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Iron in PDB 3nbt: Crystal Structure of Trimeric Cytochrome C From Horse Heart

Protein crystallography data

The structure of Crystal Structure of Trimeric Cytochrome C From Horse Heart, PDB code: 3nbt was solved by M.Taketa, H.Komori, S.Hirota, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.54 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.204, 95.661, 130.935, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Trimeric Cytochrome C From Horse Heart (pdb code 3nbt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Trimeric Cytochrome C From Horse Heart, PDB code: 3nbt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3nbt

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Iron binding site 1 out of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart


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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe105

b:24.1
occ:1.00
FE A:HEC105 0.0 24.1 1.0
NE2 A:HIS18 2.0 25.7 1.0
NB A:HEC105 2.0 24.9 1.0
NC A:HEC105 2.0 25.1 1.0
NA A:HEC105 2.0 24.7 1.0
ND A:HEC105 2.0 23.7 1.0
O A:HOH201 2.1 22.2 1.0
CD2 A:HIS18 2.9 24.1 1.0
C1B A:HEC105 3.0 23.7 1.0
C1C A:HEC105 3.0 22.3 1.0
C4A A:HEC105 3.0 24.4 1.0
C4B A:HEC105 3.0 24.8 1.0
C4C A:HEC105 3.0 23.2 1.0
CE1 A:HIS18 3.0 26.9 1.0
C1D A:HEC105 3.0 24.0 1.0
C1A A:HEC105 3.0 24.2 1.0
C4D A:HEC105 3.0 21.1 1.0
CHB A:HEC105 3.3 22.5 1.0
CHC A:HEC105 3.4 23.6 1.0
CHD A:HEC105 3.4 21.9 1.0
CHA A:HEC105 3.4 25.0 1.0
CG A:HIS18 4.0 27.6 1.0
ND1 A:HIS18 4.1 28.6 1.0
C2B A:HEC105 4.2 24.1 1.0
C3B A:HEC105 4.2 23.7 1.0
C2C A:HEC105 4.2 22.8 1.0
C3C A:HEC105 4.2 21.6 1.0
C3A A:HEC105 4.2 23.4 1.0
C2D A:HEC105 4.2 24.5 1.0
C2A A:HEC105 4.2 22.9 1.0
C3D A:HEC105 4.2 23.8 1.0
OH A:TYR67 4.4 22.8 1.0

Iron binding site 2 out of 6 in 3nbt

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Iron binding site 2 out of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart


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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe105

b:23.1
occ:1.00
FE B:HEC105 0.0 23.1 1.0
NA B:HEC105 2.0 23.1 1.0
NB B:HEC105 2.0 24.0 1.0
NC B:HEC105 2.0 23.6 1.0
ND B:HEC105 2.0 22.1 1.0
NE2 B:HIS18 2.0 24.4 1.0
O B:HOH202 2.1 23.2 1.0
CE1 B:HIS18 2.9 24.1 1.0
C4A B:HEC105 3.0 24.6 1.0
C1B B:HEC105 3.0 22.2 1.0
C4B B:HEC105 3.0 23.6 1.0
C1A B:HEC105 3.0 23.5 1.0
C1C B:HEC105 3.0 23.2 1.0
C4D B:HEC105 3.0 22.5 1.0
CD2 B:HIS18 3.0 25.3 1.0
C1D B:HEC105 3.0 23.0 1.0
C4C B:HEC105 3.0 22.6 1.0
CHB B:HEC105 3.3 22.3 1.0
CHC B:HEC105 3.4 23.8 1.0
CHA B:HEC105 3.4 21.0 1.0
CHD B:HEC105 3.4 20.1 1.0
ND1 B:HIS18 4.1 26.1 1.0
CG B:HIS18 4.1 27.3 1.0
C2B B:HEC105 4.2 23.8 1.0
C3A B:HEC105 4.2 22.9 1.0
C3B B:HEC105 4.2 22.7 1.0
C2A B:HEC105 4.2 23.8 1.0
C2C B:HEC105 4.2 24.1 1.0
C2D B:HEC105 4.2 21.7 1.0
C3D B:HEC105 4.2 22.8 1.0
C3C B:HEC105 4.2 22.7 1.0
OH B:TYR67 4.5 21.6 1.0
SD B:MET80 4.8 30.4 1.0

