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Iron in PDB 3nmi: Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2

Protein crystallography data

The structure of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmi was solved by R.J.Radford, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.05 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.290, 91.787, 130.637, 90.00, 107.99, 90.00
R / Rfree (%) 19.8 / 23.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 (pdb code 3nmi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3nmi

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Iron binding site 1 out of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:13.0
occ:1.00
FE A:HEM150 0.0 13.0 1.0
NE2 A:HIS102 1.9 12.8 1.0
NC A:HEM150 2.0 12.1 1.0
NB A:HEM150 2.0 8.5 1.0
NA A:HEM150 2.0 13.2 1.0
ND A:HEM150 2.0 12.0 1.0
SD A:MET7 2.3 13.2 1.0
CD2 A:HIS102 2.9 8.4 1.0
CE1 A:HIS102 2.9 14.0 1.0
C4B A:HEM150 3.0 6.8 1.0
C1A A:HEM150 3.0 12.4 1.0
C1B A:HEM150 3.0 9.1 1.0
C4D A:HEM150 3.0 10.4 1.0
C4C A:HEM150 3.0 15.1 1.0
C1C A:HEM150 3.1 11.6 1.0
C4A A:HEM150 3.1 14.6 1.0
C1D A:HEM150 3.1 8.4 1.0
CHA A:HEM150 3.4 11.9 1.0
CG A:MET7 3.4 9.9 1.0
CHB A:HEM150 3.4 13.6 1.0
CHC A:HEM150 3.4 7.9 1.0
CE A:MET7 3.4 7.0 1.0
CHD A:HEM150 3.4 7.6 1.0
ND1 A:HIS102 4.0 13.6 1.0
CG A:HIS102 4.0 12.1 1.0
CB A:MET7 4.2 9.8 1.0
C2A A:HEM150 4.2 16.0 1.0
C3B A:HEM150 4.2 12.8 1.0
C2B A:HEM150 4.3 10.7 1.0
C3C A:HEM150 4.3 8.0 1.0
C2C A:HEM150 4.3 13.9 1.0
C3A A:HEM150 4.3 16.3 1.0
C3D A:HEM150 4.3 10.7 1.0
C2D A:HEM150 4.3 12.1 1.0
CA A:MET7 5.0 14.3 1.0
NH2 A:ARG106 5.0 28.0 1.0

Iron binding site 2 out of 6 in 3nmi

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Iron binding site 2 out of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:13.9
occ:1.00
FE B:HEM150 0.0 13.9 1.0
NE2 B:HIS102 1.9 12.0 1.0
NC B:HEM150 2.0 12.4 1.0
ND B:HEM150 2.0 12.4 1.0
NA B:HEM150 2.1 13.5 1.0
NB B:HEM150 2.1 9.8 1.0
SD B:MET7 2.3 14.8 1.0
CE1 B:HIS102 2.9 11.5 1.0
CD2 B:HIS102 2.9 7.1 1.0
C4C B:HEM150 3.0 11.2 1.0
C1C B:HEM150 3.0 12.0 1.0
C1D B:HEM150 3.0 15.2 1.0
C4D B:HEM150 3.1 11.9 1.0
C4B B:HEM150 3.1 11.5 1.0
C1A B:HEM150 3.1 15.1 1.0
C1B B:HEM150 3.1 11.5 1.0
C4A B:HEM150 3.1 13.3 1.0
CE B:MET7 3.4 13.1 1.0
CHD B:HEM150 3.4 9.6 1.0
CHC B:HEM150 3.4 9.0 1.0
CHA B:HEM150 3.4 11.2 1.0
CG B:MET7 3.5 10.7 1.0
CHB B:HEM150 3.5 14.4 1.0
ND1 B:HIS102 4.0 12.2 1.0
CG B:HIS102 4.1 13.6 1.0
CB B:MET7 4.2 14.2 1.0
C3C B:HEM150 4.2 7.6 1.0
C2C B:HEM150 4.2 10.3 1.0
C3D B:HEM150 4.3 8.0 1.0
C2D B:HEM150 4.3 10.8 1.0
C2B B:HEM150 4.3 8.7 1.0
C2A B:HEM150 4.3 16.2 1.0
C3B B:HEM150 4.3 11.8 1.0
C3A B:HEM150 4.3 13.7 1.0
NH1 B:ARG106 5.0 31.7 0.5

