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Iron in PDB 3c62: Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination

Protein crystallography data

The structure of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c62 was solved by F.A.Tezcan, E.N.Salgado, R.A.Lewis, J.Faraone-Mennella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.23 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.968, 90.133, 49.357, 90.00, 109.64, 90.00
R / Rfree (%) 23.1 / 27.3

Other elements in 3c62:

The structure of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination also contains other interesting chemical elements:

Calcium (Ca) 5 atoms
Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination (pdb code 3c62). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c62:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3c62

Go back to Iron Binding Sites List in 3c62
Iron binding site 1 out of 4 in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:4.9
occ:1.00
FE A:HEM150 0.0 4.9 1.0
NA A:HEM150 2.0 4.4 1.0
NB A:HEM150 2.0 2.5 1.0
NC A:HEM150 2.0 2.0 1.0
ND A:HEM150 2.0 2.0 1.0
NE2 A:HIS102 2.1 4.2 1.0
SD A:MET7 2.2 6.9 1.0
C4B A:HEM150 3.0 2.4 1.0
C1A A:HEM150 3.0 3.4 1.0
CD2 A:HIS102 3.0 2.9 1.0
C4A A:HEM150 3.0 3.6 1.0
C1B A:HEM150 3.0 2.5 1.0
C1C A:HEM150 3.0 2.6 1.0
C4D A:HEM150 3.1 3.1 1.0
CE1 A:HIS102 3.1 5.6 1.0
C1D A:HEM150 3.1 3.0 1.0
C4C A:HEM150 3.1 2.0 1.0
CG A:MET7 3.4 7.8 1.0
CHC A:HEM150 3.4 2.0 1.0
CHA A:HEM150 3.4 4.3 1.0
CHB A:HEM150 3.4 4.2 1.0
CE A:MET7 3.5 8.1 1.0
CHD A:HEM150 3.5 2.0 1.0
ND1 A:HIS102 4.2 4.8 1.0
CG A:HIS102 4.2 3.1 1.0
CB A:MET7 4.2 7.9 1.0
C2A A:HEM150 4.2 4.1 1.0
C3A A:HEM150 4.2 4.8 1.0
C2B A:HEM150 4.3 2.3 1.0
C3B A:HEM150 4.3 3.5 1.0
C3D A:HEM150 4.3 3.1 1.0
C2C A:HEM150 4.3 2.0 1.0
C2D A:HEM150 4.3 2.0 1.0
C3C A:HEM150 4.4 3.7 1.0

Iron binding site 2 out of 4 in 3c62

Go back to Iron Binding Sites List in 3c62
Iron binding site 2 out of 4 in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:6.5
occ:1.00
FE B:HEM150 0.0 6.5 1.0
NE2 B:HIS102 2.0 7.9 1.0
NC B:HEM150 2.0 3.6 1.0
ND B:HEM150 2.0 4.1 1.0
NA B:HEM150 2.0 4.0 1.0
NB B:HEM150 2.0 2.6 1.0
SD B:MET7 2.3 5.9 1.0
CE1 B:HIS102 2.9 7.8 1.0
CD2 B:HIS102 3.0 8.2 1.0
C1C B:HEM150 3.0 2.3 1.0
C4C B:HEM150 3.0 3.6 1.0
C1A B:HEM150 3.1 4.7 1.0
C1D B:HEM150 3.1 3.3 1.0
C4D B:HEM150 3.1 3.9 1.0
C4B B:HEM150 3.1 3.7 1.0
C4A B:HEM150 3.1 4.1 1.0
C1B B:HEM150 3.1 3.4 1.0
CHC B:HEM150 3.4 2.9 1.0
CG B:MET7 3.4 4.0 1.0
CHD B:HEM150 3.4 3.1 1.0
CHA B:HEM150 3.4 4.4 1.0
CE B:MET7 3.5 8.7 1.0
CHB B:HEM150 3.5 3.7 1.0
ND1 B:HIS102 4.1 7.9 1.0
CG B:HIS102 4.1 6.7 1.0
CB B:MET7 4.2 6.2 1.0
C2C B:HEM150 4.3 2.4 1.0
C2D B:HEM150 4.3 3.3 1.0
C3C B:HEM150 4.3 3.2 1.0
C3D B:HEM150 4.3 4.2 1.0
C2A B:HEM150 4.3 5.1 1.0
C3A B:HEM150 4.3 4.3 1.0
C3B B:HEM150 4.3 4.2 1.0
C2B B:HEM150 4.3 3.7 1.0
CA B:MET7 5.0 6.2 1.0

Iron binding site 3 out of 4 in 3c62

Go back to Iron Binding Sites List in 3c62
Iron binding site 3 out of 4 in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:15.9
occ:1.00
FE C:HEM150 0.0 15.9 1.0
NB C:HEM150 1.9 13.1 1.0
NA C:HEM150 2.0 13.8 1.0
NE2 C:HIS102 2.1 14.1 1.0
NC C:HEM150 2.1 14.0 1.0
ND C:HEM150 2.1 14.7 1.0
SD C:MET7 2.2 15.3 1.0
CE1 C:HIS102 2.9 15.6 1.0
C4B C:HEM150 3.0 12.8 1.0
C1B C:HEM150 3.0 13.4 1.0
C4A C:HEM150 3.0 14.8 1.0
C1C C:HEM150 3.0 13.0 1.0
C1A C:HEM150 3.1 15.9 1.0
CD2 C:HIS102 3.1 15.1 1.0
C4D C:HEM150 3.2 15.3 1.0
C4C C:HEM150 3.2 14.2 1.0
C1D C:HEM150 3.2 15.8 1.0
CG C:MET7 3.4 14.1 1.0
CHC C:HEM150 3.4 13.2 1.0
CHB C:HEM150 3.4 13.7 1.0
CE C:MET7 3.4 16.5 1.0
CHA C:HEM150 3.5 15.2 1.0
CHD C:HEM150 3.6 14.6 1.0
ND1 C:HIS102 4.1 15.3 1.0
CB C:MET7 4.1 15.7 1.0
C2B C:HEM150 4.2 12.4 1.0
C3B C:HEM150 4.2 12.8 1.0
CG C:HIS102 4.2 15.3 1.0
C3A C:HEM150 4.3 16.3 1.0
C2A C:HEM150 4.3 15.7 1.0
C2C C:HEM150 4.3 13.6 1.0
C3C C:HEM150 4.4 13.6 1.0
C3D C:HEM150 4.4 16.3 1.0
C2D C:HEM150 4.4 16.0 1.0
CA C:MET7 5.0 16.4 1.0

Iron binding site 4 out of 4 in 3c62

Go back to Iron Binding Sites List in 3c62
Iron binding site 4 out of 4 in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:8.9
occ:1.00
FE D:HEM150 0.0 8.9 1.0
ND D:HEM150 1.9 3.7 1.0
NA D:HEM150 2.0 6.6 1.0
NB D:HEM150 2.0 4.6 1.0
NC D:HEM150 2.0 4.9 1.0
NE2 D:HIS102 2.0 6.2 1.0
SD D:MET7 2.3 8.6 1.0
C4D D:HEM150 3.0 6.7 1.0
C1D D:HEM150 3.0 5.4 1.0
CD2 D:HIS102 3.0 6.0 1.0
C1A D:HEM150 3.0 7.8 1.0
C4A D:HEM150 3.0 6.8 1.0
CE1 D:HIS102 3.0 6.8 1.0
C1C D:HEM150 3.1 5.0 1.0
C1B D:HEM150 3.1 5.7 1.0
C4B D:HEM150 3.1 5.8 1.0
C4C D:HEM150 3.1 5.2 1.0
CG D:MET7 3.3 4.1 1.0
CHA D:HEM150 3.4 4.5 1.0
CHD D:HEM150 3.4 4.8 1.0
CHC D:HEM150 3.4 4.9 1.0
CHB D:HEM150 3.4 6.0 1.0
CE D:MET7 3.6 4.6 1.0
CB D:MET7 4.1 4.1 1.0
ND1 D:HIS102 4.1 5.5 1.0
CG D:HIS102 4.1 6.8 1.0
C2D D:HEM150 4.2 3.9 1.0
C3D D:HEM150 4.2 5.5 1.0
C2A D:HEM150 4.3 8.5 1.0
C3A D:HEM150 4.3 7.8 1.0
C2B D:HEM150 4.3 5.4 1.0
C2C D:HEM150 4.3 5.2 1.0
C3B D:HEM150 4.3 4.6 1.0
C3C D:HEM150 4.3 3.8 1.0
CA D:MET7 4.9 5.1 1.0

Reference:

E.N.Salgado, R.A.Lewis, J.Faraone-Mennella, F.A.Tezcan. Metal-Mediated Self-Assembly of Protein Superstructures: Influence of Secondary Interactions on Protein Oligomerization and Aggregation. J.Am.Chem.Soc. V. 130 6082 2008.
ISSN: ISSN 0002-7863
PubMed: 18422313
DOI: 10.1021/JA8012177
Page generated: Sun Dec 13 15:02:24 2020

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