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Iron in PDB 3nbs: Crystal Structure of Dimeric Cytochrome C From Horse Heart

Protein crystallography data

The structure of Crystal Structure of Dimeric Cytochrome C From Horse Heart, PDB code: 3nbs 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) 19.58 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.753, 56.305, 60.815, 66.28, 89.94, 73.66
R / Rfree (%) 21.5 / 27.3

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 3nbs

Go back to Iron Binding Sites List in 3nbs
Iron binding site 1 out of 4 in the Crystal Structure of Dimeric 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 Dimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe105

b:10.7
occ:1.00
FE A:HEC105 0.0 10.7 1.0
NB A:HEC105 2.0 10.0 1.0
ND A:HEC105 2.0 12.3 1.0
NE2 A:HIS18 2.0 11.0 1.0
NC A:HEC105 2.0 10.7 1.0
NA A:HEC105 2.0 12.6 1.0
O A:HOH201 2.1 10.6 1.0
CD2 A:HIS18 2.9 10.9 1.0
CE1 A:HIS18 3.0 10.8 1.0
C1B A:HEC105 3.0 10.3 1.0
C1D A:HEC105 3.0 12.6 1.0
C1C A:HEC105 3.0 11.6 1.0
C4B A:HEC105 3.0 11.1 1.0
C4D A:HEC105 3.0 13.1 1.0
C4C A:HEC105 3.0 10.7 1.0
C4A A:HEC105 3.0 11.5 1.0
C1A A:HEC105 3.0 11.6 1.0
CHD A:HEC105 3.3 12.7 1.0
CHB A:HEC105 3.4 8.2 1.0
CHC A:HEC105 3.4 8.3 1.0
CHA A:HEC105 3.4 10.3 1.0
O A:HOH358 4.0 5.6 1.0
ND1 A:HIS18 4.1 11.5 1.0
CG A:HIS18 4.1 11.6 1.0
C2B A:HEC105 4.2 8.4 1.0
C3B A:HEC105 4.2 9.2 1.0
C2D A:HEC105 4.2 13.2 1.0
C3D A:HEC105 4.2 12.2 1.0
C2C A:HEC105 4.2 12.3 1.0
C3C A:HEC105 4.2 10.4 1.0
C3A A:HEC105 4.2 10.7 1.0
C2A A:HEC105 4.2 10.7 1.0
OH A:TYR67 4.4 12.0 1.0
CE2 B:PHE82 4.8 7.8 1.0
CD2 B:PHE82 4.9 9.8 1.0

Iron binding site 2 out of 4 in 3nbs

Go back to Iron Binding Sites List in 3nbs
Iron binding site 2 out of 4 in the Crystal Structure of Dimeric 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 Dimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe105

b:9.6
occ:1.00
FE B:HEC105 0.0 9.6 1.0
ND B:HEC105 2.0 12.8 1.0
NB B:HEC105 2.0 13.8 1.0
NA B:HEC105 2.0 14.2 1.0
NE2 B:HIS18 2.0 13.2 1.0
NC B:HEC105 2.0 13.9 1.0
O B:HOH202 2.1 13.7 1.0
CD2 B:HIS18 3.0 9.4 1.0
CE1 B:HIS18 3.0 13.5 1.0
C4D B:HEC105 3.0 11.9 1.0
C1D B:HEC105 3.0 14.1 1.0
C1B B:HEC105 3.0 13.9 1.0
C4B B:HEC105 3.0 13.9 1.0
C1C B:HEC105 3.0 14.6 1.0
C4A B:HEC105 3.0 13.7 1.0
C4C B:HEC105 3.0 14.3 1.0
C1A B:HEC105 3.0 13.3 1.0
CHB B:HEC105 3.3 13.8 1.0
CHA B:HEC105 3.4 12.5 1.0
CHC B:HEC105 3.4 14.1 1.0
CHD B:HEC105 3.4 13.8 1.0
ND1 B:HIS18 4.1 11.8 1.0
CG B:HIS18 4.1 11.3 1.0
C3D B:HEC105 4.2 12.7 1.0
C2D B:HEC105 4.2 13.8 1.0
C2B B:HEC105 4.2 13.9 1.0
C3B B:HEC105 4.2 13.4 1.0
C3C B:HEC105 4.2 15.8 1.0
C2C B:HEC105 4.2 15.2 1.0
C3A B:HEC105 4.2 13.0 1.0
C2A B:HEC105 4.2 13.2 1.0
O B:HOH284 4.4 11.2 1.0
OH B:TYR67 4.5 8.8 1.0

