Atomistry » Iron » PDB 5az3-5c0z » 5b3i
Atomistry »
  Iron »
    PDB 5az3-5c0z »
      5b3i »

Iron in PDB 5b3i: Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus

Protein crystallography data

The structure of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus, PDB code: 5b3i was solved by S.Fujii, H.Oki, K.Kawahara, D.Yamane, M.Yamanaka, T.Maruno, Y.Kobayashi, M.Masanari, S.Wakai, H.Nishihara, T.Ohkubo, Y.Sambongi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.95 / 1.89
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 54.243, 72.923, 132.365, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.3

Iron Binding Sites:

The binding sites of Iron atom in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus (pdb code 5b3i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus, PDB code: 5b3i:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5b3i

Go back to Iron Binding Sites List in 5b3i
Iron binding site 1 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:15.0
occ:1.00
FE A:HEC201 0.0 15.0 1.0
ND A:HEC201 1.9 14.8 1.0
NA A:HEC201 2.0 15.1 1.0
NC A:HEC201 2.1 15.3 1.0
NB A:HEC201 2.1 14.9 1.0
NE2 A:HIS128 2.2 15.5 1.0
C1D A:HEC201 2.9 14.8 1.0
CD1 A:TYR16 2.9 15.3 1.0
C4D A:HEC201 3.0 15.2 1.0
C1A A:HEC201 3.0 14.9 1.0
C4C A:HEC201 3.0 15.2 1.0
C4B A:HEC201 3.1 15.5 1.0
C4A A:HEC201 3.1 14.8 1.0
C1C A:HEC201 3.1 14.9 1.0
CD2 A:HIS128 3.1 15.2 1.0
C1B A:HEC201 3.1 15.1 1.0
CE1 A:HIS128 3.2 15.5 1.0
CE1 A:TYR16 3.3 15.5 1.0
CHD A:HEC201 3.3 14.9 1.0
CG A:TYR16 3.4 14.6 1.0
CHA A:HEC201 3.4 15.1 1.0
CHC A:HEC201 3.5 14.9 1.0
CHB A:HEC201 3.6 14.8 1.0
CB A:TYR16 3.9 14.2 1.0
CZ A:TYR16 4.1 15.3 1.0
C2D A:HEC201 4.2 15.1 1.0
CD2 A:TYR16 4.2 14.7 1.0
C3D A:HEC201 4.2 15.2 1.0
C2A A:HEC201 4.2 14.8 1.0
C3A A:HEC201 4.2 14.8 1.0
C3C A:HEC201 4.3 15.2 1.0
C2C A:HEC201 4.3 15.7 1.0
CG A:HIS128 4.3 16.5 1.0
ND1 A:HIS128 4.3 16.7 1.0
C3B A:HEC201 4.3 15.2 1.0
C2B A:HEC201 4.4 14.8 1.0
CE2 A:TYR16 4.5 15.3 1.0
NH1 A:ARG132 4.6 17.2 1.0
CD A:ARG132 4.9 16.4 1.0

Iron binding site 2 out of 4 in 5b3i

Go back to Iron Binding Sites List in 5b3i
Iron binding site 2 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:16.1
occ:1.00
FE B:HEC201 0.0 16.1 1.0
ND B:HEC201 1.9 15.9 1.0
NA B:HEC201 2.0 16.0 1.0
NC B:HEC201 2.1 15.8 1.0
NB B:HEC201 2.1 15.8 1.0
NE2 B:HIS128 2.2 16.7 1.0
CD1 B:TYR16 2.8 16.3 1.0
C1D B:HEC201 2.9 15.9 1.0
C4D B:HEC201 3.0 16.3 1.0
C1A B:HEC201 3.0 16.1 1.0
C4B B:HEC201 3.0 15.6 1.0
C4C B:HEC201 3.0 15.6 1.0
C4A B:HEC201 3.1 15.7 1.0
CE1 B:HIS128 3.1 16.5 1.0
C1B B:HEC201 3.1 15.8 1.0
C1C B:HEC201 3.1 15.8 1.0
CE1 B:TYR16 3.2 16.0 1.0
CD2 B:HIS128 3.2 16.6 1.0
CHD B:HEC201 3.4 15.3 1.0
CHA B:HEC201 3.4 15.8 1.0
CHC B:HEC201 3.4 15.5 1.0
CG B:TYR16 3.5 15.9 1.0
CHB B:HEC201 3.5 15.9 1.0
CZ B:TYR16 4.0 15.4 1.0
CB B:TYR16 4.1 14.9 1.0
C2D B:HEC201 4.2 15.7 1.0
C3D B:HEC201 4.2 16.2 1.0
CD2 B:TYR16 4.2 15.5 1.0
ND1 B:HIS128 4.2 17.6 1.0
C2A B:HEC201 4.2 16.0 1.0
C3A B:HEC201 4.3 16.1 1.0
C3C B:HEC201 4.3 15.2 1.0
C2C B:HEC201 4.3 15.6 1.0
C2B B:HEC201 4.3 15.9 1.0
CG B:HIS128 4.3 17.7 1.0
C3B B:HEC201 4.3 15.7 1.0
CE2 B:TYR16 4.5 15.2 1.0
NH1 B:ARG132 4.5 16.6 1.0
OH B:TYR16 4.8 15.3 1.0

