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Iron in PDB 7xma: Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso

Enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso

All present enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso:
7.1.1.9;

Protein crystallography data

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma was solved by Y.Nishida, K.Shinzawa-Itoh, N.Mizuno, T.Kumasaka, S.Yoshikawa, T.Tsukihara, S.Takashima, Y.Shintani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.8, 203.577, 177.859, 90, 90, 90
R / Rfree (%) 18.6 / 21.3

Other elements in 7xma:

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso (pdb code 7xma). 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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7xma

Go back to Iron Binding Sites List in 7xma
Iron binding site 1 out of 4 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:23.7
occ:1.00
 FE A:HEA601 0.0 23.7 1.0
NE2 A:HIS378 2.0 23.3 1.0
NE2 A:HIS61 2.0 18.3 1.0
NC A:HEA601 2.0 30.2 1.0
ND A:HEA601 2.0 26.9 1.0
NA A:HEA601 2.0 29.9 1.0
NB A:HEA601 2.0 32.7 1.0
CE1 A:HIS378 2.9 26.7 1.0
CD2 A:HIS61 3.0 20.5 1.0
CE1 A:HIS61 3.0 28.9 1.0
C1B A:HEA601 3.0 27.7 1.0
C1C A:HEA601 3.0 31.6 1.0
C4C A:HEA601 3.0 34.4 1.0
C4D A:HEA601 3.0 43.5 1.0
C4A A:HEA601 3.0 40.0 1.0
C1D A:HEA601 3.0 40.6 1.0
C1A A:HEA601 3.0 38.6 1.0
C4B A:HEA601 3.0 36.0 1.0
CD2 A:HIS378 3.1 14.5 1.0
CHB A:HEA601 3.4 23.7 1.0
CHA A:HEA601 3.5 24.9 1.0
CHC A:HEA601 3.5 23.5 1.0
CHD A:HEA601 3.5 25.4 1.0
ND1 A:HIS378 4.0 25.6 1.0
ND1 A:HIS61 4.1 19.3 1.0
CG A:HIS61 4.1 19.5 1.0
CG A:HIS378 4.2 18.9 1.0
C2C A:HEA601 4.2 25.8 1.0
C2B A:HEA601 4.2 28.8 1.0
C2D A:HEA601 4.2 26.8 1.0
C3C A:HEA601 4.2 56.3 1.0
C3A A:HEA601 4.2 30.4 1.0
C3D A:HEA601 4.2 37.8 1.0
C2A A:HEA601 4.2 29.3 1.0
C3B A:HEA601 4.2 23.2 1.0
CE1 A:PHE377 4.9 22.6 1.0

Iron binding site 2 out of 4 in 7xma

Go back to Iron Binding Sites List in 7xma
Iron binding site 2 out of 4 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:25.4
occ:1.00
 FE A:HEA602 0.0 25.4 1.0
NE2 A:HIS376 2.0 33.7 1.0
NA A:HEA602 2.0 34.0 1.0
ND A:HEA602 2.0 27.4 1.0
NC A:HEA602 2.0 26.5 1.0
NB A:HEA602 2.0 27.3 1.0
O1 A:PER606 2.7 42.5 1.0
CE1 A:HIS376 2.9 37.5 1.0
C1C A:HEA602 3.0 44.1 1.0
C4D A:HEA602 3.0 33.9 1.0
C1B A:HEA602 3.0 33.6 1.0
C1A A:HEA602 3.0 21.3 1.0
C4A A:HEA602 3.0 19.7 1.0
C1D A:HEA602 3.0 38.5 1.0
C4C A:HEA602 3.0 22.6 1.0
C4B A:HEA602 3.0 28.7 1.0
CD2 A:HIS376 3.1 39.4 1.0
CHB A:HEA602 3.5 25.2 1.0
CHD A:HEA602 3.5 18.2 1.0
CHC A:HEA602 3.5 21.6 1.0
CHA A:HEA602 3.5 21.8 1.0
O2 A:PER606 3.6 36.1 1.0
ND1 A:HIS376 4.1 19.5 1.0
CG A:HIS376 4.2 18.0 1.0
C2B A:HEA602 4.2 27.5 1.0
C2C A:HEA602 4.2 46.0 1.0
C3D A:HEA602 4.2 42.2 1.0
C3A A:HEA602 4.2 25.8 1.0
C2A A:HEA602 4.2 39.8 1.0
C3B A:HEA602 4.2 34.0 1.0
C3C A:HEA602 4.2 21.6 1.0
C2D A:HEA602 4.2 24.9 1.0
CU A:CU603 4.9 18.2 1.0

