Iron in PDB 8w1w: 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor

Enzymatic activity of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor

All present enzymatic activity of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor:
1.11.1.21;

Protein crystallography data

The structure of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor, PDB code: 8w1w was solved by A.Liu, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.99 / 2.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.674, 150.674, 311.112, 90, 90, 90
R / Rfree (%) 16.6 / 22.3

Other elements in 8w1w:

The structure of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor (pdb code 8w1w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor, PDB code: 8w1w:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8w1w

Go back to Iron Binding Sites List in 8w1w
Iron binding site 1 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:13.3
occ:1.00
 FE A:HEM801 0.0 13.3 1.0
ND A:HEM801 2.0 12.4 1.0
NA A:HEM801 2.0 10.5 1.0
NB A:HEM801 2.0 13.4 1.0
NC A:HEM801 2.1 10.6 1.0
NE2 A:HIS270 2.3 14.5 1.0
O2 A:TOX107 2.9 16.9 1.0
C4D A:HEM801 3.0 11.4 1.0
C1D A:HEM801 3.0 11.8 1.0
C1A A:HEM801 3.0 12.3 1.0
C1C A:HEM801 3.0 10.0 1.0
C4C A:HEM801 3.0 9.5 1.0
C4B A:HEM801 3.1 13.4 1.0
C4A A:HEM801 3.1 13.8 1.0
C1B A:HEM801 3.1 13.7 1.0
CD2 A:HIS270 3.1 12.0 1.0
CHD A:HEM801 3.4 11.6 1.0
CE1 A:HIS270 3.4 13.7 1.0
CHA A:HEM801 3.4 13.5 1.0
CHC A:HEM801 3.4 11.4 1.0
CHB A:HEM801 3.5 13.7 1.0
O1 A:TOX107 3.6 15.8 1.0
C3D A:HEM801 4.2 10.3 1.0
C2D A:HEM801 4.2 14.2 1.0
C2C A:HEM801 4.3 10.5 1.0
C2A A:HEM801 4.3 14.0 1.0
C3C A:HEM801 4.3 10.0 1.0
C3B A:HEM801 4.3 12.4 1.0
C2B A:HEM801 4.3 14.9 1.0
C3A A:HEM801 4.3 12.0 1.0
NE1 A:TOX107 4.3 10.4 1.0
CG A:HIS270 4.4 11.4 1.0
ND1 A:HIS270 4.4 12.2 1.0
CD1 A:TOX107 4.6 9.3 1.0
O A:HOH1366 4.7 15.9 1.0
CH2 A:TRP321 4.9 13.0 1.0
CZ2 A:TRP321 5.0 14.3 1.0

Iron binding site 2 out of 4 in 8w1w

Go back to Iron Binding Sites List in 8w1w
Iron binding site 2 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:12.2
occ:1.00
 FE B:HEM801 0.0 12.2 1.0
NB B:HEM801 1.9 11.1 1.0
NA B:HEM801 2.0 11.6 1.0
ND B:HEM801 2.0 11.1 1.0
NC B:HEM801 2.1 10.0 1.0
NE2 B:HIS270 2.3 11.8 1.0
O2 B:TOX107 2.8 13.9 1.0
C4B B:HEM801 2.9 12.0 1.0
C1B B:HEM801 3.0 11.5 1.0
C4D B:HEM801 3.0 11.3 1.0
C1A B:HEM801 3.0 12.6 1.0
C1C B:HEM801 3.0 8.9 1.0
C4A B:HEM801 3.0 11.8 1.0
C1D B:HEM801 3.0 11.0 1.0
C4C B:HEM801 3.1 9.4 1.0
CD2 B:HIS270 3.2 11.0 1.0
CHC B:HEM801 3.4 12.7 1.0
CHA B:HEM801 3.4 11.5 1.0
CE1 B:HIS270 3.4 10.5 1.0
CHB B:HEM801 3.4 11.9 1.0
CHD B:HEM801 3.5 9.2 1.0
O1 B:TOX107 3.7 18.8 1.0
C3B B:HEM801 4.1 12.3 1.0
C2B B:HEM801 4.1 13.2 1.0
C3D B:HEM801 4.2 8.8 1.0
C2D B:HEM801 4.2 11.2 1.0
C2C B:HEM801 4.3 10.6 1.0
C3A B:HEM801 4.3 13.9 1.0
C2A B:HEM801 4.3 12.2 1.0
C3C B:HEM801 4.3 9.3 1.0
NE1 B:TOX107 4.3 10.9 1.0
CG B:HIS270 4.4 11.2 1.0
ND1 B:HIS270 4.5 11.0 1.0
CD1 B:TOX107 4.6 9.8 1.0
O B:HOH1234 4.8 19.2 1.0
CH2 B:TRP321 4.8 11.2 1.0
CZ2 B:TRP321 4.9 15.7 1.0
O B:HOH1449 4.9 24.1 1.0