Iron binding site 3 out of 6 in 3nbt

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Iron binding site 3 out of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart


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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe105

b:24.2
occ:1.00
FE C:HEC105 0.0 24.2 1.0
ND C:HEC105 1.9 20.0 1.0
NB C:HEC105 1.9 22.6 1.0
NC C:HEC105 2.0 22.3 1.0
NE2 C:HIS18 2.0 23.1 1.0
NA C:HEC105 2.0 21.5 1.0
O C:HOH203 2.1 27.6 1.0
C1D C:HEC105 2.9 19.2 1.0
CE1 C:HIS18 3.0 26.4 1.0
C1B C:HEC105 3.0 23.6 1.0
CD2 C:HIS18 3.0 23.7 1.0
C4C C:HEC105 3.0 21.1 1.0
C4B C:HEC105 3.0 24.2 1.0
C4D C:HEC105 3.0 19.4 1.0
C4A C:HEC105 3.0 19.9 1.0
C1C C:HEC105 3.0 21.1 1.0
C1A C:HEC105 3.0 20.6 1.0
CHD C:HEC105 3.3 20.4 1.0
CHB C:HEC105 3.3 22.7 1.0
CHC C:HEC105 3.4 24.1 1.0
CHA C:HEC105 3.4 19.0 1.0
ND1 C:HIS18 4.1 24.9 1.0
CG C:HIS18 4.1 26.4 1.0
C2D C:HEC105 4.2 19.1 1.0
C2B C:HEC105 4.2 24.5 1.0
C3D C:HEC105 4.2 17.7 1.0
C3B C:HEC105 4.2 23.7 1.0
C3C C:HEC105 4.2 23.1 1.0
C3A C:HEC105 4.2 17.5 1.0
C2C C:HEC105 4.2 23.4 1.0
C2A C:HEC105 4.3 19.6 1.0
OH C:TYR67 4.4 25.0 1.0
CE C:MET80 4.7 31.4 1.0

Iron binding site 4 out of 6 in 3nbt

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Iron binding site 4 out of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart


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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe105

b:22.9
occ:1.00
FE D:HEC105 0.0 22.9 1.0
NC D:HEC105 2.0 23.2 1.0
ND D:HEC105 2.0 22.2 1.0
NA D:HEC105 2.0 23.2 1.0
NB D:HEC105 2.0 22.2 1.0
NE2 D:HIS18 2.0 23.2 1.0
O D:HOH204 2.1 26.4 1.0
C4C D:HEC105 3.0 23.1 1.0
CE1 D:HIS18 3.0 25.2 1.0
C1D D:HEC105 3.0 23.2 1.0
C1C D:HEC105 3.0 23.9 1.0
C4A D:HEC105 3.0 22.3 1.0
C1B D:HEC105 3.0 23.3 1.0
C4D D:HEC105 3.0 22.5 1.0
CD2 D:HIS18 3.0 20.6 1.0
C1A D:HEC105 3.0 22.9 1.0
C4B D:HEC105 3.0 23.1 1.0
CHD D:HEC105 3.3 21.8 1.0
CHB D:HEC105 3.4 21.2 1.0
CHC D:HEC105 3.4 23.6 1.0
CHA D:HEC105 3.4 21.3 1.0
ND1 D:HIS18 4.1 23.7 1.0
CG D:HIS18 4.1 23.5 1.0
C3C D:HEC105 4.2 23.6 1.0
C2C D:HEC105 4.2 23.4 1.0
C2D D:HEC105 4.2 23.4 1.0
C3D D:HEC105 4.2 23.1 1.0
C3A D:HEC105 4.2 22.3 1.0
C2B D:HEC105 4.2 25.2 1.0
C2A D:HEC105 4.2 23.0 1.0
C3B D:HEC105 4.2 25.1 1.0
OH D:TYR67 4.4 22.1 1.0
SD D:MET80 4.8 40.3 1.0

