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Iron in PDB 3de8: Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination

Protein crystallography data

The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8 was solved by E.N.Salgado, R.A.Lewis, A.L.Rheingold, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.92 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.566, 89.504, 52.019, 90.00, 111.01, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 3de8:

The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination also contains other interesting chemical elements:

Copper (Cu) 4 atoms
Calcium (Ca) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination (pdb code 3de8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3de8

Go back to Iron Binding Sites List in 3de8
Iron binding site 1 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:12.7
occ:1.00
FE A:HEM150 0.0 12.7 1.0
NA A:HEM150 2.0 10.7 1.0
NB A:HEM150 2.0 11.1 1.0
NC A:HEM150 2.0 9.8 1.0
NE2 A:HIS102 2.1 22.8 1.0
ND A:HEM150 2.1 12.8 1.0
SD A:MET7 2.3 21.6 1.0
CE1 A:HIS102 3.0 19.8 1.0
C1A A:HEM150 3.0 15.8 1.0
C4A A:HEM150 3.0 13.3 1.0
C4B A:HEM150 3.1 12.7 1.0
C1C A:HEM150 3.1 12.0 1.0
C4D A:HEM150 3.1 13.2 1.0
CD2 A:HIS102 3.1 20.1 1.0
C1B A:HEM150 3.1 12.6 1.0
C1D A:HEM150 3.1 13.5 1.0
C4C A:HEM150 3.1 12.5 1.0
CE A:MET7 3.3 20.6 1.0
CG A:MET7 3.4 19.1 1.0
CHA A:HEM150 3.4 13.7 1.0
CHB A:HEM150 3.4 13.8 1.0
CHC A:HEM150 3.4 13.6 1.0
CHD A:HEM150 3.5 13.8 1.0
ND1 A:HIS102 4.2 24.1 1.0
CG A:HIS102 4.2 21.7 1.0
CB A:MET7 4.2 19.1 1.0
C3A A:HEM150 4.3 14.7 1.0
C2B A:HEM150 4.3 11.5 1.0
C3B A:HEM150 4.3 11.3 1.0
C2A A:HEM150 4.3 13.8 1.0
C2C A:HEM150 4.3 11.4 1.0
C3D A:HEM150 4.3 15.8 1.0
C3C A:HEM150 4.3 11.3 1.0
C2D A:HEM150 4.3 12.9 1.0
NH2 A:ARG106 4.9 29.0 1.0

Iron binding site 2 out of 4 in 3de8

Go back to Iron Binding Sites List in 3de8
Iron binding site 2 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:12.3
occ:1.00
FE B:HEM150 0.0 12.3 1.0
NB B:HEM150 2.0 11.4 1.0
NC B:HEM150 2.0 11.3 1.0
NE2 B:HIS102 2.0 18.0 1.0
NA B:HEM150 2.0 12.2 1.0
ND B:HEM150 2.1 11.2 1.0
SD B:MET7 2.3 21.4 1.0
CE1 B:HIS102 3.0 20.6 1.0
CD2 B:HIS102 3.0 19.7 1.0
C1C B:HEM150 3.0 10.4 1.0
C4B B:HEM150 3.0 11.2 1.0
C4A B:HEM150 3.0 13.1 1.0
C1B B:HEM150 3.1 11.3 1.0
C4C B:HEM150 3.1 11.3 1.0
C1A B:HEM150 3.1 14.6 1.0
C1D B:HEM150 3.1 11.7 1.0
C4D B:HEM150 3.1 11.4 1.0
CG B:MET7 3.3 20.6 1.0
CE B:MET7 3.4 20.4 1.0
CHC B:HEM150 3.4 10.6 1.0
CHB B:HEM150 3.4 13.2 1.0
CHA B:HEM150 3.4 13.1 1.0
CHD B:HEM150 3.4 12.1 1.0
ND1 B:HIS102 4.1 19.7 1.0
CB B:MET7 4.1 21.5 1.0
CG B:HIS102 4.2 20.4 1.0
C2B B:HEM150 4.3 8.7 1.0
C2C B:HEM150 4.3 11.1 1.0
C3B B:HEM150 4.3 10.1 1.0
C3A B:HEM150 4.3 15.8 1.0
C2A B:HEM150 4.3 16.2 1.0
C3C B:HEM150 4.3 10.5 1.0
C2D B:HEM150 4.3 11.4 1.0
C3D B:HEM150 4.3 11.3 1.0
CA B:MET7 4.9 20.9 1.0