Iron binding site 3 out of 6 in 3nmi

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Iron binding site 3 out of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:20.7
occ:1.00
FE C:HEM150 0.0 20.7 1.0
NE2 C:HIS102 1.9 18.1 1.0
NA C:HEM150 2.0 23.3 1.0
ND C:HEM150 2.0 16.4 1.0
NB C:HEM150 2.0 18.9 1.0
NC C:HEM150 2.1 20.2 1.0
SD C:MET7 2.3 24.2 1.0
CE1 C:HIS102 2.8 14.7 1.0
CD2 C:HIS102 3.0 15.9 1.0
C1A C:HEM150 3.0 25.2 1.0
C4D C:HEM150 3.0 25.4 1.0
C4A C:HEM150 3.1 29.7 1.0
C1C C:HEM150 3.1 20.1 1.0
C1B C:HEM150 3.1 23.9 1.0
C1D C:HEM150 3.1 23.0 1.0
C4B C:HEM150 3.1 20.9 1.0
C4C C:HEM150 3.1 18.3 1.0
CE C:MET7 3.4 23.2 1.0
CHA C:HEM150 3.4 21.4 1.0
CG C:MET7 3.4 25.0 1.0
CHB C:HEM150 3.4 23.8 1.0
CHC C:HEM150 3.5 19.4 1.0
CHD C:HEM150 3.5 17.0 1.0
ND1 C:HIS102 3.9 20.3 1.0
CG C:HIS102 4.1 19.8 1.0
CB C:MET7 4.2 23.3 1.0
NH2 C:ARG106 4.2 54.0 1.0
C2A C:HEM150 4.3 27.2 1.0
C3A C:HEM150 4.3 26.0 1.0
C3D C:HEM150 4.3 18.8 1.0
C2C C:HEM150 4.3 18.4 1.0
C2B C:HEM150 4.3 24.8 1.0
C2D C:HEM150 4.3 19.9 1.0
C3B C:HEM150 4.3 25.1 1.0
C3C C:HEM150 4.3 16.8 1.0

Iron binding site 4 out of 6 in 3nmi

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Iron binding site 4 out of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:22.0
occ:1.00
FE D:HEM150 0.0 22.0 1.0
NE2 D:HIS102 1.9 23.0 1.0
NB D:HEM150 2.0 17.2 1.0
NC D:HEM150 2.0 18.7 1.0
NA D:HEM150 2.0 20.8 1.0
ND D:HEM150 2.1 21.1 1.0
SD D:MET7 2.3 25.5 1.0
CE1 D:HIS102 2.8 23.6 1.0
CD2 D:HIS102 2.9 22.1 1.0
C4B D:HEM150 3.0 19.3 1.0
C1C D:HEM150 3.0 18.1 1.0
C1B D:HEM150 3.0 18.9 1.0
C4C D:HEM150 3.0 20.5 1.0
C4A D:HEM150 3.1 21.1 1.0
C1A D:HEM150 3.1 25.8 1.0
C1D D:HEM150 3.1 18.1 1.0
C4D D:HEM150 3.1 20.9 1.0
CE D:MET7 3.3 20.8 1.0
CG D:MET7 3.3 18.6 1.0
CHC D:HEM150 3.4 17.1 1.0
CHB D:HEM150 3.4 18.8 1.0
CHD D:HEM150 3.4 22.3 1.0
CHA D:HEM150 3.5 24.0 1.0
ND1 D:HIS102 4.0 23.6 1.0
CG D:HIS102 4.1 23.0 1.0
CB D:MET7 4.2 23.2 1.0
C3B D:HEM150 4.2 17.1 1.0
C2B D:HEM150 4.2 18.4 1.0
C2C D:HEM150 4.2 19.0 1.0
C3C D:HEM150 4.2 18.1 1.0
C3A D:HEM150 4.3 18.4 1.0
C2A D:HEM150 4.3 22.7 1.0
C2D D:HEM150 4.3 20.5 1.0
C3D D:HEM150 4.3 19.4 1.0
CA D:MET7 5.0 22.4 1.0