Iron binding site 5 out of 6 in 3nbt

Go back to Iron Binding Sites List in 3nbt
Iron binding site 5 out of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe105

b:24.1
occ:1.00
FE E:HEC105 0.0 24.1 1.0
NE2 E:HIS18 2.0 26.0 1.0
NB E:HEC105 2.0 23.9 1.0
ND E:HEC105 2.0 23.7 1.0
NA E:HEC105 2.0 23.8 1.0
NC E:HEC105 2.0 24.0 1.0
O E:HOH205 2.1 22.6 1.0
CD2 E:HIS18 2.9 24.2 1.0
CE1 E:HIS18 3.0 28.8 1.0
C1B E:HEC105 3.0 24.6 1.0
C4A E:HEC105 3.0 23.6 1.0
C4D E:HEC105 3.0 20.8 1.0
C1D E:HEC105 3.0 24.1 1.0
C1C E:HEC105 3.0 24.7 1.0
C4B E:HEC105 3.0 25.5 1.0
C1A E:HEC105 3.0 22.5 1.0
C4C E:HEC105 3.0 24.9 1.0
CHB E:HEC105 3.3 23.6 1.0
CHC E:HEC105 3.4 23.4 1.0
CHD E:HEC105 3.4 24.2 1.0
CHA E:HEC105 3.4 22.7 1.0
ND1 E:HIS18 4.0 26.9 1.0
CG E:HIS18 4.0 27.7 1.0
C3D E:HEC105 4.2 23.4 1.0
C3A E:HEC105 4.2 25.9 1.0
C2D E:HEC105 4.2 23.8 1.0
C2B E:HEC105 4.2 22.6 1.0
C2A E:HEC105 4.2 26.9 1.0
C3B E:HEC105 4.2 22.8 1.0
C2C E:HEC105 4.2 25.2 1.0
C3C E:HEC105 4.2 25.0 1.0
OH E:TYR67 4.3 22.7 1.0
CE E:MET80 4.8 36.2 1.0

Iron binding site 6 out of 6 in 3nbt

Go back to Iron Binding Sites List in 3nbt
Iron binding site 6 out of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe105

b:21.9
occ:1.00
FE F:HEC105 0.0 21.9 1.0
ND F:HEC105 1.9 20.6 1.0
NA F:HEC105 2.0 22.8 1.0
NB F:HEC105 2.0 20.5 1.0
NC F:HEC105 2.0 20.9 1.0
NE2 F:HIS18 2.0 23.4 1.0
O F:HOH206 2.1 23.9 1.0
CE1 F:HIS18 2.9 23.9 1.0
C1D F:HEC105 3.0 20.8 1.0
C4A F:HEC105 3.0 22.6 1.0
C4D F:HEC105 3.0 20.6 1.0
C1B F:HEC105 3.0 20.1 1.0
C1C F:HEC105 3.0 21.0 1.0
C4C F:HEC105 3.0 18.4 1.0
CD2 F:HIS18 3.0 21.8 1.0
C1A F:HEC105 3.0 21.4 1.0
C4B F:HEC105 3.0 20.0 1.0
CHB F:HEC105 3.3 19.3 1.0
CHD F:HEC105 3.3 18.3 1.0
CHC F:HEC105 3.4 20.2 1.0
CHA F:HEC105 3.4 23.3 1.0
ND1 F:HIS18 4.1 24.0 1.0
CG F:HIS18 4.1 23.9 1.0
C3D F:HEC105 4.1 20.4 1.0
C3C F:HEC105 4.2 22.1 1.0
C2D F:HEC105 4.2 18.7 1.0
C3A F:HEC105 4.2 22.2 1.0
C2C F:HEC105 4.2 19.9 1.0
C3B F:HEC105 4.2 19.2 1.0
C2B F:HEC105 4.2 19.6 1.0
C2A F:HEC105 4.2 21.9 1.0
OH F:TYR67 4.4 26.5 1.0
CE F:MET80 4.8 39.9 1.0

Reference:

S.Hirota, Y.Hattori, S.Nagao, M.Taketa, H.Komori, H.Kamikubo, Z.Wang, I.Takahashi, S.Negi, Y.Sugiura, M.Kataoka, Y.Higuchi. Cytochrome C Polymerization By Successive Domain Swapping at the C-Terminal Helix Proc.Natl.Acad.Sci.Usa V. 107 12854 2010.
ISSN: ISSN 0027-8424
PubMed: 20615990
DOI: 10.1073/PNAS.1001839107
Page generated: Sun Aug 4 16:24:56 2024

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