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Iron 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:

Nickel (Ni) 6 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis, PDB code: 8amq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8amq

Go back to Iron Binding Sites List in 8amq
Iron binding site 1 out of 4 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe2001

b:19.9
occ:1.00
FE1 A:F3S2001 0.0 19.9 1.0
S2 A:F3S2001 2.3 20.9 1.0
S1 A:F3S2001 2.3 20.9 1.0
S3 A:F3S2001 2.3 22.9 1.0
SG A:CYS54 2.3 19.8 1.0
FE3 A:F3S2001 2.6 19.9 1.0
FE4 A:F3S2001 2.6 19.9 1.0
CB A:CYS54 3.3 17.6 1.0
S4 A:F3S2001 3.8 21.9 1.0
CA A:CYS54 4.0 18.1 1.0
CB A:ALA58 4.5 21.2 1.0
CD A:PRO55 4.5 18.4 1.0
CB A:HIS13 4.6 16.1 1.0
C A:CYS54 4.7 16.5 1.0
CD2 A:HIS13 4.7 15.8 1.0
SG A:CYS16 4.8 21.5 1.0
N A:HIS13 4.8 16.0 1.0
SG A:CYS10 4.8 23.1 1.0
N A:PRO55 4.8 16.9 1.0
N A:ALA14 4.9 15.0 1.0
N A:GLU56 5.0 18.1 1.0

Iron binding site 2 out of 4 in 8amq

Go back to Iron Binding Sites List in 8amq
Iron binding site 2 out of 4 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe2001

b:19.9
occ:1.00
FE3 A:F3S2001 0.0 19.9 1.0
S4 A:F3S2001 2.3 21.9 1.0
S3 A:F3S2001 2.3 22.9 1.0
S1 A:F3S2001 2.3 20.9 1.0
SG A:CYS16 2.3 21.5 1.0
FE1 A:F3S2001 2.6 19.9 1.0
FE4 A:F3S2001 2.7 19.9 1.0
CB A:CYS16 3.5 18.2 1.0
N A:ALA14 3.9 15.0 1.0
S2 A:F3S2001 4.0 20.9 1.0
N A:CYS16 4.0 17.1 1.0
CA A:ALA14 4.1 16.1 1.0
CB A:SER32 4.3 24.0 1.0
CA A:CYS16 4.4 18.4 1.0
N A:GLN15 4.5 20.3 0.5
N A:GLN15 4.5 20.3 0.5
CD1 A:LEU59 4.6 22.2 1.0
C A:ALA14 4.6 20.3 1.0
SG A:CYS54 4.7 19.8 1.0
O A:HOH2164 4.8 22.3 1.0
SG A:CYS10 4.8 23.1 1.0
N A:SER32 5.0 25.9 1.0
CB A:CYS54 5.0 17.6 1.0

Iron binding site 3 out of 4 in 8amq

Go back to Iron Binding Sites List in 8amq
Iron binding site 3 out of 4 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe2001

b:19.9
occ:1.00
FE4 A:F3S2001 0.0 19.9 1.0
S3 A:F3S2001 2.3 22.9 1.0
S4 A:F3S2001 2.3 21.9 1.0
S2 A:F3S2001 2.3 20.9 1.0
SG A:CYS10 2.3 23.1 1.0
FE1 A:F3S2001 2.6 19.9 1.0
FE3 A:F3S2001 2.7 19.9 1.0
CB A:CYS10 3.4 23.7 1.0
N A:GLY12 3.7 17.9 1.0
CA A:CYS10 3.8 19.3 1.0
S1 A:F3S2001 4.0 20.9 1.0
CA A:GLY12 4.1 18.8 1.0
CB A:SER32 4.1 24.0 1.0
N A:VAL11 4.1 19.7 1.0
N A:SER32 4.3 25.9 1.0
N A:HIS13 4.3 16.0 1.0
C A:CYS10 4.4 21.7 1.0
C A:GLY12 4.6 16.9 1.0
SG A:CYS54 4.7 19.8 1.0
N A:ALA14 4.8 15.0 1.0
CB A:ALA58 4.8 21.2 1.0
CA A:SER32 4.9 28.7 1.0
C A:VAL11 4.9 24.3 1.0
SG A:CYS16 4.9 21.5 1.0
CD1 A:LEU5 5.0 27.4 1.0

Iron binding site 4 out of 4 in 8amq

Go back to Iron Binding Sites List in 8amq
Iron binding site 4 out of 4 in the Crystal Structure of the Complex CYP143-Fdxe From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe2002

b:15.2
occ:1.00
FE A:HEM2002 0.0 15.2 1.0
ND A:HEM2002 2.0 14.3 1.0
NB A:HEM2002 2.1 14.7 1.0
NA A:HEM2002 2.1 13.5 1.0
NC A:HEM2002 2.1 15.2 1.0
O A:HOH2233 2.3 31.7 1.0
SG A:CYS1342 2.3 16.3 1.0
C1D A:HEM2002 3.0 20.9 1.0
C1B A:HEM2002 3.1 17.5 1.0
C4B A:HEM2002 3.1 14.2 1.0
C4D A:HEM2002 3.1 14.5 1.0
C4C A:HEM2002 3.1 16.2 1.0
C1C A:HEM2002 3.1 15.1 1.0
C1A A:HEM2002 3.1 14.8 1.0
C4A A:HEM2002 3.1 14.3 1.0
CB A:CYS1342 3.3 12.2 1.0
CHD A:HEM2002 3.4 22.3 1.0
CHC A:HEM2002 3.4 12.8 1.0
CHB A:HEM2002 3.4 18.8 1.0
CHA A:HEM2002 3.5 14.3 1.0
CA A:CYS1342 4.1 12.7 1.0
O A:HOH2444 4.2 42.6 1.0
C3C A:HEM2002 4.3 14.7 1.0
C3B A:HEM2002 4.3 13.0 1.0
C2D A:HEM2002 4.3 14.8 1.0
C3D A:HEM2002 4.3 17.7 1.0
C2B A:HEM2002 4.3 13.6 1.0
C2C A:HEM2002 4.3 14.7 1.0
C3A A:HEM2002 4.3 17.2 1.0
C2A A:HEM2002 4.3 15.4 1.0
N A:GLY1344 4.6 14.1 1.0
O A:ALA1232 4.7 26.1 1.0
C A:CYS1342 4.7 17.4 1.0
N A:LEU1343 4.8 14.4 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: Fri Aug 9 17:57:48 2024

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