Iron in PDB 5xvz: Catpo Mutant - H246W

Enzymatic activity of Catpo Mutant - H246W

All present enzymatic activity of Catpo Mutant - H246W:
1.11.1.6;

Protein crystallography data

The structure of Catpo Mutant - H246W, PDB code: 5xvz was solved by Y.Yuzugullu Karakus, G.Goc, S.Balci, A.R.Pearson, B.Yorke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.69 / 1.90
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.338, 120.785, 185.200, 90.00, 102.06, 90.00
R / Rfree (%) 15.8 / 18.7

Other elements in 5xvz:

The structure of Catpo Mutant - H246W also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Catpo Mutant - H246W (pdb code 5xvz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Catpo Mutant - H246W, PDB code: 5xvz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5xvz

Go back to Iron Binding Sites List in 5xvz
Iron binding site 1 out of 4 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.8
occ:1.00
FE A:HDD701 0.0 17.8 1.0
OH A:TYR369 1.9 16.8 1.0
ND A:HDD701 2.0 16.1 1.0
NA A:HDD701 2.0 15.6 1.0
NC A:HDD701 2.0 15.5 1.0
NB A:HDD701 2.1 16.6 1.0
CZ A:TYR369 3.0 16.7 1.0
C4A A:HDD701 3.0 15.8 1.0
C4D A:HDD701 3.0 16.2 1.0
C4C A:HDD701 3.0 16.1 1.0
C1C A:HDD701 3.0 15.0 1.0
C1A A:HDD701 3.0 14.9 1.0
C1D A:HDD701 3.1 17.0 1.0
C4B A:HDD701 3.1 16.2 1.0
C1B A:HDD701 3.1 16.5 1.0
CHB A:HDD701 3.4 16.5 1.0
CHA A:HDD701 3.4 15.6 1.0
CHC A:HDD701 3.4 15.5 1.0
CHD A:HDD701 3.5 15.5 1.0
CE2 A:TYR369 3.7 16.8 1.0
CE1 A:TYR369 3.8 15.9 1.0
NE A:ARG365 4.1 15.7 1.0
NH2 A:ARG365 4.2 14.4 1.0
C3C A:HDD701 4.3 16.1 1.0
C3B A:HDD701 4.3 16.9 1.0
C2A A:HDD701 4.3 14.8 1.0
C3A A:HDD701 4.3 14.1 1.0
C2C A:HDD701 4.3 15.2 1.0
C3D A:HDD701 4.4 18.9 1.0
C2B A:HDD701 4.4 16.8 1.0
C2D A:HDD701 4.4 18.0 1.0
CG2 A:VAL81 4.5 14.8 1.0
CZ A:PHE168 4.6 17.2 1.0
CZ A:ARG365 4.6 15.5 1.0
NE2 A:HIS82 4.8 15.6 1.0
CD2 A:HIS82 4.8 16.0 1.0
CE2 A:PHE168 4.9 17.1 1.0
CD2 A:TYR369 5.0 16.8 1.0

Iron binding site 2 out of 4 in 5xvz

Go back to Iron Binding Sites List in 5xvz
Iron binding site 2 out of 4 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:17.8
occ:1.00
FE B:HDD701 0.0 17.8 1.0
ND B:HDD701 2.0 17.1 1.0
OH B:TYR369 2.0 17.3 1.0
NC B:HDD701 2.0 16.3 1.0
NA B:HDD701 2.0 16.1 1.0
NB B:HDD701 2.1 17.4 1.0
CZ B:TYR369 3.0 16.4 1.0
C4C B:HDD701 3.0 16.9 1.0
C4D B:HDD701 3.0 17.5 1.0
C1D B:HDD701 3.0 17.9 1.0
C1A B:HDD701 3.0 16.3 1.0
C4A B:HDD701 3.0 16.2 1.0
C1B B:HDD701 3.1 17.2 1.0
C1C B:HDD701 3.1 16.1 1.0
C4B B:HDD701 3.1 16.8 1.0
CHA B:HDD701 3.4 16.5 1.0
CHD B:HDD701 3.4 16.6 1.0
CHB B:HDD701 3.4 16.7 1.0
CHC B:HDD701 3.5 16.2 1.0
CE2 B:TYR369 3.7 16.4 1.0
CE1 B:TYR369 3.8 17.1 1.0
NE B:ARG365 4.1 15.3 1.0
NH2 B:ARG365 4.2 16.4 1.0
C3C B:HDD701 4.3 16.8 1.0
C2D B:HDD701 4.3 18.6 1.0
C2A B:HDD701 4.3 16.0 1.0
C3B B:HDD701 4.3 17.5 1.0
C3D B:HDD701 4.3 19.4 1.0
C3A B:HDD701 4.3 15.4 1.0
C2C B:HDD701 4.3 16.6 1.0
C2B B:HDD701 4.4 17.1 1.0
CG2 B:VAL81 4.5 16.7 1.0
CZ B:PHE168 4.6 18.8 1.0
CZ B:ARG365 4.6 16.4 1.0
CD2 B:HIS82 4.8 15.1 1.0
NE2 B:HIS82 4.8 15.0 1.0
CE2 B:PHE168 4.9 19.0 1.0
CD2 B:TYR369 5.0 16.8 1.0