Iron binding site 3 out of 4 in 3nbs

Go back to Iron Binding Sites List in 3nbs
Iron binding site 3 out of 4 in the Crystal Structure of Dimeric 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 Dimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe105

b:8.9
occ:1.00
FE C:HEC105 0.0 8.9 1.0
NB C:HEC105 2.0 10.1 1.0
ND C:HEC105 2.0 11.4 1.0
NE2 C:HIS18 2.0 11.5 1.0
NA C:HEC105 2.0 12.6 1.0
NC C:HEC105 2.0 10.8 1.0
O C:HOH203 2.1 8.6 1.0
CD2 C:HIS18 2.9 10.5 1.0
C1D C:HEC105 3.0 10.5 1.0
C1B C:HEC105 3.0 10.1 1.0
C4B C:HEC105 3.0 10.7 1.0
C4D C:HEC105 3.0 10.9 1.0
CE1 C:HIS18 3.0 10.6 1.0
C4A C:HEC105 3.0 9.8 1.0
C4C C:HEC105 3.0 10.7 1.0
C1C C:HEC105 3.0 10.4 1.0
C1A C:HEC105 3.0 10.5 1.0
CHB C:HEC105 3.3 8.8 1.0
CHD C:HEC105 3.3 7.9 1.0
CHC C:HEC105 3.4 10.2 1.0
CHA C:HEC105 3.4 11.4 1.0
CG C:HIS18 4.1 10.1 1.0
ND1 C:HIS18 4.1 11.1 1.0
C3D C:HEC105 4.1 10.6 1.0
C2B C:HEC105 4.1 9.6 1.0
C2D C:HEC105 4.1 11.4 1.0
C3B C:HEC105 4.2 9.3 1.0
C3A C:HEC105 4.2 12.0 1.0
O C:HOH362 4.2 18.3 1.0
C2A C:HEC105 4.2 11.3 1.0
C3C C:HEC105 4.2 9.1 1.0
C2C C:HEC105 4.2 11.6 1.0
OH C:TYR67 4.4 9.5 1.0

Iron binding site 4 out of 4 in 3nbs

Go back to Iron Binding Sites List in 3nbs
Iron binding site 4 out of 4 in the Crystal Structure of Dimeric 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 Dimeric Cytochrome C From Horse Heart within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe105

b:12.4
occ:1.00
FE D:HEC105 0.0 12.4 1.0
ND D:HEC105 1.9 10.2 1.0
NE2 D:HIS18 2.0 12.4 1.0
NB D:HEC105 2.0 10.9 1.0
NC D:HEC105 2.0 11.8 1.0
NA D:HEC105 2.0 10.9 1.0
O D:HOH204 2.1 14.5 1.0
CE1 D:HIS18 2.9 13.7 1.0
C4D D:HEC105 3.0 12.4 1.0
C1D D:HEC105 3.0 12.1 1.0
C1C D:HEC105 3.0 12.1 1.0
C1B D:HEC105 3.0 10.9 1.0
CD2 D:HIS18 3.0 13.2 1.0
C1A D:HEC105 3.0 10.4 1.0
C4B D:HEC105 3.0 11.1 1.0
C4A D:HEC105 3.0 10.0 1.0
C4C D:HEC105 3.0 12.4 1.0
CHD D:HEC105 3.3 10.8 1.0
CHA D:HEC105 3.4 10.1 1.0
CHC D:HEC105 3.4 10.0 1.0
CHB D:HEC105 3.4 8.4 1.0
ND1 D:HIS18 4.0 14.7 1.0
CG D:HIS18 4.1 14.9 1.0
C3D D:HEC105 4.1 12.6 1.0
C2D D:HEC105 4.1 12.3 1.0
C2C D:HEC105 4.2 12.9 1.0
C2A D:HEC105 4.2 10.6 1.0
C2B D:HEC105 4.2 10.3 1.0
C3B D:HEC105 4.2 10.2 1.0
O D:HOH312 4.2 12.5 1.0
C3A D:HEC105 4.2 10.4 1.0
C3C D:HEC105 4.2 12.8 1.0
OH D:TYR67 4.4 9.8 1.0
CE1 C:PHE82 4.8 14.5 1.0
CD1 C:PHE82 4.8 13.7 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 Dec 13 15:14:00 2020

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