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Iron in PDB 6j8m: Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray

Enzymatic activity of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray

All present enzymatic activity of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray:
1.9.3.1;

Protein crystallography data

The structure of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray, PDB code: 6j8m was solved by G.Ueno, A.Shimada, E.Yamashita, K.Hasegawa, T.Kumasaka, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, M.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.020, 203.540, 177.410, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 6j8m:

The structure of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Copper (Cu) 6 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray (pdb code 6j8m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray, PDB code: 6j8m:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6j8m

Go back to Iron Binding Sites List in 6j8m
Iron binding site 1 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:28.4
occ:1.00
 FE A:HEA601 0.0 28.4 1.0
NE2 A:HIS378 2.0 27.3 1.0
NC A:HEA601 2.1 24.2 1.0
NB A:HEA601 2.1 26.2 1.0
NE2 A:HIS61 2.1 26.8 1.0
NA A:HEA601 2.1 26.9 1.0
ND A:HEA601 2.1 25.5 1.0
CE1 A:HIS378 3.0 26.5 1.0
CE1 A:HIS61 3.0 26.2 1.0
CD2 A:HIS378 3.0 25.0 1.0
C1C A:HEA601 3.0 23.7 1.0
C4C A:HEA601 3.1 24.7 1.0
C4A A:HEA601 3.1 26.9 1.0
C1D A:HEA601 3.1 25.0 1.0
C4B A:HEA601 3.1 26.1 1.0
C1B A:HEA601 3.1 26.8 1.0
CD2 A:HIS61 3.1 27.1 1.0
C1A A:HEA601 3.1 26.1 1.0
C4D A:HEA601 3.1 26.4 1.0
CHC A:HEA601 3.4 22.8 1.0
CHB A:HEA601 3.4 25.9 1.0
CHD A:HEA601 3.4 23.3 1.0
CHA A:HEA601 3.5 26.0 1.0
ND1 A:HIS378 4.1 26.0 1.0
ND1 A:HIS61 4.1 26.0 1.0
CG A:HIS378 4.2 23.9 1.0
CG A:HIS61 4.2 27.3 1.0
C3A A:HEA601 4.3 26.1 1.0
C3B A:HEA601 4.3 25.6 1.0
C2A A:HEA601 4.3 26.7 1.0
C2C A:HEA601 4.3 23.1 1.0
C2D A:HEA601 4.3 24.8 1.0
C3C A:HEA601 4.3 24.4 1.0
C3D A:HEA601 4.3 26.6 1.0
C2B A:HEA601 4.3 26.4 1.0
CE1 A:PHE377 4.9 26.0 1.0

Iron binding site 2 out of 4 in 6j8m

Go back to Iron Binding Sites List in 6j8m
Iron binding site 2 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:27.7
occ:1.00
 FE A:HEA602 0.0 27.7 1.0
NC A:HEA602 2.0 26.2 1.0
NA A:HEA602 2.1 26.6 1.0
ND A:HEA602 2.1 25.8 1.0
NB A:HEA602 2.1 27.3 1.0
NE2 A:HIS376 2.2 27.0 1.0
O1 A:PER607 2.3 19.6 0.9
O1 A:PER607 3.0 15.1 0.1
C1C A:HEA602 3.0 26.6 1.0
C1A A:HEA602 3.0 25.5 1.0
C4C A:HEA602 3.1 26.0 1.0
C4A A:HEA602 3.1 25.9 1.0
C4D A:HEA602 3.1 25.7 1.0
C4B A:HEA602 3.1 26.1 1.0
C1B A:HEA602 3.1 27.4 1.0
C1D A:HEA602 3.1 26.0 1.0
CE1 A:HIS376 3.1 28.4 1.0
CD2 A:HIS376 3.2 28.1 1.0
CHC A:HEA602 3.4 25.6 1.0
CHA A:HEA602 3.5 23.7 1.0
CHB A:HEA602 3.5 26.5 1.0
CHD A:HEA602 3.5 24.7 1.0
O2 A:PER607 3.7 25.6 0.9
C2A A:HEA602 4.3 24.8 1.0
C3A A:HEA602 4.3 26.0 1.0
ND1 A:HIS376 4.3 26.2 1.0
C2C A:HEA602 4.3 26.5 1.0
C3C A:HEA602 4.3 25.8 1.0
C3D A:HEA602 4.3 25.9 1.0
CG A:HIS376 4.3 27.7 1.0
C3B A:HEA602 4.3 26.7 1.0
C2D A:HEA602 4.3 24.6 1.0
C2B A:HEA602 4.3 26.3 1.0
O2 A:PER607 4.4 15.0 0.1
CU A:CU603 4.8 27.9 1.0

