Zinc in PDB 6om4: The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca

The structure of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca, PDB code: 6om4 was solved by S.-H.Dong, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.98 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.094, 76.059, 131.902, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 19.9

The structure of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca (pdb code 6om4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca, PDB code: 6om4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:19.0 occ:1.00 SG A:CYS257 2.2 17.4 1.0 SG A:CYS343 2.3 20.1 1.0 SG A:CYS260 2.3 20.5 1.0 SG A:CYS346 2.4 21.1 1.0 CB A:CYS343 3.1 21.1 1.0 CB A:CYS257 3.3 16.7 1.0 CB A:CYS346 3.4 20.5 1.0 CB A:CYS260 3.5 20.4 1.0 N A:CYS260 3.5 22.7 1.0 CA A:CYS260 3.5 22.2 1.0 N A:CYS257 3.6 18.1 1.0 N A:CYS346 3.9 19.1 1.0 CA A:CYS257 3.9 17.0 1.0 CA A:CYS346 4.2 21.3 1.0 C A:GLU259 4.3 22.4 1.0 C A:CYS257 4.3 16.5 1.0 O A:CYS257 4.4 16.3 1.0 CA A:CYS343 4.6 22.2 1.0 N A:GLU259 4.7 20.9 1.0 CB A:VAL345 4.7 20.3 1.0 O A:HOH509 4.7 34.1 1.0 C A:CYS346 4.8 24.0 1.0 C A:GLY256 4.8 20.0 1.0 CA A:GLU259 4.9 23.0 1.0 C A:VAL345 4.9 19.6 1.0 O A:GLU259 4.9 22.0 1.0 N A:GLY347 5.0 24.1 1.0

Zinc binding site 2 out of 2 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.1 occ:1.00 SG B:CYS260 2.1 23.6 1.0 SG B:CYS343 2.3 26.4 1.0 SG B:CYS257 2.3 19.3 1.0 SG B:CYS346 2.3 25.0 1.0 CB B:CYS343 3.2 29.9 1.0 CB B:CYS257 3.4 20.3 1.0 CB B:CYS346 3.4 23.7 1.0 CB B:CYS260 3.4 23.2 1.0 N B:CYS260 3.5 24.9 1.0 CA B:CYS260 3.6 25.8 1.0 N B:CYS257 3.8 18.1 1.0 N B:CYS346 3.8 27.4 1.0 CA B:CYS257 4.0 18.5 1.0 CA B:CYS346 4.2 28.4 1.0 C B:GLU259 4.3 25.9 1.0 C B:CYS257 4.4 18.3 1.0 O B:CYS257 4.5 19.3 1.0 O B:HOH513 4.6 34.9 1.0 CA B:CYS343 4.6 33.3 1.0 O B:HOH525 4.7 23.9 1.0 N B:GLU259 4.7 24.8 1.0 CB B:VAL345 4.7 33.8 1.0 C B:VAL345 4.8 28.4 1.0 CA B:GLU259 4.9 27.5 1.0 C B:GLY256 4.9 20.6 1.0 CB B:GLU259 5.0 30.6 1.0 C B:CYS346 5.0 31.6 1.0

S.H.Dong, A.Kulikovsky, I.Zukher, P.Estrada, S.Dubiley, K.Severinov, S.K.Nair. Biosynthesis of the Ripp Trojan Horse Nucleotide Antibiotic Microcin C Is Directed By Then-Formyl of the Peptide Precursor. Chem Sci V. 10 2391 2019.
ISSN: ISSN 2041-6520
PubMed: 30881667
DOI: 10.1039/C8SC03173H