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Iron in PDB 8w1y: 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute

Enzymatic activity of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute

All present enzymatic activity of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute:
1.11.1.21;

Protein crystallography data

The structure of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute, PDB code: 8w1y was solved by J.Li, R.Duan, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.93 / 2.30
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 150.511, 150.511, 155.225, 90, 90, 90
R / Rfree (%) 19.1 / 24.7

Other elements in 8w1y:

The structure of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute (pdb code 8w1y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute, PDB code: 8w1y:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8w1y

Go back to Iron Binding Sites List in 8w1y
Iron binding site 1 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:27.8
occ:1.00
 FE A:HEM801 0.0 27.8 1.0
NB A:HEM801 2.0 25.9 1.0
NA A:HEM801 2.0 30.1 1.0
ND A:HEM801 2.1 25.8 1.0
NC A:HEM801 2.1 27.7 1.0
NE2 A:HIS270 2.3 28.6 1.0
O2 A:TOX107 2.7 25.7 0.3
C4B A:HEM801 3.0 26.3 1.0
C1B A:HEM801 3.0 25.7 1.0
C4A A:HEM801 3.0 23.3 1.0
C1A A:HEM801 3.1 30.5 1.0
C4D A:HEM801 3.1 30.4 1.0
C1D A:HEM801 3.1 30.2 1.0
C1C A:HEM801 3.1 23.9 1.0
C4C A:HEM801 3.1 27.3 1.0
CD2 A:HIS270 3.2 32.2 1.0
O1 A:TOX107 3.2 39.2 1.0
CE1 A:HIS270 3.3 29.1 1.0
CHC A:HEM801 3.4 28.1 1.0
CHB A:HEM801 3.4 21.2 1.0
CHA A:HEM801 3.4 30.6 1.0
CHD A:HEM801 3.5 25.5 1.0
NE1 A:TOX107 4.1 27.0 1.0
C3B A:HEM801 4.2 25.2 1.0
C2B A:HEM801 4.2 31.5 1.0
C3A A:HEM801 4.3 27.3 1.0
C2D A:HEM801 4.3 30.1 1.0
C3D A:HEM801 4.3 28.7 1.0
C2A A:HEM801 4.3 25.2 1.0
O2 A:TOX107 4.3 28.7 0.7
C2C A:HEM801 4.3 23.6 1.0
CG A:HIS270 4.4 35.2 1.0
C3C A:HEM801 4.4 29.8 1.0
ND1 A:HIS270 4.4 30.7 1.0
CD1 A:TOX107 4.4 24.9 1.0
O A:HOH1056 4.9 27.8 1.0
CH2 A:TRP321 4.9 33.3 1.0

Iron binding site 2 out of 4 in 8w1y

Go back to Iron Binding Sites List in 8w1y
Iron binding site 2 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:27.1
occ:1.00
 FE B:HEM801 0.0 27.1 1.0
ND B:HEM801 1.9 28.1 1.0
NA B:HEM801 2.0 25.1 1.0
NC B:HEM801 2.0 22.7 1.0
NB B:HEM801 2.1 20.8 1.0
NE2 B:HIS270 2.4 27.1 1.0
O2 B:TOX107 2.7 22.2 0.4
C1D B:HEM801 2.9 23.5 1.0
C4D B:HEM801 2.9 25.2 1.0
C1A B:HEM801 2.9 22.7 1.0
C4C B:HEM801 3.0 25.3 1.0
C4A B:HEM801 3.0 22.8 1.0
C1B B:HEM801 3.0 20.4 1.0
C4B B:HEM801 3.0 22.2 1.0
C1C B:HEM801 3.0 25.4 1.0
O1 B:TOX107 3.3 36.1 1.0
CD2 B:HIS270 3.3 25.9 1.0
CHD B:HEM801 3.3 22.5 1.0
CHA B:HEM801 3.3 26.2 1.0
CHB B:HEM801 3.4 20.5 1.0
CHC B:HEM801 3.4 24.4 1.0
CE1 B:HIS270 3.4 25.3 1.0
C2A B:HEM801 4.1 24.3 1.0
C3A B:HEM801 4.1 24.1 1.0
C2D B:HEM801 4.1 24.9 1.0
C3D B:HEM801 4.1 24.6 1.0
C3C B:HEM801 4.1 25.6 1.0
C2C B:HEM801 4.2 24.1 1.0
NE1 B:TOX107 4.2 30.8 1.0
C2B B:HEM801 4.2 23.1 1.0
C3B B:HEM801 4.2 22.9 1.0
O2 B:TOX107 4.4 28.4 0.6
CG B:HIS270 4.5 26.3 1.0
ND1 B:HIS270 4.5 26.2 1.0
CD1 B:TOX107 4.5 23.8 1.0
O B:HOH1129 4.9 26.4 1.0
CH2 B:TRP321 5.0 28.4 1.0

Iron binding site 3 out of 4 in 8w1y

Go back to Iron Binding Sites List in 8w1y
Iron binding site 3 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:25.4
occ:1.00
 FE C:HEM801 0.0 25.4 1.0
NA C:HEM801 2.0 26.1 1.0
NB C:HEM801 2.0 26.6 1.0
ND C:HEM801 2.1 26.7 1.0
NC C:HEM801 2.1 25.3 1.0
NE2 C:HIS270 2.4 27.2 1.0
O2 C:TOX107 2.6 23.7 0.5
C4B C:HEM801 3.0 30.1 1.0
C4A C:HEM801 3.0 21.6 1.0
C1A C:HEM801 3.0 27.3 1.0
C4D C:HEM801 3.0 26.7 1.0
C1B C:HEM801 3.1 23.4 1.0
C1C C:HEM801 3.1 24.6 1.0
C1D C:HEM801 3.1 25.9 1.0
O1 C:TOX107 3.2 38.7 1.0
C4C C:HEM801 3.2 24.7 1.0
CD2 C:HIS270 3.2 29.0 1.0
CHC C:HEM801 3.4 28.5 1.0
CHA C:HEM801 3.4 27.8 1.0
CHB C:HEM801 3.4 20.9 1.0
CE1 C:HIS270 3.5 30.0 1.0
CHD C:HEM801 3.5 24.1 1.0
NE1 C:TOX107 4.1 26.0 1.0
C3B C:HEM801 4.2 30.5 1.0
O2 C:TOX107 4.2 30.4 0.5
C2B C:HEM801 4.2 28.6 1.0
C3A C:HEM801 4.2 25.3 1.0
C3D C:HEM801 4.3 24.8 1.0
C2A C:HEM801 4.3 24.7 1.0
C2D C:HEM801 4.3 27.1 1.0
C2C C:HEM801 4.3 23.8 1.0
C3C C:HEM801 4.4 28.9 1.0
CG C:HIS270 4.4 31.1 1.0
CD1 C:TOX107 4.5 23.8 1.0
ND1 C:HIS270 4.5 30.9 1.0
O C:HOH1094 4.8 30.6 1.0
CH2 C:TRP321 4.9 31.7 1.0
CZ2 C:TRP321 5.0 31.7 1.0

Iron binding site 4 out of 4 in 8w1y

Go back to Iron Binding Sites List in 8w1y
Iron binding site 4 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:26.4
occ:1.00
 FE D:HEM801 0.0 26.4 1.0
NA D:HEM801 2.0 26.1 1.0
NC D:HEM801 2.0 22.0 1.0
NB D:HEM801 2.0 18.1 1.0
ND D:HEM801 2.1 27.7 1.0
NE2 D:HIS270 2.4 28.1 1.0
O2 D:TOX107 2.8 21.9 0.4
C1A D:HEM801 3.0 24.9 1.0
C4A D:HEM801 3.0 24.2 1.0
C4C D:HEM801 3.0 22.0 1.0
C1C D:HEM801 3.0 22.4 1.0
C4B D:HEM801 3.0 22.2 1.0
C1D D:HEM801 3.1 22.2 1.0
C1B D:HEM801 3.1 19.1 1.0
C4D D:HEM801 3.1 24.8 1.0
CD2 D:HIS270 3.2 27.3 1.0
O1 D:TOX107 3.4 35.0 1.0
CHD D:HEM801 3.4 21.7 1.0
CHC D:HEM801 3.4 22.1 1.0
CHB D:HEM801 3.4 19.3 1.0
CHA D:HEM801 3.4 25.0 1.0
CE1 D:HIS270 3.4 23.7 1.0
NE1 D:TOX107 4.2 25.9 1.0
C2A D:HEM801 4.2 27.3 1.0
C3A D:HEM801 4.2 24.7 1.0
C2C D:HEM801 4.3 25.6 1.0
C2D D:HEM801 4.3 24.2 1.0
C3C D:HEM801 4.3 23.2 1.0
C2B D:HEM801 4.3 25.1 1.0
C3B D:HEM801 4.3 21.7 1.0
O2 D:TOX107 4.3 26.7 0.6
C3D D:HEM801 4.3 27.5 1.0
CG D:HIS270 4.4 30.8 1.0
CD1 D:TOX107 4.5 23.2 1.0
ND1 D:HIS270 4.5 26.2 1.0
O D:HOH1168 4.7 29.3 1.0
CH2 D:TRP321 5.0 28.0 1.0

Reference:

J.Li, R.Duan, E.S.Traore, R.C.Nguyen, I.Davis, W.P.Griffth, D.C.Goodwin, A.A.Jarzecki, A.Liu. Indole-N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions. Angew.Chem.Int.Ed.Engl. 07018 2024.
ISSN: ESSN 1521-3773
PubMed: 39300819
DOI: 10.1002/ANIE.202407018
Page generated: Thu Oct 31 20:49:22 2024

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