Iron binding site 3 out of 4 in 3de8

Go back to Iron Binding Sites List in 3de8
Iron binding site 3 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:17.8
occ:1.00
FE C:HEM150 0.0 17.8 1.0
NE2 C:HIS102 2.0 18.6 1.0
NC C:HEM150 2.0 18.0 1.0
ND C:HEM150 2.1 17.7 1.0
NA C:HEM150 2.1 19.8 1.0
NB C:HEM150 2.1 17.4 1.0
SD C:MET7 2.3 20.7 1.0
CE1 C:HIS102 3.0 19.4 1.0
C4C C:HEM150 3.0 17.4 1.0
C1C C:HEM150 3.0 17.7 1.0
CD2 C:HIS102 3.0 21.6 1.0
C4B C:HEM150 3.1 17.8 1.0
C4A C:HEM150 3.1 19.2 1.0
C1A C:HEM150 3.1 21.4 1.0
C1D C:HEM150 3.1 17.0 1.0
C4D C:HEM150 3.1 18.7 1.0
C1B C:HEM150 3.1 17.7 1.0
CE C:MET7 3.3 23.0 1.0
CG C:MET7 3.4 21.5 1.0
CHC C:HEM150 3.4 16.3 1.0
CHD C:HEM150 3.4 18.3 1.0
CHA C:HEM150 3.5 19.7 1.0
CHB C:HEM150 3.5 18.4 1.0
ND1 C:HIS102 4.1 20.7 1.0
CG C:HIS102 4.2 20.3 1.0
CB C:MET7 4.2 22.9 1.0
C2C C:HEM150 4.3 18.1 1.0
C3C C:HEM150 4.3 18.3 1.0
C3A C:HEM150 4.3 20.7 1.0
C2A C:HEM150 4.3 20.1 1.0
C3B C:HEM150 4.3 15.8 1.0
C2B C:HEM150 4.3 17.7 1.0
C3D C:HEM150 4.3 18.5 1.0
C2D C:HEM150 4.3 18.2 1.0

Iron binding site 4 out of 4 in 3de8

Go back to Iron Binding Sites List in 3de8
Iron binding site 4 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:26.8
occ:1.00
FE D:HEM150 0.0 26.8 1.0
NE2 D:HIS102 2.0 21.5 1.0
ND D:HEM150 2.0 29.1 1.0
NC D:HEM150 2.1 28.3 1.0
NA D:HEM150 2.1 28.2 1.0
NB D:HEM150 2.1 26.0 1.0
SD D:MET7 2.5 24.1 1.0
CE1 D:HIS102 2.9 19.7 1.0
CD2 D:HIS102 3.0 21.1 1.0
C4D D:HEM150 3.1 29.9 1.0
C1D D:HEM150 3.1 30.1 1.0
C4C D:HEM150 3.1 28.9 1.0
C4A D:HEM150 3.1 27.9 1.0
C1B D:HEM150 3.1 26.0 1.0
C1A D:HEM150 3.1 29.6 1.0
C1C D:HEM150 3.1 27.9 1.0
C4B D:HEM150 3.1 26.3 1.0
CHA D:HEM150 3.4 30.6 1.0
CHD D:HEM150 3.4 29.1 1.0
CHB D:HEM150 3.4 27.2 1.0
CHC D:HEM150 3.5 26.7 1.0
CE D:MET7 3.5 22.6 1.0
CG D:MET7 3.7 23.6 1.0
ND1 D:HIS102 4.0 19.7 1.0
CG D:HIS102 4.1 20.5 1.0
C2D D:HEM150 4.3 29.4 1.0
C3D D:HEM150 4.3 30.2 1.0
C3C D:HEM150 4.3 28.1 1.0
C3A D:HEM150 4.3 28.7 1.0
C2C D:HEM150 4.3 27.6 1.0
C2B D:HEM150 4.3 24.4 1.0
C3B D:HEM150 4.3 24.3 1.0
C2A D:HEM150 4.3 29.9 1.0
CB D:MET7 4.5 23.3 1.0
NH2 D:ARG106 4.8 28.2 1.0
O D:CYS98 5.0 21.9 1.0

Reference:

E.N.Salgado, R.A.Lewis, S.Mossin, A.L.Rheingold, F.A.Tezcan. Control of Protein Oligomerization Symmetry By Metal Coordination: C2 and C3 Symmetrical Assemblies Through Cu(II) and Ni(II) Coordination. Inorg.Chem. V. 48 2726 2009.
ISSN: ISSN 0020-1669
PubMed: 19267481
DOI: 10.1021/IC9001237
Page generated: Tue Aug 5 00:36:05 2025

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