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Iron in PDB 4j20: X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum

Protein crystallography data

The structure of X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum, PDB code: 4j20 was solved by M.Unno, L.J.Yu, Z.Y.Wang-Otomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.824, 33.826, 47.333, 90.00, 107.83, 90.00
R / Rfree (%) 15 / 17

Other elements in 4j20:

The structure of X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum (pdb code 4j20). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum, PDB code: 4j20:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4j20

Go back to Iron Binding Sites List in 4j20
Iron binding site 1 out of 2 in the X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:9.3
occ:1.00
FE A:HEB107 0.0 9.3 1.0
NC A:HEB107 2.0 9.7 1.0
NB A:HEB107 2.0 9.5 1.0
ND A:HEB107 2.0 9.7 1.0
NA A:HEB107 2.0 9.0 1.0
NE2 A:HIS20 2.0 8.7 1.0
SD A:MET62 2.3 10.0 1.0
CE1 A:HIS20 2.9 9.0 1.0
C1C A:HEB107 3.0 9.2 1.0
C4D A:HEB107 3.0 10.0 1.0
C1D A:HEB107 3.0 9.5 1.0
C4A A:HEB107 3.0 8.6 1.0
C1A A:HEB107 3.1 9.1 1.0
C4B A:HEB107 3.1 8.6 1.0
C1B A:HEB107 3.1 8.6 1.0
C4C A:HEB107 3.1 9.5 1.0
CD2 A:HIS20 3.1 9.0 1.0
CE A:MET62 3.3 10.6 1.0
CHC A:HEB107 3.4 10.1 1.0
CHA A:HEB107 3.4 9.4 1.0
CHD A:HEB107 3.4 10.5 1.0
CHB A:HEB107 3.4 8.3 1.0
CG A:MET62 3.5 10.2 1.0
ND1 A:HIS20 4.1 8.8 1.0
CG A:HIS20 4.2 8.7 1.0
CB A:MET62 4.2 10.3 1.0
C3C A:HEB107 4.3 10.1 1.0
C2C A:HEB107 4.3 9.9 1.0
C3A A:HEB107 4.3 8.5 1.0
C2A A:HEB107 4.3 9.2 1.0
C3D A:HEB107 4.3 10.9 1.0
C2D A:HEB107 4.3 9.6 1.0
C3B A:HEB107 4.3 9.5 1.0
C2B A:HEB107 4.3 8.9 1.0
CA A:MET62 4.6 10.5 1.0

Iron binding site 2 out of 2 in 4j20

Go back to Iron Binding Sites List in 4j20
Iron binding site 2 out of 2 in the X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Cytochrome C-554 From Chlorobaculum Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe104

b:13.1
occ:1.00
FE B:HEB104 0.0 13.1 1.0
NB B:HEB104 2.0 11.7 1.0
NC B:HEB104 2.0 13.8 1.0
NE2 B:HIS20 2.0 10.6 1.0
ND B:HEB104 2.0 13.2 1.0
NA B:HEB104 2.0 12.2 1.0
SD B:MET62 2.3 14.5 1.0
CE1 B:HIS20 3.0 11.4 1.0
C1D B:HEB104 3.0 14.6 1.0
C1B B:HEB104 3.0 10.9 1.0
C4C B:HEB104 3.0 13.8 1.0
C4B B:HEB104 3.0 12.1 1.0
C1C B:HEB104 3.0 13.3 1.0
C4A B:HEB104 3.0 11.8 1.0
CD2 B:HIS20 3.1 11.4 1.0
C4D B:HEB104 3.1 13.7 1.0
C1A B:HEB104 3.1 12.2 1.0
CE B:MET62 3.4 14.2 1.0
CHD B:HEB104 3.4 15.6 1.0
CHC B:HEB104 3.4 12.6 1.0
CHB B:HEB104 3.4 12.2 1.0
CHA B:HEB104 3.4 12.3 1.0
CG B:MET62 3.5 14.3 1.0
ND1 B:HIS20 4.1 12.9 1.0
CG B:HIS20 4.2 11.8 1.0
CB B:MET62 4.2 15.6 1.0
C2C B:HEB104 4.2 14.3 1.0
C3C B:HEB104 4.2 14.9 1.0
C2B B:HEB104 4.3 11.6 1.0
C3B B:HEB104 4.3 11.4 1.0
C2D B:HEB104 4.3 16.4 1.0
C3A B:HEB104 4.3 14.0 1.0
C2A B:HEB104 4.3 12.4 1.0
C3D B:HEB104 4.3 14.6 1.0
CA B:MET62 4.7 17.8 1.0

Reference:

L.J.Yu, M.Unno, Y.Kimura, K.Yanagimoto, H.Oh-Oka, Z.Y.Wang-Otomo. Structure Analysis and Characterization of the Cytochrome C-554 From Thermophilic Green Sulfur Photosynthetic Bacterium Chlorobaculum Tepidum Photosynth.Res. V. 118 249 2013.
ISSN: ISSN 0166-8595
PubMed: 24052268
DOI: 10.1007/S11120-013-9922-2
Page generated: Mon Aug 5 04:34:37 2024

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