Iron in PDB 7xmc: Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso

All present enzymatic activity of Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso:
7.1.1.3;

The structure of Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Iron atom in the Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso (pdb code 7xmc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso, PDB code: 7xmc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, 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 Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:74.2 occ:1.00 FE A:HEO701 0.0 74.2 1.0 ND A:HEO701 1.9 74.2 1.0 NA A:HEO701 2.0 74.2 1.0 NE2 A:HIS419 2.1 71.5 1.0 NC A:HEO701 2.1 74.2 1.0 NB A:HEO701 2.1 74.2 1.0 CE1 A:HIS419 2.8 71.5 1.0 C4D A:HEO701 2.9 74.2 1.0 C1D A:HEO701 2.9 74.2 1.0 C1A A:HEO701 2.9 74.2 1.0 C4A A:HEO701 3.0 74.2 1.0 C4C A:HEO701 3.0 74.2 1.0 C1B A:HEO701 3.1 74.2 1.0 C4B A:HEO701 3.1 74.2 1.0 C1C A:HEO701 3.1 74.2 1.0 CD2 A:HIS419 3.3 71.5 1.0 CHA A:HEO701 3.3 74.2 1.0 CHD A:HEO701 3.4 74.2 1.0 CHB A:HEO701 3.5 74.2 1.0 CHC A:HEO701 3.5 74.2 1.0 ND1 A:HIS419 4.0 71.5 1.0 C3D A:HEO701 4.1 74.2 1.0 C2D A:HEO701 4.1 74.2 1.0 C2A A:HEO701 4.2 74.2 1.0 C3A A:HEO701 4.2 74.2 1.0 CG A:HIS419 4.3 71.5 1.0 C3C A:HEO701 4.3 74.2 1.0 C2C A:HEO701 4.3 74.2 1.0 C2B A:HEO701 4.3 74.2 1.0 C3B A:HEO701 4.3 74.2 1.0 CG2 A:VAL423 4.6 71.7 1.0 CE1 A:HIS284 4.9 71.5 1.0 CB A:PHE420 5.0 69.7 1.0

Iron binding site 2 out of 2 in the Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, 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 Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, Apo Structure with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:68.8 occ:1.00 FE A:HEM702 0.0 68.8 1.0 ND A:HEM702 1.9 68.8 1.0 NE2 A:HIS421 2.0 69.1 1.0 NA A:HEM702 2.0 68.8 1.0 NE2 A:HIS106 2.0 68.5 1.0 NC A:HEM702 2.1 68.8 1.0 NB A:HEM702 2.1 68.8 1.0 CE1 A:HIS421 2.7 69.1 1.0 C4D A:HEM702 2.9 68.8 1.0 CD2 A:HIS106 2.9 68.5 1.0 C1D A:HEM702 2.9 68.8 1.0 C1A A:HEM702 2.9 68.8 1.0 C4C A:HEM702 3.0 68.8 1.0 C4A A:HEM702 3.0 68.8 1.0 CE1 A:HIS106 3.0 68.5 1.0 C1B A:HEM702 3.1 68.8 1.0 C4B A:HEM702 3.1 68.8 1.0 C1C A:HEM702 3.1 68.8 1.0 CD2 A:HIS421 3.1 69.1 1.0 CHA A:HEM702 3.3 68.8 1.0 CHD A:HEM702 3.4 68.8 1.0 CHB A:HEM702 3.5 68.8 1.0 CHC A:HEM702 3.5 68.8 1.0 ND1 A:HIS421 3.9 69.1 1.0 CG A:HIS106 4.1 68.5 1.0 ND1 A:HIS106 4.1 68.5 1.0 C3D A:HEM702 4.1 68.8 1.0 C2D A:HEM702 4.1 68.8 1.0 CG A:HIS421 4.1 69.1 1.0 C2A A:HEM702 4.2 68.8 1.0 C3A A:HEM702 4.2 68.8 1.0 C3C A:HEM702 4.2 68.8 1.0 C2C A:HEM702 4.3 68.8 1.0 C2B A:HEM702 4.3 68.8 1.0 C3B A:HEM702 4.4 68.8 1.0 CE1 A:PHE420 4.8 69.7 1.0

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