Iron in PDB 7xmd: Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, the Structure Complexed with An Allosteric Inhibitor N4

All present enzymatic activity of Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, the Structure Complexed with An Allosteric Inhibitor N4:
7.1.1.3;

The structure of Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, the Structure Complexed with An Allosteric Inhibitor N4 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, the Structure Complexed with An Allosteric Inhibitor N4 (pdb code 7xmd). 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, the Structure Complexed with An Allosteric Inhibitor N4, PDB code: 7xmd:
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, the Structure Complexed with An Allosteric Inhibitor N4


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, the Structure Complexed with An Allosteric Inhibitor N4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:69.8 occ:1.00 FE A:HEO701 0.0 69.8 1.0 ND A:HEO701 1.9 69.8 1.0 NA A:HEO701 2.0 69.8 1.0 NE2 A:HIS419 2.0 65.6 1.0 NC A:HEO701 2.1 69.8 1.0 NB A:HEO701 2.1 69.8 1.0 CE1 A:HIS419 2.8 65.6 1.0 C4D A:HEO701 2.8 69.8 1.0 C1D A:HEO701 2.9 69.8 1.0 C1A A:HEO701 3.0 69.8 1.0 C4A A:HEO701 3.0 69.8 1.0 C4C A:HEO701 3.0 69.8 1.0 C1B A:HEO701 3.1 69.8 1.0 C4B A:HEO701 3.1 69.8 1.0 C1C A:HEO701 3.1 69.8 1.0 CD2 A:HIS419 3.2 65.6 1.0 CHA A:HEO701 3.3 69.8 1.0 CHD A:HEO701 3.4 69.8 1.0 CHB A:HEO701 3.5 69.8 1.0 CHC A:HEO701 3.5 69.8 1.0 ND1 A:HIS419 4.0 65.6 1.0 CU A:CU703 4.0 86.4 1.0 C3D A:HEO701 4.1 69.8 1.0 C2D A:HEO701 4.1 69.8 1.0 C2A A:HEO701 4.2 69.8 1.0 C3A A:HEO701 4.2 69.8 1.0 CG A:HIS419 4.2 65.6 1.0 C3C A:HEO701 4.2 69.8 1.0 C2C A:HEO701 4.3 69.8 1.0 C2B A:HEO701 4.3 69.8 1.0 C3B A:HEO701 4.3 69.8 1.0 CE1 A:HIS334 4.9 66.9 1.0 NE2 A:HIS333 5.0 67.6 1.0

Iron binding site 2 out of 2 in the Cryo-Em Structure of Cytochrome BO3 From Escherichia Coli, the Structure Complexed with An Allosteric Inhibitor N4


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, the Structure Complexed with An Allosteric Inhibitor N4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:64.0 occ:1.00 FE A:HEM702 0.0 64.0 1.0 ND A:HEM702 1.9 64.0 1.0 NE2 A:HIS421 2.0 63.7 1.0 NA A:HEM702 2.0 64.0 1.0 NE2 A:HIS106 2.0 63.5 1.0 NC A:HEM702 2.1 64.0 1.0 NB A:HEM702 2.1 64.0 1.0 CD2 A:HIS106 2.7 63.5 1.0 CE1 A:HIS421 2.8 63.7 1.0 C4D A:HEM702 2.9 64.0 1.0 C1D A:HEM702 2.9 64.0 1.0 C1A A:HEM702 2.9 64.0 1.0 C4C A:HEM702 3.0 64.0 1.0 C4A A:HEM702 3.0 64.0 1.0 CD2 A:HIS421 3.1 63.7 1.0 C1B A:HEM702 3.1 64.0 1.0 C4B A:HEM702 3.1 64.0 1.0 C1C A:HEM702 3.1 64.0 1.0 CE1 A:HIS106 3.1 63.5 1.0 CHA A:HEM702 3.3 64.0 1.0 CHD A:HEM702 3.4 64.0 1.0 CHB A:HEM702 3.5 64.0 1.0 CHC A:HEM702 3.5 64.0 1.0 CG A:HIS106 3.9 63.5 1.0 ND1 A:HIS421 4.0 63.7 1.0 ND1 A:HIS106 4.1 63.5 1.0 C3D A:HEM702 4.1 64.0 1.0 CG A:HIS421 4.1 63.7 1.0 C2D A:HEM702 4.1 64.0 1.0 C2A A:HEM702 4.1 64.0 1.0 C3A A:HEM702 4.2 64.0 1.0 C3C A:HEM702 4.2 64.0 1.0 C2C A:HEM702 4.3 64.0 1.0 C2B A:HEM702 4.3 64.0 1.0 C3B A:HEM702 4.3 64.0 1.0 CE1 A:PHE420 4.9 64.7 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