Nickel in PDB 8amq: Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis

The structure of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis, PDB code: 8amq was solved by S.Bukhdruker, T.Varaksa, S.Smolskaya, E.Marin, I.Kapranov, K.Kovalev, A.Gilep, N.Strushkevich, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.15 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.2, 54.354, 69.037, 67.71, 77.21, 61.63
R / Rfree (%)	17.7 / 20.7

The structure of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis (pdb code 8amq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis, PDB code: 8amq:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2003 b:36.3 occ:1.00 NE2 A:HIS72 1.9 33.2 1.0 O A:HOH2119 2.0 36.2 1.0 OD1 A:ASP65 2.1 35.0 1.0 O A:HOH2299 2.2 53.1 1.0 NE2 A:HIS70 2.2 39.9 1.0 O A:HOH2431 2.5 41.3 1.0 CE1 A:HIS72 2.7 40.4 1.0 CG A:ASP65 3.0 40.5 1.0 CD2 A:HIS70 3.1 34.0 1.0 CD2 A:HIS72 3.1 43.2 1.0 OD2 A:ASP65 3.2 40.5 1.0 CE1 A:HIS70 3.3 37.5 1.0 ND1 A:HIS72 3.9 42.5 1.0 CG A:HIS72 4.1 46.9 1.0 O A:GLU63 4.3 36.5 1.0 CG A:HIS70 4.3 37.3 1.0 ND1 A:HIS70 4.4 42.1 1.0 CB A:ASP65 4.4 45.4 1.0 O A:HOH2417 4.4 45.5 1.0 O A:HOH2439 4.5 43.4 1.0 C A:ASP65 4.7 41.1 1.0 N A:ALA66 4.7 35.5 1.0 N A:ASP65 4.8 34.2 1.0 CA A:ASP65 4.8 35.5 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2004 b:78.6 occ:1.00 NE2 A:HIS1 2.1 57.4 1.0 O A:HOH2179 3.0 65.4 1.0 CD2 A:HIS1 3.0 47.7 1.0 CE1 A:HIS1 3.1 57.7 1.0 OE2 A:GLU63 3.2 64.7 1.0 CG A:GLU63 3.8 55.0 1.0 CD A:GLU63 3.9 68.0 1.0 CG A:HIS1 4.2 48.4 1.0 ND1 A:HIS1 4.2 52.4 1.0 O A:HIS-1 4.8 61.1 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2005 b:63.9 occ:1.00 N A:HIS-4 2.0 76.8 1.0 N A:ALA-5 2.0 71.6 1.0 ND1 A:HIS-4 2.0 61.2 1.0 C A:ALA-5 2.6 67.5 1.0 CA A:ALA-5 2.6 80.5 1.0 CE1 A:HIS-4 2.8 70.9 1.0 CG A:HIS-4 3.0 65.0 1.0 CA A:HIS-4 3.1 75.4 1.0 CB A:ALA-5 3.3 76.2 1.0 CB A:HIS-4 3.4 61.9 1.0 N A:HIS-3 3.7 77.0 1.0 O A:ALA-5 3.7 66.0 1.0 C A:HIS-4 3.8 77.5 1.0 NE2 A:HIS-4 3.9 70.8 1.0 CD2 A:HIS-4 4.0 68.4 1.0 CD2 A:HIS-3 4.1 70.0 1.0 NE2 A:HIS-3 4.4 74.2 1.0 CG A:HIS-3 4.6 66.7 1.0 O A:HIS-4 5.0 76.5 1.0 CE1 A:HIS-3 5.0 67.3 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2006 b:106.8 occ:1.00 CE1 A:HIS0 2.4 77.9 1.0 NE2 A:HIS0 2.4 86.5 1.0 CE1 A:HIS-2 3.5 63.3 1.0 NE2 A:HIS-2 3.6 50.5 1.0 ND1 A:HIS0 3.8 73.9 1.0 CD2 A:HIS0 3.8 70.0 1.0 CG A:HIS0 4.4 70.3 1.0 ND1 A:HIS-2 4.7 73.1 1.0 CD2 A:HIS-2 4.9 64.2 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2007 b:77.0 occ:1.00 NE2 A:HIS-4 2.4 70.8 1.0 CD2 A:HIS-4 3.3 68.4 1.0 CE1 A:HIS-4 3.4 70.9 1.0 CE1 A:HIS-3 4.1 67.3 1.0 ND1 A:HIS-4 4.4 61.2 1.0 CG A:HIS-4 4.5 65.0 1.0 NE2 A:HIS-3 4.6 74.2 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2008 b:65.7 occ:1.00 O A:HOH2426 2.3 50.3 1.0 NE2 A:HIS-1 3.1 60.2 1.0 CD2 A:HIS-1 3.5 63.2 1.0 O A:HOH2533 4.1 52.9 1.0 CE1 A:HIS-1 4.2 61.1 1.0 O A:HOH2167 4.3 44.1 1.0 OD2 A:ASP65 4.7 40.5 1.0 CG A:HIS-1 4.8 68.3 1.0 CB A:ASP65 4.9 45.4 1.0 OE1 A:GLU63 5.0 63.8 1.0

A.Gilep, T.Varaksa, S.Bukhdruker, A.Kavaleuski, Y.Ryzhykau, S.Smolskaya, T.Sushko, K.Tsumoto, I.Grabovec, I.Kapranov, I.Okhrimenko, E.Marin, M.Shevtsov, A.Mishin, K.Kovalev, A.Kuklin, V.Gordeliy, L.Kaluzhskiy, O.Gnedenko, E.Yablokov, A.Ivanov, V.Borshchevskiy, N.Strushkevich. Structural Insights Into 3FE-4S Ferredoxins Diversity in M. Tuberculosis Highlighted By A First Redox Complex with P450. Front Mol Biosci V. 9 00032 2022.
ISSN: ESSN 2296-889X
PubMed: 36699703
DOI: 10.3389/FMOLB.2022.1100032