Iron binding site 3 out of 4 in 8w1w

Go back to Iron Binding Sites List in 8w1w
Iron binding site 3 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:10.9
occ:1.00
 FE C:HEM801 0.0 10.9 1.0
NA C:HEM801 2.0 11.7 1.0
NB C:HEM801 2.0 9.9 1.0
ND C:HEM801 2.1 11.1 1.0
NC C:HEM801 2.1 9.1 1.0
NE2 C:HIS270 2.3 12.7 1.0
O2 C:TOX107 3.0 16.2 1.0
C4B C:HEM801 3.0 11.6 1.0
C1D C:HEM801 3.0 7.8 1.0
C1A C:HEM801 3.0 11.4 1.0
C4D C:HEM801 3.0 11.2 1.0
C1B C:HEM801 3.1 10.6 1.0
C4A C:HEM801 3.1 11.7 1.0
C4C C:HEM801 3.1 9.2 1.0
C1C C:HEM801 3.1 9.0 1.0
CD2 C:HIS270 3.1 9.5 1.0
CHD C:HEM801 3.3 7.7 1.0
CE1 C:HIS270 3.4 10.2 1.0
CHA C:HEM801 3.4 10.2 1.0
CHC C:HEM801 3.4 8.5 1.0
CHB C:HEM801 3.5 12.2 1.0
O1 C:TOX107 3.7 14.7 1.0
C3B C:HEM801 4.2 10.2 1.0
C2D C:HEM801 4.2 8.4 1.0
C2B C:HEM801 4.2 10.9 1.0
C3D C:HEM801 4.2 10.1 1.0
C2A C:HEM801 4.3 10.1 1.0
C3A C:HEM801 4.3 10.3 1.0
C2C C:HEM801 4.3 8.4 1.0
C3C C:HEM801 4.3 7.6 1.0
CG C:HIS270 4.4 11.4 1.0
NE1 C:TOX107 4.4 11.4 1.0
ND1 C:HIS270 4.4 9.2 1.0
CD1 C:TOX107 4.7 9.3 1.0
O C:HOH1336 4.8 16.5 1.0
CH2 C:TRP321 4.9 10.6 1.0
O C:HOH1430 4.9 24.7 1.0
CZ2 C:TRP321 5.0 9.4 1.0

Iron binding site 4 out of 4 in 8w1w

Go back to Iron Binding Sites List in 8w1w
Iron binding site 4 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:11.6
occ:1.00
 FE D:HEM801 0.0 11.6 1.0
NC D:HEM801 2.0 8.6 1.0
ND D:HEM801 2.0 9.3 1.0
NB D:HEM801 2.1 9.9 1.0
NA D:HEM801 2.1 10.9 1.0
NE2 D:HIS270 2.3 10.7 1.0
O2 D:TOX107 3.0 15.8 1.0
C4D D:HEM801 3.0 10.8 1.0
C4B D:HEM801 3.0 8.6 1.0
C1C D:HEM801 3.0 10.3 1.0
C1D D:HEM801 3.0 11.0 1.0
C4C D:HEM801 3.0 9.5 1.0
CD2 D:HIS270 3.1 9.5 1.0
C1A D:HEM801 3.1 10.5 1.0
C1B D:HEM801 3.1 11.0 1.0
C4A D:HEM801 3.1 12.1 1.0
CHC D:HEM801 3.4 12.0 1.0
CE1 D:HIS270 3.4 11.7 1.0
CHA D:HEM801 3.4 9.2 1.0
CHD D:HEM801 3.4 8.3 1.0
CHB D:HEM801 3.5 10.5 1.0
O1 D:TOX107 3.6 13.0 1.0
C2D D:HEM801 4.2 10.7 1.0
C3D D:HEM801 4.2 8.6 1.0
C3C D:HEM801 4.3 7.8 1.0
C3B D:HEM801 4.3 11.0 1.0
C2C D:HEM801 4.3 8.0 1.0
C2B D:HEM801 4.3 10.5 1.0
CG D:HIS270 4.3 9.2 1.0
C2A D:HEM801 4.3 12.7 1.0
C3A D:HEM801 4.3 12.9 1.0
NE1 D:TOX107 4.3 11.3 1.0
ND1 D:HIS270 4.4 9.8 1.0
CD1 D:TOX107 4.6 8.4 1.0
CH2 D:TRP321 4.7 10.2 1.0
CZ2 D:TRP321 4.9 11.1 1.0
O D:HOH1347 4.9 17.1 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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