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Iron in PDB 3o1y: Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface

Protein crystallography data

The structure of Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface, PDB code: 3o1y was solved by M.De March, R.De Zorzi, N.Demitri, C.Gabbiani, A.Guerri, A.Casini, L.Messori, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.01 / 1.75
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.695, 79.695, 89.247, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 24.8

Iron Binding Sites:

The binding sites of Iron atom in the Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface (pdb code 3o1y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface, PDB code: 3o1y:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3o1y

Go back to Iron Binding Sites List in 3o1y
Iron binding site 1 out of 3 in the Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe105

b:12.2
occ:1.00
FE A:HEC105 0.0 12.2 1.0
NE2 A:HIS18 2.0 10.3 1.0
ND A:HEC105 2.0 8.1 1.0
NA A:HEC105 2.0 9.2 1.0
NC A:HEC105 2.1 10.2 1.0
NB A:HEC105 2.1 7.3 1.0
SD A:MET80 2.3 11.9 1.0
CE1 A:HIS18 2.9 10.2 1.0
C1D A:HEC105 3.0 9.1 1.0
C4D A:HEC105 3.0 11.2 1.0
C1A A:HEC105 3.1 10.1 1.0
C4C A:HEC105 3.1 9.0 1.0
C4B A:HEC105 3.1 10.1 1.0
C1B A:HEC105 3.1 9.9 1.0
CD2 A:HIS18 3.1 10.5 1.0
C1C A:HEC105 3.1 9.8 1.0
C4A A:HEC105 3.1 11.7 1.0
CHA A:HEC105 3.4 9.5 1.0
CHD A:HEC105 3.4 8.6 1.0
CG A:MET80 3.4 8.5 1.0
CE A:MET80 3.4 10.0 1.0
CHC A:HEC105 3.5 10.0 1.0
CHB A:HEC105 3.5 8.6 1.0
ND1 A:HIS18 4.1 11.8 1.0
CG A:HIS18 4.2 9.2 1.0
C2D A:HEC105 4.2 10.3 1.0
C3B A:HEC105 4.3 8.6 1.0
C3D A:HEC105 4.3 9.5 1.0
C2B A:HEC105 4.3 9.0 1.0
C3C A:HEC105 4.3 9.3 1.0
CB A:MET80 4.3 10.1 1.0
C2C A:HEC105 4.3 8.4 1.0
C2A A:HEC105 4.3 11.1 1.0
C3A A:HEC105 4.3 11.2 1.0
OH A:TYR67 4.5 11.7 1.0

Iron binding site 2 out of 3 in 3o1y

Go back to Iron Binding Sites List in 3o1y
Iron binding site 2 out of 3 in the Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe105

b:12.3
occ:1.00
FE B:HEC105 0.0 12.3 1.0
NE2 B:HIS18 2.0 11.2 1.0
NB B:HEC105 2.0 9.7 1.0
NC B:HEC105 2.1 10.8 1.0
NA B:HEC105 2.1 8.6 1.0
ND B:HEC105 2.1 10.9 1.0
SD B:MET80 2.4 11.0 1.0
CE1 B:HIS18 2.9 9.2 1.0
C1B B:HEC105 3.0 12.0 1.0
CD2 B:HIS18 3.0 9.8 1.0
C4B B:HEC105 3.0 14.2 1.0
C4A B:HEC105 3.0 13.8 1.0
C4C B:HEC105 3.0 11.5 1.0
C1D B:HEC105 3.1 12.4 1.0
C1A B:HEC105 3.1 11.3 1.0
C4D B:HEC105 3.1 12.8 1.0
C1C B:HEC105 3.1 12.8 1.0
CHB B:HEC105 3.4 10.6 1.0
CHD B:HEC105 3.4 10.2 1.0
CE B:MET80 3.4 9.9 1.0
CHA B:HEC105 3.4 10.0 1.0
CHC B:HEC105 3.5 11.1 1.0
CG B:MET80 3.5 8.8 1.0
ND1 B:HIS18 4.0 11.6 1.0
CG B:HIS18 4.1 9.6 1.0
C2B B:HEC105 4.2 11.0 1.0
C3B B:HEC105 4.2 11.0 1.0
C3A B:HEC105 4.3 7.9 1.0
C3C B:HEC105 4.3 9.6 1.0
CB B:MET80 4.3 9.9 1.0
C2D B:HEC105 4.3 11.6 1.0
C2A B:HEC105 4.3 11.0 1.0
C3D B:HEC105 4.3 9.3 1.0
C2C B:HEC105 4.3 9.5 1.0
OH B:TYR67 4.5 13.1 1.0

Iron binding site 3 out of 3 in 3o1y

Go back to Iron Binding Sites List in 3o1y
Iron binding site 3 out of 3 in the Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Electron Transfer Complexes: Experimental Mapping of the Redox- Dependent Cytochrome C Electrostatic Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe105

b:11.1
occ:1.00
FE C:HEC105 0.0 11.1 1.0
NE2 C:HIS18 2.0 11.2 1.0
NB C:HEC105 2.0 8.9 1.0
NC C:HEC105 2.1 9.0 1.0
ND C:HEC105 2.1 10.1 1.0
NA C:HEC105 2.1 10.7 1.0
SD C:MET80 2.3 10.8 1.0
CE1 C:HIS18 2.9 8.5 1.0
C1B C:HEC105 3.0 7.8 1.0
C4B C:HEC105 3.0 8.4 1.0
CD2 C:HIS18 3.0 9.5 1.0
C4A C:HEC105 3.0 11.6 1.0
C1D C:HEC105 3.0 11.1 1.0
C1C C:HEC105 3.1 11.0 1.0
C4C C:HEC105 3.1 9.1 1.0
C1A C:HEC105 3.1 9.5 1.0
C4D C:HEC105 3.1 10.9 1.0
CHB C:HEC105 3.4 10.3 1.0
CE C:MET80 3.4 10.7 1.0
CHC C:HEC105 3.4 10.7 1.0
CHD C:HEC105 3.4 8.1 1.0
CG C:MET80 3.5 9.9 1.0
CHA C:HEC105 3.5 9.7 1.0
ND1 C:HIS18 4.0 11.4 1.0
CG C:HIS18 4.1 9.7 1.0
C3B C:HEC105 4.2 10.6 1.0
C2B C:HEC105 4.2 10.8 1.0
C3A C:HEC105 4.3 8.7 1.0
C2D C:HEC105 4.3 9.3 1.0
C3C C:HEC105 4.3 8.9 1.0
C2C C:HEC105 4.3 8.6 1.0
C2A C:HEC105 4.3 10.0 1.0
CB C:MET80 4.3 10.0 1.0
C3D C:HEC105 4.3 11.1 1.0
OH C:TYR67 4.5 11.5 1.0

Reference:

M.De March, N.Demitri, R.De Zorzi, A.Casini, C.Gabbiani, A.Guerri, L.Messori, S.Geremia. Nitrate As A Probe of Cytochrome C Surface: Crystallographic Identification of Crucial "Hot Spots" For Protein-Protein Recognition. J. Inorg. Biochem. V. 135 58 2014.
ISSN: ISSN 1873-3344
PubMed: 24662464
DOI: 10.1016/J.JINORGBIO.2014.02.015
Page generated: Sun Dec 13 15:15:27 2020

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