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Iron in PDB 6by0: Crystal Structure of Catalase Hpii From E. Coli in Space Group P1

Enzymatic activity of Crystal Structure of Catalase Hpii From E. Coli in Space Group P1

All present enzymatic activity of Crystal Structure of Catalase Hpii From E. Coli in Space Group P1:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of Catalase Hpii From E. Coli in Space Group P1, PDB code: 6by0 was solved by M.N.Lisa, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.93
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.337, 90.141, 114.764, 107.10, 105.60, 95.98
R / Rfree (%) 18.3 / 23.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1 (pdb code 6by0). 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 Catalase Hpii From E. Coli in Space Group P1, PDB code: 6by0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6by0

Go back to Iron Binding Sites List in 6by0
Iron binding site 1 out of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1


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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:13.7
occ:1.00
FE A:HEM801 0.0 13.7 1.0
NA A:HEM801 1.9 14.1 1.0
NC A:HEM801 1.9 13.6 1.0
NB A:HEM801 2.0 14.0 1.0
ND A:HEM801 2.0 13.5 1.0
OH A:TYR415 2.1 32.6 1.0
C4A A:HEM801 2.9 14.4 1.0
C1B A:HEM801 2.9 14.7 1.0
C1A A:HEM801 3.0 14.1 1.0
C4C A:HEM801 3.0 13.5 1.0
C1C A:HEM801 3.0 13.8 1.0
C4B A:HEM801 3.0 14.5 1.0
CZ A:TYR415 3.0 27.4 1.0
C1D A:HEM801 3.1 13.6 1.0
C4D A:HEM801 3.1 13.6 1.0
CHB A:HEM801 3.2 15.1 1.0
CHC A:HEM801 3.4 14.8 1.0
CHD A:HEM801 3.4 14.0 1.0
CHA A:HEM801 3.5 14.2 1.0
CE2 A:TYR415 3.7 21.9 1.0
CE1 A:TYR415 3.9 17.8 1.0
C3A A:HEM801 4.1 15.0 1.0
C3C A:HEM801 4.2 13.9 1.0
C2A A:HEM801 4.2 14.8 1.0
C2C A:HEM801 4.2 14.2 1.0
NE A:ARG411 4.2 19.5 1.0
C2B A:HEM801 4.2 15.2 1.0
NH2 A:ARG411 4.2 15.1 1.0
C3B A:HEM801 4.3 15.4 1.0
C3D A:HEM801 4.4 13.7 1.0
C2D A:HEM801 4.4 13.6 1.0
CG2 A:VAL127 4.5 17.5 1.0
CD2 A:HIS128 4.6 12.2 1.0
CZ A:ARG411 4.6 26.9 1.0
NE2 A:HIS128 4.7 11.0 1.0
CZ A:PHE214 4.7 12.0 1.0
CD2 A:TYR415 4.9 21.2 1.0

Iron binding site 2 out of 4 in 6by0

Go back to Iron Binding Sites List in 6by0
Iron binding site 2 out of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1


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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:14.8
occ:1.00
FE B:HEM801 0.0 14.8 1.0
NC B:HEM801 1.9 14.9 1.0
ND B:HEM801 1.9 14.8 1.0
NB B:HEM801 1.9 14.7 1.0
NA B:HEM801 2.0 14.9 1.0
OH B:TYR415 2.1 12.5 1.0
C4D B:HEM801 2.9 15.0 1.0
C4C B:HEM801 2.9 15.0 1.0
C1C B:HEM801 2.9 15.0 1.0
C4B B:HEM801 3.0 15.2 1.0
C1B B:HEM801 3.0 15.1 1.0
C1D B:HEM801 3.0 15.1 1.0
C1A B:HEM801 3.0 15.0 1.0
C4A B:HEM801 3.1 14.9 1.0
CZ B:TYR415 3.1 23.9 1.0
CHC B:HEM801 3.3 15.8 1.0
CHA B:HEM801 3.3 15.4 1.0
CHD B:HEM801 3.4 15.6 1.0
CHB B:HEM801 3.4 15.4 1.0
CE2 B:TYR415 3.8 22.2 1.0
CE1 B:TYR415 3.9 24.6 1.0
NE B:ARG411 4.1 19.2 1.0
C3C B:HEM801 4.1 15.4 1.0
C2C B:HEM801 4.2 15.5 1.0
C3D B:HEM801 4.2 15.4 1.0
NH2 B:ARG411 4.2 23.9 1.0
C3B B:HEM801 4.2 15.8 1.0
C2B B:HEM801 4.2 15.4 1.0
C2A B:HEM801 4.3 15.3 1.0
C2D B:HEM801 4.3 15.3 1.0
C3A B:HEM801 4.3 15.3 1.0
CZ B:ARG411 4.5 30.1 1.0
CG2 B:VAL127 4.6 14.4 1.0
CZ B:PHE214 4.6 24.7 1.0
NE2 B:HIS128 4.7 27.1 1.0
CD2 B:HIS128 4.7 27.2 1.0

