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Iron in PDB 8dwr: Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis, PDB code: 8dwr was solved by A.Diaz-Vilchis, B.Uribe-Vazquez, A.Avila-Linares, E.Rudino-Pinera, X.Soberon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.671, 150.817, 127.037, 90, 90.45, 90
R / Rfree (%) 18.1 / 22.7

Other elements in 8dwr:

The structure of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis (pdb code 8dwr). 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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis, PDB code: 8dwr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8dwr

Go back to Iron Binding Sites List in 8dwr
Iron binding site 1 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium 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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:15.0
occ:1.00
FE A:HEM801 0.0 15.0 1.0
NC A:HEM801 2.0 11.6 1.0
NA A:HEM801 2.0 14.1 1.0
ND A:HEM801 2.1 14.6 1.0
NB A:HEM801 2.1 12.2 1.0
NE2 A:HIS270 2.6 14.1 1.0
O2 A:TOX107 2.7 19.0 1.0
C4D A:HEM801 3.0 12.3 1.0
C1D A:HEM801 3.0 12.7 1.0
C1C A:HEM801 3.1 15.1 1.0
C1A A:HEM801 3.1 11.3 1.0
C4B A:HEM801 3.1 14.2 1.0
C4C A:HEM801 3.1 11.5 1.0
C4A A:HEM801 3.1 15.4 1.0
C1B A:HEM801 3.1 14.5 1.0
CD2 A:HIS270 3.3 14.0 1.0
CHA A:HEM801 3.4 12.8 1.0
CHC A:HEM801 3.4 12.1 1.0
CHD A:HEM801 3.4 9.5 1.0
CHB A:HEM801 3.5 11.0 1.0
O1 A:TOX107 3.5 23.5 1.0
CE1 A:HIS270 3.7 10.5 1.0
C2D A:HEM801 4.2 10.6 1.0
C3D A:HEM801 4.2 13.7 1.0
NE1 A:TOX107 4.3 11.8 1.0
C2A A:HEM801 4.3 13.5 1.0
C2C A:HEM801 4.3 11.5 1.0
C3C A:HEM801 4.3 10.1 1.0
C3B A:HEM801 4.3 12.0 1.0
C3A A:HEM801 4.3 17.5 1.0
C2B A:HEM801 4.3 13.9 1.0
O A:HOH1195 4.4 18.1 1.0
CD1 A:TOX107 4.4 11.1 1.0
CG A:HIS270 4.6 16.9 1.0
ND1 A:HIS270 4.7 15.9 1.0
O A:HOH1404 4.9 25.5 1.0

Iron binding site 2 out of 4 in 8dwr

Go back to Iron Binding Sites List in 8dwr
Iron binding site 2 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium 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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:16.1
occ:1.00
FE B:HEM802 0.0 16.1 1.0
NA B:HEM802 2.0 14.9 1.0
ND B:HEM802 2.0 14.5 1.0
NC B:HEM802 2.1 14.6 1.0
NB B:HEM802 2.1 12.7 1.0
NE2 B:HIS270 2.6 19.5 1.0
O2 B:TOX107 2.7 21.5 1.0
C1D B:HEM802 3.0 14.1 1.0
C4D B:HEM802 3.1 14.4 1.0
C4B B:HEM802 3.1 15.8 1.0
C1A B:HEM802 3.1 15.0 1.0
C4C B:HEM802 3.1 13.7 1.0
C1B B:HEM802 3.1 14.5 1.0
C4A B:HEM802 3.1 15.5 1.0
C1C B:HEM802 3.1 13.8 1.0
CD2 B:HIS270 3.3 13.8 1.0
CHD B:HEM802 3.4 13.2 1.0
CHA B:HEM802 3.4 14.0 1.0
CHC B:HEM802 3.4 14.4 1.0
CHB B:HEM802 3.4 15.7 1.0
O1 B:TOX107 3.5 25.7 1.0
CE1 B:HIS270 3.7 15.0 1.0
C2D B:HEM802 4.2 13.2 1.0
C3D B:HEM802 4.2 11.8 1.0
C3B B:HEM802 4.3 17.8 1.0
C2B B:HEM802 4.3 16.3 1.0
NE1 B:TOX107 4.3 17.2 1.0
C2A B:HEM802 4.3 15.7 1.0
C3A B:HEM802 4.3 17.3 1.0
C3C B:HEM802 4.3 13.9 1.0
C2C B:HEM802 4.3 13.5 1.0
CD1 B:TOX107 4.5 14.8 1.0
CG B:HIS270 4.6 15.9 1.0
O B:HOH1349 4.7 26.8 1.0
ND1 B:HIS270 4.7 17.4 1.0
O B:HOH1219 4.9 19.3 1.0