Iron binding site 3 out of 4 in 5b3i

Go back to Iron Binding Sites List in 5b3i
Iron binding site 3 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:16.2
occ:1.00
FE C:HEC201 0.0 16.2 1.0
ND C:HEC201 1.9 15.7 1.0
NA C:HEC201 2.0 16.5 1.0
NC C:HEC201 2.1 16.1 1.0
NB C:HEC201 2.1 16.0 1.0
NE2 C:HIS128 2.2 17.0 1.0
C1D C:HEC201 2.9 16.0 1.0
CD1 C:TYR16 3.0 16.0 1.0
C4D C:HEC201 3.0 16.2 1.0
C4B C:HEC201 3.0 15.8 1.0
C1A C:HEC201 3.0 16.0 1.0
C4C C:HEC201 3.0 16.7 1.0
C1C C:HEC201 3.1 15.9 1.0
C4A C:HEC201 3.1 16.3 1.0
C1B C:HEC201 3.1 15.7 1.0
CD2 C:HIS128 3.1 17.0 1.0
CE1 C:HIS128 3.2 17.7 1.0
CE1 C:TYR16 3.3 15.8 1.0
CG C:TYR16 3.3 15.3 1.0
CHD C:HEC201 3.4 16.0 1.0
CHC C:HEC201 3.4 15.2 1.0
CHA C:HEC201 3.5 15.9 1.0
CHB C:HEC201 3.5 15.7 1.0
CB C:TYR16 3.9 15.0 1.0
CD2 C:TYR16 4.0 15.0 1.0
CZ C:TYR16 4.0 15.7 1.0
C2D C:HEC201 4.2 15.9 1.0
C3D C:HEC201 4.2 15.8 1.0
C2A C:HEC201 4.3 16.0 1.0
C2C C:HEC201 4.3 16.1 1.0
C3C C:HEC201 4.3 16.6 1.0
ND1 C:HIS128 4.3 17.7 1.0
C3B C:HEC201 4.3 15.7 1.0
C3A C:HEC201 4.3 15.9 1.0
C2B C:HEC201 4.3 15.2 1.0
CG C:HIS128 4.3 18.4 1.0
CE2 C:TYR16 4.3 15.2 1.0
NH1 C:ARG132 4.5 18.3 1.0
OH C:TYR16 4.9 16.5 1.0

Iron binding site 4 out of 4 in 5b3i

Go back to Iron Binding Sites List in 5b3i
Iron binding site 4 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:15.4
occ:1.00
FE D:HEC201 0.0 15.4 1.0
ND D:HEC201 1.9 15.5 1.0
NA D:HEC201 2.0 15.3 1.0
NC D:HEC201 2.1 15.6 1.0
NB D:HEC201 2.1 15.2 1.0
NE2 D:HIS128 2.2 16.5 1.0
CD1 D:TYR16 2.8 15.5 1.0
C1D D:HEC201 2.9 14.9 1.0
C4D D:HEC201 3.0 15.1 1.0
C1A D:HEC201 3.0 15.4 1.0
C4B D:HEC201 3.0 15.4 1.0
C4C D:HEC201 3.0 16.2 1.0
C4A D:HEC201 3.1 15.6 1.0
C1C D:HEC201 3.1 15.7 1.0
C1B D:HEC201 3.1 15.1 1.0
CD2 D:HIS128 3.1 16.6 1.0
CE1 D:HIS128 3.2 16.9 1.0
CE1 D:TYR16 3.2 16.1 1.0
CG D:TYR16 3.3 14.9 1.0
CHD D:HEC201 3.3 15.4 1.0
CHA D:HEC201 3.4 15.8 1.0
CHC D:HEC201 3.4 15.6 1.0
CHB D:HEC201 3.5 15.2 1.0
CB D:TYR16 3.8 14.7 1.0
CZ D:TYR16 4.0 15.4 1.0
CD2 D:TYR16 4.0 15.4 1.0
C2D D:HEC201 4.2 15.8 1.0
C3D D:HEC201 4.2 15.7 1.0
C2A D:HEC201 4.2 15.9 1.0
C3A D:HEC201 4.3 15.5 1.0
ND1 D:HIS128 4.3 17.2 1.0
C2C D:HEC201 4.3 15.8 1.0
C3C D:HEC201 4.3 15.4 1.0
CG D:HIS128 4.3 17.5 1.0
C2B D:HEC201 4.3 15.2 1.0
C3B D:HEC201 4.3 15.6 1.0
CE2 D:TYR16 4.3 15.1 1.0
NH1 D:ARG132 4.5 18.7 1.0
OH D:TYR16 4.9 15.1 1.0

Reference:

S.Fujii, H.Oki, K.Kawahara, D.Yamane, M.Yamanaka, T.Maruno, Y.Kobayashi, M.Masanari, S.Wakai, H.Nishihara, T.Ohkubo, Y.Sambongi. Structural and Functional Insights Into Thermally Stable Cytochrome C' From A Thermophile Protein Sci. V. 26 737 2017.
ISSN: ESSN 1469-896X
PubMed: 28097774
DOI: 10.1002/PRO.3120
Page generated: Sun Dec 13 15:56:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy