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Iron in PDB 1i8p: Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris

Protein crystallography data

The structure of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris, PDB code: 1i8p was solved by G.Garau, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.119, 71.706, 67.357, 90.00, 93.67, 90.00
R / Rfree (%) 16.1 / 23.7

Iron Binding Sites:

The binding sites of Iron atom in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris (pdb code 1i8p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris, PDB code: 1i8p:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1i8p

Go back to Iron Binding Sites List in 1i8p
Iron binding site 1 out of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe115

b:9.8
occ:1.00
FE A:HEC115 0.0 9.8 1.0
ND A:HEC115 1.9 13.4 1.0
NE2 A:HIS17 2.0 7.0 1.0
NC A:HEC115 2.0 8.8 1.0
NA A:HEC115 2.0 10.2 1.0
NB A:HEC115 2.1 9.9 1.0
SD A:MET93 2.4 10.8 1.0
CE1 A:HIS17 2.9 10.1 1.0
C1D A:HEC115 3.0 12.8 1.0
CD2 A:HIS17 3.0 3.8 1.0
C4D A:HEC115 3.0 12.6 1.0
C4C A:HEC115 3.0 6.3 1.0
C1A A:HEC115 3.1 10.8 1.0
C4B A:HEC115 3.1 6.1 1.0
C1B A:HEC115 3.1 9.3 1.0
C1C A:HEC115 3.1 11.8 1.0
C4A A:HEC115 3.1 8.0 1.0
CHD A:HEC115 3.4 9.9 1.0
CHA A:HEC115 3.4 11.6 1.0
CE A:MET93 3.4 2.7 1.0
CG A:MET93 3.5 13.7 1.0
CHC A:HEC115 3.5 3.7 1.0
CHB A:HEC115 3.5 5.6 1.0
ND1 A:HIS17 4.1 9.8 1.0
CG A:HIS17 4.1 12.2 1.0
C2D A:HEC115 4.2 11.7 1.0
C3D A:HEC115 4.2 12.6 1.0
CB A:MET93 4.3 12.6 1.0
C2B A:HEC115 4.3 7.4 1.0
C3C A:HEC115 4.3 9.1 1.0
C2A A:HEC115 4.3 7.8 1.0
C3B A:HEC115 4.3 6.3 1.0
C2C A:HEC115 4.3 13.9 1.0
C3A A:HEC115 4.3 6.4 1.0
OH A:TYR66 5.0 12.4 1.0

Iron binding site 2 out of 4 in 1i8p

Go back to Iron Binding Sites List in 1i8p
Iron binding site 2 out of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe115

b:9.2
occ:1.00
FE B:HEC115 0.0 9.2 1.0
ND B:HEC115 2.0 12.1 1.0
NE2 B:HIS17 2.0 8.5 1.0
NC B:HEC115 2.0 8.7 1.0
NA B:HEC115 2.0 9.2 1.0
NB B:HEC115 2.0 9.3 1.0
SD B:MET93 2.3 9.4 1.0
CE1 B:HIS17 3.0 11.0 1.0
C1D B:HEC115 3.0 12.3 1.0
C4A B:HEC115 3.0 5.8 1.0
C4D B:HEC115 3.0 11.2 1.0
C1A B:HEC115 3.0 10.4 1.0
C4B B:HEC115 3.0 6.3 1.0
C1C B:HEC115 3.0 12.9 1.0
C1B B:HEC115 3.1 9.2 1.0
C4C B:HEC115 3.1 6.0 1.0
CD2 B:HIS17 3.1 3.9 1.0
CE B:MET93 3.3 4.6 1.0
CHA B:HEC115 3.4 11.6 1.0
CHB B:HEC115 3.4 6.3 1.0
CHC B:HEC115 3.4 4.3 1.0
CHD B:HEC115 3.4 9.0 1.0
CG B:MET93 3.4 13.3 1.0
ND1 B:HIS17 4.1 9.0 1.0
CG B:HIS17 4.2 12.5 1.0
CB B:MET93 4.3 12.3 1.0
C3D B:HEC115 4.3 13.8 1.0
C2D B:HEC115 4.3 12.9 1.0
C3A B:HEC115 4.3 8.1 1.0
C2A B:HEC115 4.3 6.7 1.0
C2B B:HEC115 4.3 6.5 1.0
C2C B:HEC115 4.3 13.2 1.0
C3B B:HEC115 4.3 6.3 1.0
C3C B:HEC115 4.3 10.5 1.0
OH B:TYR66 5.0 11.4 1.0

