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Iron in PDB 8j4r: Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli

Enzymatic activity of Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli

All present enzymatic activity of Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli, PDB code: 8j4r was solved by Y.Yoo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.679, 150.643, 164.869, 90, 90, 90
R / Rfree (%) 15.3 / 21

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli (pdb code 8j4r). 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 Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli, PDB code: 8j4r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8j4r

Go back to Iron Binding Sites List in 8j4r
Iron binding site 1 out of 4 in the Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli


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 Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:32.9
occ:1.00
 FE A:HEM801 0.0 32.9 1.0
OH A:TYR415 1.8 30.7 1.0
NA A:HEM801 2.0 30.1 1.0
NC A:HEM801 2.0 32.5 1.0
ND A:HEM801 2.0 30.6 1.0
NB A:HEM801 2.0 36.3 1.0
O A:HOH934 2.5 30.0 1.0
CZ A:TYR415 3.0 28.9 1.0
C4D A:HEM801 3.0 29.1 1.0
C4C A:HEM801 3.0 28.3 1.0
C1B A:HEM801 3.0 32.1 1.0
C1A A:HEM801 3.0 28.7 1.0
C1D A:HEM801 3.0 31.4 1.0
C4B A:HEM801 3.0 31.2 1.0
C1C A:HEM801 3.0 31.7 1.0
C4A A:HEM801 3.1 32.3 1.0
CHD A:HEM801 3.4 28.1 1.0
CHA A:HEM801 3.4 27.6 1.0
CHC A:HEM801 3.4 30.0 1.0
CHB A:HEM801 3.4 30.6 1.0
CE1 A:TYR415 3.7 28.9 1.0
CE2 A:TYR415 3.8 27.4 1.0
NE A:ARG411 4.0 30.9 1.0
C3C A:HEM801 4.2 31.6 1.0
C2A A:HEM801 4.2 27.9 1.0
C2B A:HEM801 4.2 36.2 1.0
C2C A:HEM801 4.2 33.6 1.0
C3A A:HEM801 4.2 29.7 1.0
C3D A:HEM801 4.2 31.5 1.0
C3B A:HEM801 4.2 37.9 1.0
C2D A:HEM801 4.2 31.0 1.0
O A:HOH953 4.3 32.8 1.0
NH2 A:ARG411 4.4 29.6 1.0
CZ A:PHE214 4.4 27.2 1.0
CZ A:ARG411 4.6 36.4 1.0
CG2 A:VAL127 4.7 24.5 1.0
NE2 A:HIS128 4.8 27.1 1.0
CD A:ARG411 4.8 26.5 1.0
CE2 A:PHE214 4.8 26.9 1.0
CD2 A:HIS128 4.9 32.6 1.0
CD1 A:TYR415 5.0 31.5 1.0

Iron binding site 2 out of 4 in 8j4r

Go back to Iron Binding Sites List in 8j4r
Iron binding site 2 out of 4 in the Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli


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 Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:32.9
occ:1.00
 FE B:HEM801 0.0 32.9 1.0
OH B:TYR415 1.8 30.7 1.0
NA B:HEM801 2.0 30.1 1.0
ND B:HEM801 2.0 30.6 1.0
NC B:HEM801 2.0 32.5 1.0
NB B:HEM801 2.0 36.3 1.0
O B:HOH1078 2.5 30.0 1.0
CZ B:TYR415 3.0 28.9 1.0
C4D B:HEM801 3.0 29.1 1.0
C4C B:HEM801 3.0 28.3 1.0
C1B B:HEM801 3.0 32.1 1.0
C1A B:HEM801 3.0 28.7 1.0
C1D B:HEM801 3.0 31.4 1.0
C4B B:HEM801 3.0 31.2 1.0
C1C B:HEM801 3.0 31.7 1.0
C4A B:HEM801 3.1 32.3 1.0
CHD B:HEM801 3.4 28.1 1.0
CHA B:HEM801 3.4 27.6 1.0
CHC B:HEM801 3.4 30.0 1.0
CHB B:HEM801 3.4 30.6 1.0
CE1 B:TYR415 3.7 28.9 1.0
CE2 B:TYR415 3.8 27.4 1.0
NE B:ARG411 4.1 28.4 1.0
C3C B:HEM801 4.2 31.6 1.0
C2A B:HEM801 4.2 27.9 1.0
C2B B:HEM801 4.2 36.2 1.0
C2C B:HEM801 4.2 33.6 1.0
C3A B:HEM801 4.2 29.7 1.0
C3D B:HEM801 4.2 31.5 1.0
C3B B:HEM801 4.2 37.9 1.0
C2D B:HEM801 4.2 31.0 1.0
NH2 B:ARG411 4.2 26.6 1.0
CZ B:PHE214 4.5 30.0 1.0
CZ B:ARG411 4.6 33.7 1.0
CG2 B:VAL127 4.6 25.5 1.0
O B:HOH1040 4.7 27.7 1.0
NE2 B:HIS128 4.7 29.1 1.0
CD2 B:HIS128 4.9 25.2 1.0
CE2 B:PHE214 4.9 28.1 1.0
CD B:ARG411 5.0 28.4 1.0
CD1 B:TYR415 5.0 31.5 1.0