Iron binding site 5 out of 6 in 3nmi

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Iron binding site 5 out of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe150

b:23.0
occ:1.00
FE E:HEM150 0.0 23.0 1.0
NE2 E:HIS102 1.9 23.9 1.0
NB E:HEM150 2.0 16.9 1.0
NA E:HEM150 2.0 19.9 1.0
ND E:HEM150 2.0 19.0 1.0
NC E:HEM150 2.0 22.2 1.0
SD E:MET7 2.3 22.5 1.0
CE1 E:HIS102 2.8 18.3 1.0
CD2 E:HIS102 2.9 18.6 1.0
C1B E:HEM150 3.0 20.8 1.0
C1D E:HEM150 3.0 20.8 1.0
C4B E:HEM150 3.0 21.0 1.0
C4C E:HEM150 3.0 21.2 1.0
C4A E:HEM150 3.0 23.5 1.0
C1A E:HEM150 3.0 23.2 1.0
C4D E:HEM150 3.1 22.1 1.0
C1C E:HEM150 3.1 22.1 1.0
CE E:MET7 3.4 24.6 1.0
CHD E:HEM150 3.4 21.6 1.0
CG E:MET7 3.4 21.2 1.0
CHB E:HEM150 3.4 21.6 1.0
CHA E:HEM150 3.4 21.2 1.0
CHC E:HEM150 3.5 23.6 1.0
ND1 E:HIS102 4.0 21.4 1.0
CG E:HIS102 4.0 20.7 1.0
CB E:MET7 4.2 20.3 1.0
C2B E:HEM150 4.2 18.4 1.0
C3B E:HEM150 4.2 17.4 1.0
C2A E:HEM150 4.3 23.4 1.0
C3A E:HEM150 4.3 24.4 1.0
C3C E:HEM150 4.3 18.2 1.0
C2D E:HEM150 4.3 22.8 1.0
C3D E:HEM150 4.3 22.3 1.0
C2C E:HEM150 4.3 18.0 1.0

Iron binding site 6 out of 6 in 3nmi

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Iron binding site 6 out of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe150

b:21.8
occ:1.00
FE F:HEM150 0.0 21.8 1.0
NE2 F:HIS102 1.9 20.9 1.0
NB F:HEM150 2.0 21.3 1.0
ND F:HEM150 2.0 16.7 1.0
NA F:HEM150 2.0 23.2 1.0
NC F:HEM150 2.1 19.6 1.0
SD F:MET7 2.3 27.0 1.0
CE1 F:HIS102 2.7 27.0 1.0
CD2 F:HIS102 3.0 17.0 1.0
C1B F:HEM150 3.0 25.6 1.0
C4B F:HEM150 3.0 23.2 1.0
C4A F:HEM150 3.0 24.2 1.0
C1D F:HEM150 3.1 23.4 1.0
C1A F:HEM150 3.1 29.4 1.0
C4D F:HEM150 3.1 26.6 1.0
C1C F:HEM150 3.1 21.0 1.0
C4C F:HEM150 3.1 20.4 1.0
CG F:MET7 3.4 25.5 1.0
CE F:MET7 3.4 24.3 1.0
CHB F:HEM150 3.4 26.5 1.0
CHC F:HEM150 3.4 21.8 1.0
CHD F:HEM150 3.4 15.6 1.0
CHA F:HEM150 3.5 23.1 1.0
ND1 F:HIS102 3.9 23.6 1.0
CG F:HIS102 4.1 21.9 1.0
CB F:MET7 4.2 27.4 1.0
C2B F:HEM150 4.2 27.8 1.0
C3B F:HEM150 4.3 27.9 1.0
C3A F:HEM150 4.3 27.9 1.0
C2A F:HEM150 4.3 24.9 1.0
C2D F:HEM150 4.3 18.1 1.0
C3D F:HEM150 4.3 20.7 1.0
C2C F:HEM150 4.3 20.1 1.0
C3C F:HEM150 4.3 17.0 1.0
NH2 F:ARG106 4.8 52.2 1.0

Reference:

R.J.Radford, M.Lawrenz, P.C.Nguyen, J.A.Mccammon, F.A.Tezcan. Porous Protein Frameworks with Unsaturated Metal Centers in Sterically Encumbered Coordination Sites. Chem.Commun.(Camb.) V. 47 313 2011.
ISSN: ISSN 1359-7345
PubMed: 20740227
DOI: 10.1039/C0CC02168G
Page generated: Sun Aug 4 16:32:54 2024

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