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Iron in PDB 3vrd: Crystal Structure of Flavocytochrome C From Thermochromatium Tepidum

Protein crystallography data

The structure of Crystal Structure of Flavocytochrome C From Thermochromatium Tepidum, PDB code: 3vrd was solved by Y.Hirano, Y.Kimura, H.Suzuki, K.Miki, Z.-Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 140.617, 140.617, 57.720, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Flavocytochrome C From Thermochromatium Tepidum (pdb code 3vrd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Flavocytochrome C From Thermochromatium Tepidum, PDB code: 3vrd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3vrd

Go back to Iron Binding Sites List in 3vrd
Iron binding site 1 out of 2 in the Crystal Structure of Flavocytochrome C From Thermochromatium Tepidum


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 Flavocytochrome C From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:6.4
occ:1.00
FE A:HEC201 0.0 6.4 1.0
NE2 A:HIS15 2.0 6.5 1.0
NB A:HEC201 2.0 5.9 1.0
ND A:HEC201 2.0 5.3 1.0
NC A:HEC201 2.0 6.0 1.0
NA A:HEC201 2.0 6.0 1.0
SD A:MET54 2.3 6.5 1.0
CE1 A:HIS15 3.0 5.8 1.0
C4A A:HEC201 3.0 6.7 1.0
C1B A:HEC201 3.0 6.3 1.0
C4C A:HEC201 3.0 6.4 1.0
C1C A:HEC201 3.0 6.6 1.0
C1D A:HEC201 3.0 5.8 1.0
C4B A:HEC201 3.0 6.5 1.0
CD2 A:HIS15 3.1 6.5 1.0
C4D A:HEC201 3.1 5.7 1.0
C1A A:HEC201 3.1 6.5 1.0
CE A:MET54 3.3 7.7 1.0
CG A:MET54 3.3 7.2 1.0
CHB A:HEC201 3.4 6.8 1.0
CHC A:HEC201 3.5 6.7 1.0
CHD A:HEC201 3.5 5.7 1.0
CHA A:HEC201 3.5 5.5 1.0
ND1 A:HIS15 4.1 6.0 1.0
CG A:HIS15 4.2 7.0 1.0
C3B A:HEC201 4.2 6.6 1.0
C3A A:HEC201 4.3 6.0 1.0
C2D A:HEC201 4.3 5.8 1.0
C3C A:HEC201 4.3 7.7 1.0
C2B A:HEC201 4.3 6.7 1.0
C3D A:HEC201 4.3 5.8 1.0
C2C A:HEC201 4.3 6.9 1.0
C2A A:HEC201 4.3 6.4 1.0
CB A:MET54 4.7 8.0 1.0

Iron binding site 2 out of 2 in 3vrd

Go back to Iron Binding Sites List in 3vrd
Iron binding site 2 out of 2 in the Crystal Structure of Flavocytochrome C From Thermochromatium Tepidum


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 Flavocytochrome C From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:10.4
occ:1.00
FE A:HEC202 0.0 10.4 1.0
NB A:HEC202 2.0 10.0 1.0
ND A:HEC202 2.0 9.7 1.0
NE2 A:HIS105 2.0 8.6 1.0
NA A:HEC202 2.0 8.4 1.0
NC A:HEC202 2.0 9.7 1.0
SD A:MET147 2.4 11.1 1.0
C4C A:HEC202 2.9 10.0 1.0
C4A A:HEC202 2.9 8.7 1.0
C1B A:HEC202 3.0 10.3 1.0
CE1 A:HIS105 3.0 10.5 1.0
C1D A:HEC202 3.0 10.2 1.0
C4B A:HEC202 3.0 10.2 1.0
CD2 A:HIS105 3.0 9.4 1.0
C4D A:HEC202 3.1 9.7 1.0
C1A A:HEC202 3.1 9.6 1.0
C1C A:HEC202 3.1 10.7 1.0
CE A:MET147 3.3 10.7 1.0
CHD A:HEC202 3.3 11.3 1.0
CHB A:HEC202 3.4 9.6 1.0
CHC A:HEC202 3.4 11.6 1.0
CHA A:HEC202 3.4 9.3 1.0
CG A:MET147 3.5 10.9 1.0
ND1 A:HIS105 4.1 10.6 1.0
CG A:HIS105 4.2 10.2 1.0
C3C A:HEC202 4.2 12.4 1.0
CB A:MET147 4.2 11.1 1.0
C3B A:HEC202 4.2 9.6 1.0
C2C A:HEC202 4.3 12.5 1.0
C2A A:HEC202 4.3 8.8 1.0
C2B A:HEC202 4.3 10.5 1.0
C3A A:HEC202 4.3 9.2 1.0
C2D A:HEC202 4.3 11.6 1.0
C3D A:HEC202 4.3 11.0 1.0
O A:HOH375 4.8 18.8 1.0

Reference:

Y.Hirano, Y.Kimura, H.Suzuki, K.Miki, Z.-Y.Wang. Structure Analysis and Comparative Characterization of the Cytochrome C' and Flavocytochrome C From Thermophilic Purple Photosynthetic Bacterium Thermochromatium Tepidum Biochemistry V. 51 6556 2012.
ISSN: ISSN 0006-2960
PubMed: 22827326
DOI: 10.1021/BI3005522
Page generated: Sun Dec 13 15:25:07 2020

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