Iron binding site 3 out of 4 in 8j4r

Go back to Iron Binding Sites List in 8j4r
Iron binding site 3 out of 4 in the Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli


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 Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:32.9
occ:1.00
 FE C:HEM801 0.0 32.9 1.0
OH C:TYR415 1.8 30.7 1.0
NA C:HEM801 2.0 30.1 1.0
NC C:HEM801 2.0 32.5 1.0
ND C:HEM801 2.0 30.6 1.0
NB C:HEM801 2.0 36.3 1.0
O C:HOH941 2.5 35.9 1.0
CZ C:TYR415 3.0 28.9 1.0
C4D C:HEM801 3.0 29.1 1.0
C4C C:HEM801 3.0 28.3 1.0
C1B C:HEM801 3.0 32.1 1.0
C1D C:HEM801 3.0 31.4 1.0
C1A C:HEM801 3.0 28.7 1.0
C4B C:HEM801 3.0 31.2 1.0
C1C C:HEM801 3.0 31.7 1.0
C4A C:HEM801 3.1 32.3 1.0
CHD C:HEM801 3.4 28.1 1.0
CHA C:HEM801 3.4 27.6 1.0
CHC C:HEM801 3.4 30.0 1.0
CHB C:HEM801 3.4 30.6 1.0
CE1 C:TYR415 3.7 28.9 1.0
CE2 C:TYR415 3.8 27.4 1.0
NE C:ARG411 4.1 26.7 1.0
C3C C:HEM801 4.2 31.6 1.0
C2A C:HEM801 4.2 27.9 1.0
C2B C:HEM801 4.2 36.2 1.0
C2C C:HEM801 4.2 33.6 1.0
C3A C:HEM801 4.2 29.7 1.0
C3D C:HEM801 4.2 31.5 1.0
C3B C:HEM801 4.2 37.9 1.0
C2D C:HEM801 4.2 31.0 1.0
NH2 C:ARG411 4.3 26.1 1.0
O C:HOH922 4.4 29.4 1.0
CZ C:PHE214 4.6 25.1 1.0
CZ C:ARG411 4.6 29.1 1.0
CG2 C:VAL127 4.6 23.5 1.0
NE2 C:HIS128 4.7 23.4 1.0
CD2 C:HIS128 4.8 23.7 1.0
CD C:ARG411 4.9 29.6 1.0

Iron binding site 4 out of 4 in 8j4r

Go back to Iron Binding Sites List in 8j4r
Iron binding site 4 out of 4 in the Crystal Structure of Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli


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 Ekate (Extra Kate) F413Y Mutant From Atypical E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:32.9
occ:1.00
 FE D:HEM801 0.0 32.9 1.0
OH D:TYR415 1.9 30.7 1.0
NA D:HEM801 2.0 30.1 1.0
NC D:HEM801 2.0 32.5 1.0
ND D:HEM801 2.0 30.6 1.0
NB D:HEM801 2.0 36.3 1.0
O D:HOH934 2.5 30.0 1.0
C4D D:HEM801 3.0 29.1 1.0
CZ D:TYR415 3.0 28.9 1.0
C4C D:HEM801 3.0 28.3 1.0
C1B D:HEM801 3.0 32.1 1.0
C1A D:HEM801 3.0 28.7 1.0
C1D D:HEM801 3.0 31.4 1.0
C4B D:HEM801 3.0 31.2 1.0
C1C D:HEM801 3.0 31.7 1.0
C4A D:HEM801 3.1 32.3 1.0
CHD D:HEM801 3.4 28.1 1.0
CHA D:HEM801 3.4 27.6 1.0
CHC D:HEM801 3.4 30.0 1.0
CHB D:HEM801 3.4 30.6 1.0
CE1 D:TYR415 3.7 28.9 1.0
CE2 D:TYR415 3.8 27.4 1.0
NE D:ARG411 4.1 22.5 1.0
C3C D:HEM801 4.2 31.6 1.0
C2A D:HEM801 4.2 27.9 1.0
C2B D:HEM801 4.2 36.2 1.0
C2C D:HEM801 4.2 33.6 1.0
C3A D:HEM801 4.2 29.7 1.0
C3D D:HEM801 4.2 31.5 1.0
C3B D:HEM801 4.2 37.9 1.0
C2D D:HEM801 4.2 31.0 1.0
NH2 D:ARG411 4.3 23.8 1.0
O D:HOH970 4.5 36.6 1.0
CZ D:PHE214 4.6 28.4 1.0
CZ D:ARG411 4.6 28.3 1.0
CG2 D:VAL127 4.8 24.1 1.0
NE2 D:HIS128 4.9 26.4 1.0
CD2 D:HIS128 5.0 23.6 1.0
CD D:ARG411 5.0 25.4 1.0
CD1 D:TYR415 5.0 31.5 1.0

Reference:

Y.Yoo, Y.Yoo. N/A N/A.
Page generated: Thu Aug 7 18:26:49 2025

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