Iron binding site 3 out of 4 in 5xvz

Go back to Iron Binding Sites List in 5xvz
Iron binding site 3 out of 4 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe701

b:18.4
occ:1.00
FE C:HDD701 0.0 18.4 1.0
OH C:TYR369 1.9 15.4 1.0
ND C:HDD701 2.0 17.9 1.0
NC C:HDD701 2.0 19.1 1.0
NA C:HDD701 2.1 17.8 1.0
NB C:HDD701 2.1 18.9 1.0
O C:HOH1184 2.9 34.7 1.0
CZ C:TYR369 3.0 17.3 1.0
C1D C:HDD701 3.0 18.8 1.0
C4C C:HDD701 3.0 19.0 1.0
C4D C:HDD701 3.0 17.1 1.0
C4A C:HDD701 3.0 17.6 1.0
C1C C:HDD701 3.1 18.9 1.0
C1A C:HDD701 3.1 17.6 1.0
C4B C:HDD701 3.1 18.9 1.0
C1B C:HDD701 3.1 19.2 1.0
CHD C:HDD701 3.4 18.6 1.0
CHC C:HDD701 3.4 18.2 1.0
CHB C:HDD701 3.4 18.4 1.0
CHA C:HDD701 3.4 16.1 1.0
CE2 C:TYR369 3.8 17.4 1.0
CE1 C:TYR369 3.8 17.2 1.0
NE C:ARG365 4.1 16.8 1.0
NH2 C:ARG365 4.2 15.1 1.0
C3C C:HDD701 4.3 19.0 1.0
C3D C:HDD701 4.4 18.9 1.0
C3A C:HDD701 4.4 17.5 1.0
C2D C:HDD701 4.4 19.5 1.0
C2A C:HDD701 4.4 16.2 1.0
C2C C:HDD701 4.4 18.3 1.0
O C:HOH1052 4.4 22.8 1.0
C3B C:HDD701 4.4 20.1 1.0
C2B C:HDD701 4.4 20.8 1.0
CG2 C:VAL81 4.5 15.2 1.0
CZ C:PHE168 4.5 18.0 1.0
CZ C:ARG365 4.6 17.4 1.0
NE2 C:HIS82 4.8 19.2 1.0
CD2 C:HIS82 4.8 18.5 1.0
CE2 C:PHE168 4.9 18.8 1.0

Iron binding site 4 out of 4 in 5xvz

Go back to Iron Binding Sites List in 5xvz
Iron binding site 4 out of 4 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe701

b:18.3
occ:1.00
FE D:HDD701 0.0 18.3 1.0
OH D:TYR369 2.0 15.8 1.0
ND D:HDD701 2.0 18.6 1.0
NA D:HDD701 2.0 17.7 1.0
NC D:HDD701 2.1 19.4 1.0
NB D:HDD701 2.1 19.5 1.0
O D:HOH1149 2.8 39.6 1.0
CZ D:TYR369 3.0 18.1 1.0
C4A D:HDD701 3.0 18.3 1.0
C1B D:HDD701 3.1 19.0 1.0
C1D D:HDD701 3.1 18.6 1.0
C4B D:HDD701 3.1 20.7 1.0
C4C D:HDD701 3.1 18.0 1.0
C4D D:HDD701 3.1 17.9 1.0
C1C D:HDD701 3.1 19.0 1.0
C1A D:HDD701 3.1 17.9 1.0
CHB D:HDD701 3.4 18.6 1.0
CHC D:HDD701 3.4 19.5 1.0
CHD D:HDD701 3.4 18.1 1.0
CHA D:HDD701 3.5 17.4 1.0
CE2 D:TYR369 3.7 18.1 1.0
CE1 D:TYR369 3.8 18.6 1.0
NE D:ARG365 4.1 17.7 1.0
NH2 D:ARG365 4.2 18.0 1.0
C3C D:HDD701 4.3 17.9 1.0
C3A D:HDD701 4.3 18.3 1.0
C3B D:HDD701 4.3 20.1 1.0
C2B D:HDD701 4.3 19.1 1.0
C2A D:HDD701 4.3 16.9 1.0
C2C D:HDD701 4.4 17.9 1.0
C3D D:HDD701 4.4 18.7 1.0
C2D D:HDD701 4.4 19.5 1.0
O D:HOH1105 4.5 21.3 1.0
CG2 D:VAL81 4.5 16.8 1.0
CZ D:ARG365 4.6 18.4 1.0
CZ D:PHE168 4.6 20.3 1.0
CD2 D:HIS82 4.7 19.5 1.0
NE2 D:HIS82 4.8 20.0 1.0

Reference:

Y.Yuzugullu Karakus, G.Goc, S.Balci, B.A.Yorke, C.H.Trinh, M.J.Mcpherson, A.R.Pearson. Identification of the Site of Oxidase Substrate Binding in Scytalidium Thermophilum Catalase. Acta Crystallogr D Struct V. 74 979 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289408
DOI: 10.1107/S2059798318010628
Page generated: Sun Dec 13 16:18:01 2020

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