7 1.0
FE2 B:SF487 2.7 4.8 1.0
FE1 B:SF487 2.7 4.6 1.0
FE3 B:SF487 2.7 4.7 1.0
CB B:CYS77 3.3 4.3 1.0
N B:CYS77 3.6 4.5 1.0
CA B:CYS77 3.9 4.5 1.0
S4 B:SF487 3.9 4.6 1.0
C B:CYS77 4.3 4.2 1.0
O B:CYS77 4.3 4.7 1.0
N B:TRP80 4.4 5.2 1.0
C B:TRP76 4.4 4.7 1.0
C B:SER79 4.6 5.0 1.0
SG B:CYS63 4.7 5.7 1.0
CA B:TRP80 4.7 4.9 1.0
SG B:CYS43 4.8 5.0 1.0
N B:SER79 4.8 5.1 1.0
SG B:CYS46 4.8 4.8 1.0
CB B:SER79 4.8 5.8 1.0
CA B:SER79 5.0 5.2 1.0

Reference:

E.Parisini, F.Capozzi, P.Lubini, V.Lamzin, C.Luchinat, G.M.Sheldrick. Ab Initio Solution and Refinement of Two High-Potential Iron Protein Structures at Atomic Resolution. Acta Crystallogr.,Sect.D V. 55 1773 1999.
ISSN: ISSN 0907-4449
PubMed: 10531472
DOI: 10.1107/S0907444999009129
Page generated: Sat Aug 3 03:22:04 2024

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