Iron binding site 3 out of 4 in 8dwr

Go back to Iron Binding Sites List in 8dwr
Iron binding site 3 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium 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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:20.7
occ:1.00
FE C:HEM801 0.0 20.7 1.0
ND C:HEM801 2.0 17.6 1.0
NC C:HEM801 2.0 15.6 1.0
NA C:HEM801 2.0 18.0 1.0
NB C:HEM801 2.1 17.9 1.0
NE2 C:HIS270 2.6 23.4 1.0
O2 C:TOX107 2.7 21.3 1.0
C1D C:HEM801 3.0 17.2 1.0
C4D C:HEM801 3.0 20.9 1.0
C4C C:HEM801 3.1 13.0 1.0
C1A C:HEM801 3.1 18.8 1.0
C4B C:HEM801 3.1 20.6 1.0
C1C C:HEM801 3.1 21.0 1.0
C4A C:HEM801 3.1 17.6 1.0
C1B C:HEM801 3.1 16.4 1.0
CD2 C:HIS270 3.3 19.5 1.0
CHD C:HEM801 3.4 16.5 1.0
CHA C:HEM801 3.4 20.4 1.0
CHC C:HEM801 3.4 18.8 1.0
CHB C:HEM801 3.5 17.2 1.0
O1 C:TOX107 3.5 25.4 1.0
CE1 C:HIS270 3.7 21.0 1.0
NE1 C:TOX107 4.2 18.1 1.0
C2D C:HEM801 4.2 18.5 1.0
C3D C:HEM801 4.2 18.3 1.0
C2C C:HEM801 4.3 15.8 1.0
C3C C:HEM801 4.3 18.6 1.0
C2A C:HEM801 4.3 17.1 1.0
C3B C:HEM801 4.3 19.5 1.0
C2B C:HEM801 4.3 19.3 1.0
C3A C:HEM801 4.3 18.8 1.0
CD1 C:TOX107 4.4 16.7 1.0
O C:HOH1192 4.5 26.8 1.0
CG C:HIS270 4.5 23.4 1.0
ND1 C:HIS270 4.7 22.8 1.0
CH2 C:TRP321 5.0 19.1 1.0

Iron binding site 4 out of 4 in 8dwr

Go back to Iron Binding Sites List in 8dwr
Iron binding site 4 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium 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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:21.6
occ:1.00
FE D:HEM801 0.0 21.6 1.0
NC D:HEM801 2.0 22.3 1.0
ND D:HEM801 2.0 16.7 1.0
NA D:HEM801 2.0 21.5 1.0
NB D:HEM801 2.1 15.8 1.0
NE2 D:HIS270 2.6 25.4 1.0
O2 D:TOX107 2.7 26.2 1.0
C1D D:HEM801 3.0 16.5 1.0
C4C D:HEM801 3.0 18.4 1.0
C4D D:HEM801 3.1 21.8 1.0
C1C D:HEM801 3.1 18.4 1.0
C4A D:HEM801 3.1 18.4 1.0
C4B D:HEM801 3.1 21.7 1.0
C1B D:HEM801 3.1 21.9 1.0
C1A D:HEM801 3.1 19.7 1.0
CD2 D:HIS270 3.3 20.2 1.0
CHD D:HEM801 3.4 18.2 1.0
O1 D:TOX107 3.4 32.0 1.0
CHA D:HEM801 3.4 20.4 1.0
CHC D:HEM801 3.4 22.3 1.0
CHB D:HEM801 3.4 21.1 1.0
CE1 D:HIS270 3.7 22.5 1.0
NE1 D:TOX107 4.1 23.8 1.0
C2D D:HEM801 4.2 20.1 1.0
C3D D:HEM801 4.2 16.3 1.0
C3C D:HEM801 4.3 19.2 1.0
C2C D:HEM801 4.3 17.6 1.0
C2B D:HEM801 4.3 20.7 1.0
C3B D:HEM801 4.3 18.4 1.0
C2A D:HEM801 4.3 20.9 1.0
C3A D:HEM801 4.3 20.3 1.0
CD1 D:TOX107 4.3 19.3 1.0
CG D:HIS270 4.6 20.8 1.0
ND1 D:HIS270 4.7 27.6 1.0
O D:HOH1256 4.7 32.7 1.0
O D:HOH1137 4.7 25.2 1.0
CH2 D:TRP321 5.0 23.4 1.0

Reference:

B.Uribe-Vazquez, A.Diaz-Vilchis, A.Avila-Linares, G.Saab-Rincon, Y.Marin-Tovar, H.Flores-Soto, N.Pastor-Colon, E.Rudino-Pinera, X.Soberon. Crystal Structure and Biochemical Characterization of the Mycobacterium Tuberculosis Katg-L333V From A Clinical Isolate To Be Published.
Page generated: Thu Dec 28 05:56:22 2023

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