Iron binding site 3 out of 4 in 1i8p

Go back to Iron Binding Sites List in 1i8p
Iron binding site 3 out of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe115

b:9.7
occ:1.00
FE C:HEC115 0.0 9.7 1.0
ND C:HEC115 2.0 11.4 1.0
NE2 C:HIS17 2.0 8.7 1.0
NC C:HEC115 2.0 8.9 1.0
NA C:HEC115 2.0 10.0 1.0
NB C:HEC115 2.1 9.5 1.0
SD C:MET93 2.4 9.4 1.0
CE1 C:HIS17 3.0 10.3 1.0
C1D C:HEC115 3.0 12.0 1.0
C4C C:HEC115 3.0 6.3 1.0
C4D C:HEC115 3.0 11.8 1.0
C1B C:HEC115 3.1 8.5 1.0
C1A C:HEC115 3.1 11.1 1.0
C1C C:HEC115 3.1 11.4 1.0
CD2 C:HIS17 3.1 4.6 1.0
C4B C:HEC115 3.1 5.9 1.0
C4A C:HEC115 3.1 6.8 1.0
CG C:MET93 3.3 13.1 1.0
CHD C:HEC115 3.4 9.6 1.0
CHB C:HEC115 3.4 5.6 1.0
CHC C:HEC115 3.5 2.5 1.0
CHA C:HEC115 3.5 12.1 1.0
CE C:MET93 3.5 3.8 1.0
ND1 C:HIS17 4.1 8.7 1.0
CG C:HIS17 4.2 12.8 1.0
C2D C:HEC115 4.2 12.5 1.0
C3D C:HEC115 4.2 13.1 1.0
CB C:MET93 4.2 12.5 1.0
C3C C:HEC115 4.3 8.9 1.0
C2B C:HEC115 4.3 7.4 1.0
C2C C:HEC115 4.3 13.2 1.0
C2A C:HEC115 4.3 6.4 1.0
C3B C:HEC115 4.3 6.6 1.0
C3A C:HEC115 4.3 7.2 1.0
OH C:TYR66 4.9 12.9 1.0

Iron binding site 4 out of 4 in 1i8p

Go back to Iron Binding Sites List in 1i8p
Iron binding site 4 out of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe115

b:9.1
occ:1.00
FE D:HEC115 0.0 9.1 1.0
ND D:HEC115 2.0 12.4 1.0
NE2 D:HIS17 2.0 8.6 1.0
NC D:HEC115 2.0 8.5 1.0
NB D:HEC115 2.0 9.7 1.0
NA D:HEC115 2.1 10.4 1.0
SD D:MET93 2.4 9.6 1.0
CE1 D:HIS17 2.9 9.2 1.0
C1D D:HEC115 3.0 13.3 1.0
CD2 D:HIS17 3.0 5.1 1.0
C4D D:HEC115 3.0 12.6 1.0
C4C D:HEC115 3.0 6.8 1.0
C1C D:HEC115 3.0 11.3 1.0
C1A D:HEC115 3.1 11.2 1.0
C4B D:HEC115 3.1 7.0 1.0
C4A D:HEC115 3.1 5.8 1.0
C1B D:HEC115 3.1 10.1 1.0
CHA D:HEC115 3.4 11.2 1.0
CHD D:HEC115 3.4 9.5 1.0
CHC D:HEC115 3.4 5.2 1.0
CE D:MET93 3.4 4.8 1.0
CG D:MET93 3.4 13.8 1.0
CHB D:HEC115 3.5 5.3 1.0
ND1 D:HIS17 4.1 9.8 1.0
CG D:HIS17 4.1 13.5 1.0
C2D D:HEC115 4.2 12.8 1.0
C3D D:HEC115 4.3 13.4 1.0
C3C D:HEC115 4.3 10.1 1.0
C2C D:HEC115 4.3 13.8 1.0
CB D:MET93 4.3 12.7 1.0
C2A D:HEC115 4.3 7.8 1.0
C3B D:HEC115 4.3 6.8 1.0
C3A D:HEC115 4.3 7.2 1.0
C2B D:HEC115 4.3 6.9 1.0
OH D:TYR66 5.0 12.1 1.0

Reference:

S.Geremia, G.Garau, L.Vaccari, R.Sgarra, M.S.Viezzoli, M.Calligaris, L.Randaccio. Cleavage of the Iron-Methionine Bond in C-Type Cytochromes: Crystal Structure of Oxidized and Reduced Cytochrome C(2) From Rhodopseudomonas Palustris and Its Ammonia Complex. Protein Sci. V. 11 6 2002.
ISSN: ISSN 0961-8368
PubMed: 11742117
DOI: 10.1110/PS.PS.13102
Page generated: Sat Aug 3 08:01:49 2024

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