Iron binding site 3 out of 4 in 6by0

Go back to Iron Binding Sites List in 6by0
Iron binding site 3 out of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1


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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:15.7
occ:1.00
FE C:HEM801 0.0 15.7 1.0
ND C:HEM801 1.9 15.4 1.0
NA C:HEM801 1.9 15.8 1.0
NC C:HEM801 1.9 15.6 1.0
NB C:HEM801 2.0 15.9 1.0
OH C:TYR415 2.1 27.5 1.0
C4D C:HEM801 2.9 15.5 1.0
C1C C:HEM801 3.0 15.8 1.0
C1A C:HEM801 3.0 15.7 1.0
C1B C:HEM801 3.0 16.5 1.0
C4C C:HEM801 3.0 15.6 1.0
C4B C:HEM801 3.0 16.4 1.0
C1D C:HEM801 3.0 15.6 1.0
C4A C:HEM801 3.0 16.0 1.0
CZ C:TYR415 3.0 25.8 1.0
CHA C:HEM801 3.3 15.9 1.0
CHB C:HEM801 3.4 16.7 1.0
CHC C:HEM801 3.4 16.8 1.0
CHD C:HEM801 3.5 16.1 1.0
CE2 C:TYR415 3.7 17.4 1.0
CE1 C:TYR415 3.9 18.1 1.0
C2C C:HEM801 4.1 16.3 1.0
C3C C:HEM801 4.2 16.1 1.0
C3D C:HEM801 4.2 15.6 1.0
C2A C:HEM801 4.2 16.2 1.0
NE C:ARG411 4.2 22.2 1.0
C3A C:HEM801 4.2 16.4 1.0
C2B C:HEM801 4.2 16.9 1.0
C3B C:HEM801 4.3 17.2 1.0
NH2 C:ARG411 4.3 19.5 1.0
C2D C:HEM801 4.3 15.6 1.0
CG2 C:VAL127 4.5 10.4 1.0
CZ C:PHE214 4.6 9.8 1.0
CD2 C:HIS128 4.6 18.3 1.0
CZ C:ARG411 4.7 25.6 1.0
NE2 C:HIS128 4.7 18.4 1.0
CD2 C:TYR415 4.9 17.0 1.0

Iron binding site 4 out of 4 in 6by0

Go back to Iron Binding Sites List in 6by0
Iron binding site 4 out of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1


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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:16.8
occ:1.00
FE D:HEM801 0.0 16.8 1.0
NC D:HEM801 1.9 16.6 1.0
ND D:HEM801 2.0 16.7 1.0
NA D:HEM801 2.0 17.2 1.0
NB D:HEM801 2.0 16.9 1.0
OH D:TYR415 2.1 6.5 1.0
C4C D:HEM801 2.9 16.7 1.0
C1D D:HEM801 3.0 16.9 1.0
C1B D:HEM801 3.0 17.4 1.0
C1C D:HEM801 3.0 16.7 1.0
C4B D:HEM801 3.0 17.2 1.0
C4D D:HEM801 3.0 17.0 1.0
C4A D:HEM801 3.1 17.4 1.0
C1A D:HEM801 3.1 17.3 1.0
CZ D:TYR415 3.1 22.6 1.0
CHD D:HEM801 3.3 17.3 1.0
CHB D:HEM801 3.4 17.9 1.0
CHC D:HEM801 3.5 17.6 1.0
CHA D:HEM801 3.5 17.5 1.0
O D:HOH974 3.7 7.9 1.0
CE2 D:TYR415 3.8 25.4 1.0
CE1 D:TYR415 4.0 26.6 1.0
C2B D:HEM801 4.1 17.8 1.0
NE D:ARG411 4.1 13.1 1.0
C3C D:HEM801 4.2 17.0 1.0
NH2 D:ARG411 4.2 23.5 1.0
C2C D:HEM801 4.2 17.2 1.0
C3B D:HEM801 4.2 17.9 1.0
C2A D:HEM801 4.2 17.8 1.0
C3A D:HEM801 4.2 18.0 1.0
C3D D:HEM801 4.3 17.3 1.0
C2D D:HEM801 4.3 17.1 1.0
CZ D:ARG411 4.5 28.7 1.0
NE2 D:HIS128 4.6 19.2 1.0
CD2 D:HIS128 4.6 19.7 1.0
CG2 D:VAL127 4.6 13.4 1.0
CZ D:PHE214 4.7 25.0 1.0

Reference:

A.J.Simpkin, F.Simkovic, J.M.H.Thomas, M.Savko, A.Lebedev, V.Uski, C.Ballard, M.Wojdyr, R.Wu, R.Sanishvili, Y.Xu, M.N.Lisa, A.Buschiazzo, W.Shepard, D.J.Rigden, R.M.Keegan. Simbad: A Sequence-Independent Molecular-Replacement Pipeline. Acta Crystallogr D Struct V. 74 595 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29968670
DOI: 10.1107/S2059798318005752
Page generated: Sun Dec 13 16:22:00 2020

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