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Iron in PDB 1ynr: Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution

Protein crystallography data

The structure of Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution, PDB code: 1ynr was solved by C.Travaglini-Allocatelli, S.Gianni, V.K.Dubey, A.Borgia, A.Di Matteo, D.Bonivento, F.Cutruzzola, K.L.Bren, M.Brunori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.712, 56.712, 220.179, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution (pdb code 1ynr). 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 the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution, PDB code: 1ynr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1ynr

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Iron binding site 1 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution


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 Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe81

b:2.0
occ:1.00
FE A:HEC81 0.0 2.0 1.0
NA A:HEC81 2.0 2.0 1.0
NB A:HEC81 2.0 2.0 1.0
ND A:HEC81 2.0 2.0 1.0
NC A:HEC81 2.0 2.0 1.0
NE2 A:HIS14 2.1 8.4 1.0
SD A:MET59 2.4 8.9 1.0
C4D A:HEC81 3.0 2.0 1.0
C1A A:HEC81 3.0 2.0 1.0
C4B A:HEC81 3.0 2.0 1.0
CE1 A:HIS14 3.0 7.6 1.0
C1C A:HEC81 3.1 2.0 1.0
C1B A:HEC81 3.1 2.0 1.0
C4A A:HEC81 3.1 2.0 1.0
C4C A:HEC81 3.1 2.0 1.0
C1D A:HEC81 3.1 2.0 1.0
CD2 A:HIS14 3.1 10.8 1.0
CE A:MET59 3.3 8.1 1.0
CHA A:HEC81 3.3 2.0 1.0
CG A:MET59 3.4 9.6 1.0
CHC A:HEC81 3.4 2.0 1.0
CHB A:HEC81 3.5 2.0 1.0
CHD A:HEC81 3.5 2.0 1.0
ND1 A:HIS14 4.2 7.3 1.0
CB A:MET59 4.2 8.8 1.0
C3B A:HEC81 4.2 2.0 1.0
CG A:HIS14 4.2 7.2 1.0
C2A A:HEC81 4.2 2.0 1.0
C2B A:HEC81 4.2 2.0 1.0
C3D A:HEC81 4.3 2.0 1.0
C3A A:HEC81 4.3 2.0 1.0
C2C A:HEC81 4.3 2.0 1.0
C3C A:HEC81 4.3 2.0 1.0
C2D A:HEC81 4.3 2.0 1.0

Iron binding site 2 out of 4 in 1ynr

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Iron binding site 2 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution


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 Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe81

b:2.0
occ:1.00
FE B:HEC81 0.0 2.0 1.0
NB B:HEC81 2.0 2.0 1.0
ND B:HEC81 2.0 2.0 1.0
NE2 B:HIS14 2.1 10.3 1.0
NA B:HEC81 2.1 2.0 1.0
NC B:HEC81 2.1 2.0 1.0
SD B:MET59 2.3 8.1 1.0
CE1 B:HIS14 3.0 6.2 1.0
C1B B:HEC81 3.0 2.0 1.0
C4D B:HEC81 3.0 2.0 1.0
C4B B:HEC81 3.1 2.0 1.0
C1D B:HEC81 3.1 2.0 1.0
C4A B:HEC81 3.1 2.0 1.0
C1A B:HEC81 3.1 2.0 1.0
C4C B:HEC81 3.1 2.0 1.0
CD2 B:HIS14 3.1 6.0 1.0
C1C B:HEC81 3.1 2.0 1.0
CE B:MET59 3.3 8.0 1.0
CG B:MET59 3.4 6.9 1.0
CHB B:HEC81 3.4 2.0 1.0
CHA B:HEC81 3.4 2.0 1.0
CHD B:HEC81 3.4 2.0 1.0
CHC B:HEC81 3.5 2.0 1.0
CB B:MET59 4.1 8.1 1.0
ND1 B:HIS14 4.1 5.9 1.0
CG B:HIS14 4.2 6.3 1.0
C2B B:HEC81 4.3 2.0 1.0
C3B B:HEC81 4.3 2.0 1.0
C3D B:HEC81 4.3 2.0 1.0
C2D B:HEC81 4.3 2.0 1.0
C3A B:HEC81 4.3 2.0 1.0
C2A B:HEC81 4.3 2.0 1.0
C3C B:HEC81 4.3 2.0 1.0
C2C B:HEC81 4.3 2.0 1.0

Iron binding site 3 out of 4 in 1ynr

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Iron binding site 3 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution


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 Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe81

b:2.2
occ:1.00
FE C:HEC81 0.0 2.2 1.0
NC C:HEC81 2.0 2.0 1.0
NA C:HEC81 2.0 2.3 1.0
NE2 C:HIS14 2.1 6.5 1.0
NB C:HEC81 2.1 2.0 1.0
ND C:HEC81 2.1 2.0 1.0
SD C:MET59 2.3 9.2 1.0
C1A C:HEC81 3.0 2.3 1.0
CD2 C:HIS14 3.0 6.6 1.0
C4C C:HEC81 3.0 2.0 1.0
C1C C:HEC81 3.0 2.0 1.0
CE1 C:HIS14 3.1 8.6 1.0
C4A C:HEC81 3.1 4.5 1.0
C4B C:HEC81 3.1 2.0 1.0
C4D C:HEC81 3.1 2.0 1.0
C1B C:HEC81 3.1 2.0 1.0
C1D C:HEC81 3.1 2.0 1.0
CG C:MET59 3.4 6.5 1.0
CHC C:HEC81 3.4 2.0 1.0
CHA C:HEC81 3.4 2.0 1.0
CE C:MET59 3.4 6.4 1.0
CHD C:HEC81 3.4 2.0 1.0
CHB C:HEC81 3.5 2.0 1.0
CB C:MET59 4.2 8.7 1.0
ND1 C:HIS14 4.2 5.1 1.0
CG C:HIS14 4.2 6.7 1.0
C2A C:HEC81 4.2 2.6 1.0
C3C C:HEC81 4.3 2.0 1.0
C2C C:HEC81 4.3 2.0 1.0
C3A C:HEC81 4.3 3.0 1.0
C2B C:HEC81 4.3 2.0 1.0
C3B C:HEC81 4.3 2.0 1.0
C3D C:HEC81 4.4 2.0 1.0
C2D C:HEC81 4.4 2.0 1.0

Iron binding site 4 out of 4 in 1ynr

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Iron binding site 4 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution


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 Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe81

b:2.0
occ:1.00
FE D:HEC81 0.0 2.0 1.0
NA D:HEC81 2.0 2.0 1.0
NE2 D:HIS14 2.0 5.3 1.0
NC D:HEC81 2.0 2.0 1.0
ND D:HEC81 2.1 2.0 1.0
NB D:HEC81 2.1 2.0 1.0
SD D:MET59 2.3 6.6 1.0
CE1 D:HIS14 3.0 5.7 1.0
C4A D:HEC81 3.0 2.0 1.0
C4C D:HEC81 3.1 2.0 1.0
C1D D:HEC81 3.1 2.0 1.0
C1A D:HEC81 3.1 2.0 1.0
C1C D:HEC81 3.1 2.0 1.0
C1B D:HEC81 3.1 2.0 1.0
CD2 D:HIS14 3.1 5.7 1.0
C4D D:HEC81 3.1 2.0 1.0
C4B D:HEC81 3.1 2.0 1.0
CG D:MET59 3.4 4.8 1.0
CHB D:HEC81 3.4 2.0 1.0
CHD D:HEC81 3.4 2.0 1.0
CE D:MET59 3.4 9.4 1.0
CHA D:HEC81 3.5 2.0 1.0
CHC D:HEC81 3.5 2.0 1.0
ND1 D:HIS14 4.1 5.2 1.0
CB D:MET59 4.1 7.1 1.0
CG D:HIS14 4.2 4.4 1.0
C3A D:HEC81 4.2 2.0 1.0
C2A D:HEC81 4.3 2.0 1.0
C3C D:HEC81 4.3 2.0 1.0
C2C D:HEC81 4.3 2.0 1.0
C2D D:HEC81 4.3 2.0 1.0
C3D D:HEC81 4.3 2.0 1.0
C2B D:HEC81 4.3 2.0 1.0
C3B D:HEC81 4.4 2.0 1.0

Reference:

C.Travaglini-Allocatelli, S.Gianni, V.K.Dubey, A.Borgia, A.Di Matteo, D.Bonivento, F.Cutruzzola, K.L.Bren, M.Brunori. An Obligatory Intermediate in the Folding Pathway of Cytochrome C552 From Hydrogenobacter Thermophilus J.Biol.Chem. V. 280 25729 2005.
ISSN: ISSN 0021-9258
PubMed: 15883159
DOI: 10.1074/JBC.M502628200
Page generated: Sun Dec 13 14:38:00 2020

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