Iron binding site 3 out of 4 in 6j8m

Go back to Iron Binding Sites List in 6j8m
Iron binding site 3 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:31.8
occ:1.00
 FE N:HEA601 0.0 31.8 1.0
NB N:HEA601 2.0 31.3 1.0
NA N:HEA601 2.1 31.1 1.0
NE2 N:HIS378 2.1 31.7 1.0
NE2 N:HIS61 2.1 30.2 1.0
ND N:HEA601 2.1 30.3 1.0
NC N:HEA601 2.1 30.6 1.0
CD2 N:HIS61 3.0 30.0 1.0
C1A N:HEA601 3.0 30.6 1.0
C1B N:HEA601 3.0 31.1 1.0
CE1 N:HIS378 3.0 31.2 1.0
C4B N:HEA601 3.0 31.6 1.0
C4A N:HEA601 3.1 31.4 1.0
CD2 N:HIS378 3.1 29.5 1.0
C1D N:HEA601 3.1 29.9 1.0
CE1 N:HIS61 3.1 29.2 1.0
C1C N:HEA601 3.1 30.1 1.0
C4D N:HEA601 3.1 29.9 1.0
C4C N:HEA601 3.1 30.4 1.0
CHC N:HEA601 3.4 29.0 1.0
CHB N:HEA601 3.4 31.0 1.0
CHA N:HEA601 3.4 29.3 1.0
CHD N:HEA601 3.5 28.7 1.0
ND1 N:HIS378 4.2 30.2 1.0
CG N:HIS61 4.2 30.4 1.0
ND1 N:HIS61 4.2 28.7 1.0
CG N:HIS378 4.2 29.9 1.0
C2A N:HEA601 4.2 30.5 1.0
C3A N:HEA601 4.2 31.4 1.0
C2B N:HEA601 4.3 31.0 1.0
C3B N:HEA601 4.3 30.1 1.0
C2D N:HEA601 4.3 30.6 1.0
C3D N:HEA601 4.3 28.8 1.0
C2C N:HEA601 4.3 28.6 1.0
C3C N:HEA601 4.4 28.8 1.0
CE1 N:PHE377 4.8 28.9 1.0

Iron binding site 4 out of 4 in 6j8m

Go back to Iron Binding Sites List in 6j8m
Iron binding site 4 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:29.2
occ:1.00
 FE N:HEA602 0.0 29.2 1.0
NC N:HEA602 2.0 28.7 1.0
NB N:HEA602 2.1 28.7 1.0
ND N:HEA602 2.1 29.0 1.0
NA N:HEA602 2.1 28.9 1.0
NE2 N:HIS376 2.2 29.4 1.0
O1 N:PER607 2.3 21.5 0.9
C1C N:HEA602 3.0 29.2 1.0
C1A N:HEA602 3.1 28.2 1.0
C4C N:HEA602 3.1 28.8 1.0
C1B N:HEA602 3.1 28.1 1.0
C4B N:HEA602 3.1 27.9 1.0
C1D N:HEA602 3.1 30.1 1.0
C4D N:HEA602 3.1 29.8 1.0
C4A N:HEA602 3.1 27.9 1.0
O1 N:PER607 3.2 19.7 0.1
CE1 N:HIS376 3.2 29.4 1.0
CD2 N:HIS376 3.2 29.1 1.0
CHA N:HEA602 3.5 27.5 1.0
CHD N:HEA602 3.5 27.7 1.0
CHC N:HEA602 3.5 29.6 1.0
CHB N:HEA602 3.5 27.6 1.0
O2 N:PER607 3.6 25.4 0.9
C2C N:HEA602 4.3 29.6 1.0
C2A N:HEA602 4.3 27.9 1.0
C3C N:HEA602 4.3 29.2 1.0
C2D N:HEA602 4.3 29.3 1.0
C3D N:HEA602 4.3 29.9 1.0
C3A N:HEA602 4.3 28.1 1.0
C2B N:HEA602 4.3 27.0 1.0
C3B N:HEA602 4.3 27.6 1.0
ND1 N:HIS376 4.3 29.1 1.0
CG N:HIS376 4.4 28.6 1.0
O2 N:PER607 4.4 19.6 0.1
CU N:CU603 4.8 29.4 1.0

Reference:

G.Ueno, A.Shimada, E.Yamashita, K.Hasegawa, T.Kumasaka, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, M.Yamamoto. Low-Dose X-Ray Structure Analysis of Cytochrome C Oxidase Utilizing High-Energy X-Rays. J.Synchrotron Radiat. V. 26 912 2019.
ISSN: ESSN 1600-5775
PubMed: 31274413
DOI: 10.1107/S1600577519006805
Page generated: Tue Aug 6 23:19:08 2024

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