Atomistry » Nickel » PDB 7z5r-8cja » 8amq
Atomistry »
  Nickel »
    PDB 7z5r-8cja »
      8amq »

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

Protein crystallography data

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

Other elements in 8amq:

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

Iron (Fe) 4 atoms

Nickel Binding Sites:

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 8amq

Go back to Nickel Binding Sites List in 8amq
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 8amq

Go back to Nickel Binding Sites List in 8amq
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 8amq

Go back to Nickel Binding Sites List in 8amq
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 8amq

Go back to Nickel Binding Sites List in 8amq
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 8amq

Go back to Nickel Binding Sites List in 8amq
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 8amq

Go back to Nickel Binding Sites List in 8amq
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

Reference:

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
Page generated: Thu Oct 10 09:34:59 2024

Last articles

Zn in 1IJL
Zn in 1IJ1
Zn in 1IJ0
Zn in 1IGB
Zn in 1IF9
Zn in 1IF8
Zn in 1IF7
Zn in 1IF6
Zn in 1IF5
Zn in 1IF4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy