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Iron in PDB 2bc5: Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages

Protein crystallography data

The structure of Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages, PDB code: 2bc5 was solved by J.Faraone-Mennella, F.A.Tezcan, H.B.Gray, J.R.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.40 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.861, 68.158, 90.440, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 27.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages (pdb code 2bc5). 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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages, PDB code: 2bc5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2bc5

Go back to Iron Binding Sites List in 2bc5
Iron binding site 1 out of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages


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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:23.6
occ:1.00
FE A:HEM150 0.0 23.6 1.0
ND A:HEM150 2.0 25.5 1.0
NC A:HEM150 2.0 23.9 1.0
NE2 A:HIS102 2.0 28.9 1.0
NB A:HEM150 2.0 17.5 1.0
NA A:HEM150 2.1 24.4 1.0
SD A:MET7 2.4 28.4 1.0
CD2 A:HIS102 2.9 27.5 1.0
C1C A:HEM150 3.0 22.3 1.0
C4B A:HEM150 3.0 20.3 1.0
C4D A:HEM150 3.0 28.2 1.0
C1D A:HEM150 3.0 26.5 1.0
C4C A:HEM150 3.0 25.4 1.0
C1A A:HEM150 3.1 25.9 1.0
CE1 A:HIS102 3.1 30.7 1.0
C1B A:HEM150 3.2 20.9 1.0
C4A A:HEM150 3.2 21.6 1.0
CHC A:HEM150 3.3 21.3 1.0
CHA A:HEM150 3.4 26.6 1.0
CHD A:HEM150 3.4 23.3 1.0
CE A:MET7 3.5 20.1 1.0
CHB A:HEM150 3.6 18.4 1.0
CG A:MET7 3.6 26.2 1.0
CG A:HIS102 4.1 26.2 1.0
ND1 A:HIS102 4.2 29.4 1.0
C2C A:HEM150 4.2 22.2 1.0
C3C A:HEM150 4.2 22.7 1.0
C3D A:HEM150 4.3 31.5 1.0
C2D A:HEM150 4.3 25.6 1.0
C3B A:HEM150 4.3 18.9 1.0
C2A A:HEM150 4.4 31.4 1.0
C2B A:HEM150 4.4 20.9 1.0
CB A:MET7 4.4 28.7 1.0
C3A A:HEM150 4.4 27.2 1.0
NH1 A:ARG106 5.0 40.1 1.0

Iron binding site 2 out of 4 in 2bc5

Go back to Iron Binding Sites List in 2bc5
Iron binding site 2 out of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages


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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:20.7
occ:1.00
FE B:HEM150 0.0 20.7 1.0
ND B:HEM150 2.0 18.0 1.0
NE2 B:HIS102 2.0 20.2 1.0
NB B:HEM150 2.0 16.2 1.0
NC B:HEM150 2.1 14.1 1.0
NA B:HEM150 2.1 19.5 1.0
SD B:MET7 2.4 31.6 1.0
CD2 B:HIS102 3.0 18.2 1.0
C4D B:HEM150 3.0 24.4 1.0
C1D B:HEM150 3.0 22.8 1.0
C1A B:HEM150 3.0 25.1 1.0
C4B B:HEM150 3.0 18.1 1.0
CE1 B:HIS102 3.0 19.2 1.0
C1C B:HEM150 3.0 12.8 1.0
C4C B:HEM150 3.1 17.4 1.0
C1B B:HEM150 3.1 22.8 1.0
C4A B:HEM150 3.1 21.8 1.0
CHA B:HEM150 3.3 17.4 1.0
CHC B:HEM150 3.4 16.3 1.0
CHD B:HEM150 3.4 19.2 1.0
CHB B:HEM150 3.5 20.3 1.0
CG B:MET7 3.5 31.6 1.0
CE B:MET7 3.6 35.6 1.0
CG B:HIS102 4.1 19.1 1.0
ND1 B:HIS102 4.1 17.6 1.0
C3D B:HEM150 4.2 23.1 1.0
C2D B:HEM150 4.2 22.1 1.0
C3B B:HEM150 4.3 13.7 1.0
C2C B:HEM150 4.3 16.1 1.0
C2A B:HEM150 4.3 27.9 1.0
C3C B:HEM150 4.3 13.7 1.0
CB B:MET7 4.3 26.4 1.0
C2B B:HEM150 4.3 18.5 1.0
C3A B:HEM150 4.4 26.2 1.0
NH1 B:ARG106 4.8 39.3 1.0

Iron binding site 3 out of 4 in 2bc5

Go back to Iron Binding Sites List in 2bc5
Iron binding site 3 out of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages


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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:18.6
occ:1.00
FE C:HEM150 0.0 18.6 1.0
ND C:HEM150 2.0 16.7 1.0
NE2 C:HIS102 2.0 22.5 1.0
NB C:HEM150 2.0 17.1 1.0
NC C:HEM150 2.1 15.0 1.0
NA C:HEM150 2.1 23.4 1.0
SD C:MET7 2.4 16.8 1.0
CD2 C:HIS102 2.9 16.3 1.0
C4D C:HEM150 3.0 22.9 1.0
CE1 C:HIS102 3.0 17.8 1.0
C4B C:HEM150 3.0 18.2 1.0
C1D C:HEM150 3.0 18.6 1.0
C1C C:HEM150 3.0 16.3 1.0
C1B C:HEM150 3.1 18.3 1.0
C1A C:HEM150 3.1 25.6 1.0
C4C C:HEM150 3.1 17.3 1.0
C4A C:HEM150 3.1 22.7 1.0
CHC C:HEM150 3.3 17.1 1.0
CHA C:HEM150 3.4 19.9 1.0
CHD C:HEM150 3.4 14.7 1.0
CHB C:HEM150 3.4 21.1 1.0
CE C:MET7 3.5 23.5 1.0
CG C:MET7 3.6 24.3 1.0
ND1 C:HIS102 4.1 20.5 1.0
CG C:HIS102 4.1 16.0 1.0
C3D C:HEM150 4.2 23.1 1.0
C2D C:HEM150 4.3 18.1 1.0
C3B C:HEM150 4.3 16.4 1.0
C2B C:HEM150 4.3 18.1 1.0
C2C C:HEM150 4.3 17.3 1.0
C3C C:HEM150 4.3 11.6 1.0
C2A C:HEM150 4.4 28.9 1.0
C3A C:HEM150 4.4 25.5 1.0
CB C:MET7 4.4 22.0 1.0

Iron binding site 4 out of 4 in 2bc5

Go back to Iron Binding Sites List in 2bc5
Iron binding site 4 out of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages


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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:29.4
occ:1.00
FE D:HEM150 0.0 29.4 1.0
NA D:HEM150 2.0 30.6 1.0
NE2 D:HIS102 2.0 33.6 1.0
ND D:HEM150 2.0 31.2 1.0
NB D:HEM150 2.0 25.9 1.0
NC D:HEM150 2.1 24.3 1.0
SD D:MET7 2.2 29.6 1.0
C1A D:HEM150 3.0 32.8 1.0
CE1 D:HIS102 3.0 33.5 1.0
C4D D:HEM150 3.0 33.3 1.0
CD2 D:HIS102 3.0 34.4 1.0
C4B D:HEM150 3.0 26.5 1.0
C1C D:HEM150 3.0 21.5 1.0
C4A D:HEM150 3.1 30.5 1.0
C1D D:HEM150 3.1 32.6 1.0
C1B D:HEM150 3.1 28.6 1.0
C4C D:HEM150 3.1 27.7 1.0
CHA D:HEM150 3.3 32.1 1.0
CHC D:HEM150 3.3 23.6 1.0
CG D:MET7 3.5 25.6 1.0
CHB D:HEM150 3.5 28.1 1.0
CHD D:HEM150 3.5 28.6 1.0
CE D:MET7 3.5 25.5 1.0
ND1 D:HIS102 4.1 35.0 1.0
CG D:HIS102 4.1 33.6 1.0
C2A D:HEM150 4.2 37.3 1.0
C3D D:HEM150 4.2 36.2 1.0
CB D:MET7 4.3 26.8 1.0
C3A D:HEM150 4.3 36.5 1.0
C2D D:HEM150 4.3 32.2 1.0
C3B D:HEM150 4.3 25.8 1.0
C2C D:HEM150 4.3 23.8 1.0
C2B D:HEM150 4.3 26.8 1.0
C3C D:HEM150 4.4 25.1 1.0
NH1 D:ARG106 5.0 46.1 1.0

Reference:

J.Faraone-Mennella, F.A.Tezcan, H.B.Gray, J.R.Winkler. Stability and Folding Kinetics of Structurally Characterized Cytochrome C-B(562). Biochemistry V. 45 10504 2006.
ISSN: ISSN 0006-2960
PubMed: 16939202
DOI: 10.1021/BI060242X
Page generated: Sat Aug 3 19:32:57 2024

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