Iron binding site 3 out of 4 in 7xma

Go back to Iron Binding Sites List in 7xma
Iron binding site 3 out of 4 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:24.9
occ:1.00
 FE N:HEA601 0.0 24.9 1.0
NE2 N:HIS378 2.0 20.3 1.0
NE2 N:HIS61 2.0 20.8 1.0
NC N:HEA601 2.0 34.8 1.0
ND N:HEA601 2.0 32.3 1.0
NA N:HEA601 2.0 30.0 1.0
NB N:HEA601 2.0 28.5 1.0
CE1 N:HIS378 2.9 34.8 1.0
CD2 N:HIS61 3.0 23.5 1.0
C1B N:HEA601 3.0 34.8 1.0
C1C N:HEA601 3.0 33.3 1.0
C4C N:HEA601 3.0 48.7 1.0
C4D N:HEA601 3.0 44.2 1.0
CE1 N:HIS61 3.0 35.0 1.0
C1D N:HEA601 3.0 41.8 1.0
C4A N:HEA601 3.0 44.3 1.0
C1A N:HEA601 3.0 34.2 1.0
C4B N:HEA601 3.1 39.7 1.0
CD2 N:HIS378 3.1 20.2 1.0
CHB N:HEA601 3.4 20.3 1.0
CHA N:HEA601 3.5 22.3 1.0
CHD N:HEA601 3.5 31.6 1.0
CHC N:HEA601 3.5 23.1 1.0
ND1 N:HIS378 4.0 24.9 1.0
CG N:HIS61 4.1 20.0 1.0
ND1 N:HIS61 4.1 25.2 1.0
CG N:HIS378 4.2 26.4 1.0
C2C N:HEA601 4.2 38.6 1.0
C2B N:HEA601 4.2 37.1 1.0
C2D N:HEA601 4.2 46.6 1.0
C3C N:HEA601 4.2 42.4 1.0
C3D N:HEA601 4.2 30.8 1.0
C3A N:HEA601 4.2 39.8 1.0
C2A N:HEA601 4.2 38.0 1.0
C3B N:HEA601 4.2 32.7 1.0
CE1 N:PHE377 4.9 27.9 1.0

Iron binding site 4 out of 4 in 7xma

Go back to Iron Binding Sites List in 7xma
Iron binding site 4 out of 4 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


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 Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:24.0
occ:1.00
 FE N:HEA602 0.0 24.0 1.0
NE2 N:HIS376 2.0 32.7 1.0
NA N:HEA602 2.0 27.9 1.0
ND N:HEA602 2.0 26.4 1.0
NC N:HEA602 2.0 22.7 1.0
NB N:HEA602 2.0 28.9 1.0
O1 N:PER606 2.7 38.3 1.0
CE1 N:HIS376 2.9 37.4 1.0
C1C N:HEA602 3.0 45.2 1.0
C4D N:HEA602 3.0 21.9 1.0
C1B N:HEA602 3.0 45.7 1.0
C1A N:HEA602 3.0 26.9 1.0
C4A N:HEA602 3.0 30.7 1.0
C1D N:HEA602 3.0 36.0 1.0
C4B N:HEA602 3.0 34.0 1.0
C4C N:HEA602 3.0 36.1 1.0
CD2 N:HIS376 3.1 40.2 1.0
O2 N:PER606 3.5 46.7 1.0
CHA N:HEA602 3.5 18.5 1.0
CHC N:HEA602 3.5 23.4 1.0
CHB N:HEA602 3.5 27.7 1.0
CHD N:HEA602 3.5 22.2 1.0
ND1 N:HIS376 4.1 27.1 1.0
CG N:HIS376 4.2 21.0 1.0
C2C N:HEA602 4.2 35.8 1.0
C2B N:HEA602 4.2 23.4 1.0
C3D N:HEA602 4.2 54.4 1.0
C2A N:HEA602 4.2 31.6 1.0
C3A N:HEA602 4.2 22.5 1.0
C2D N:HEA602 4.2 29.6 1.0
C3C N:HEA602 4.2 33.5 1.0
C3B N:HEA602 4.2 27.3 1.0
CU N:CU603 4.9 18.9 1.0

Reference:

Y.Nishida, S.Yanagisawa, R.Morita, H.Shigematsu, K.Shinzawa-Itoh, H.Yuki, S.Ogasawara, K.Shimuta, T.Iwamoto, C.Nakabayashi, W.Matsumura, H.Kato, C.Gopalasingam, T.Nagao, T.Qaqorh, Y.Takahashi, S.Yamazaki, K.Kamiya, R.Harada, N.Mizuno, H.Takahashi, Y.Akeda, M.Ohnishi, Y.Ishii, T.Kumasaka, T.Murata, K.Muramoto, T.Tosha, Y.Shiro, T.Honma, Y.Shigeta, M.Kubo, S.Takashima, Y.Shintani. Identifying Antibiotics Based on Structural Differences in the Conserved Allostery From Mitochondrial Heme-Copper Oxidases. Nat Commun V. 13 7591 2022.
ISSN: ESSN 2041-1723
PubMed: 36481732
DOI: 10.1038/S41467-022-34771-Y
Page generated: Fri Aug 9 11:02:45 2024

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