Atomistry » Iron » PDB 1y4r-1yeu » 1ye9
Atomistry »
  Iron »
    PDB 1y4r-1yeu »
      1ye9 »

Iron in PDB 1ye9: Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli

Enzymatic activity of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli

All present enzymatic activity of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli, PDB code: 1ye9 was solved by P.C.Loewen, P.Chelikani, X.Carpena, I.Fita, R.Perez-Luque, L.J.Donald, J.Switala, H.W.Duckworth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.011, 152.888, 135.287, 90.00, 97.54, 90.00
R / Rfree (%) 21.7 / 26.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli (pdb code 1ye9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli, PDB code: 1ye9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 1 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From 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 Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe760

b:24.1
occ:1.00
FE E:HDD760 0.0 24.1 1.0
ND E:HDD760 1.9 26.1 1.0
OH E:TYR415 1.9 23.9 1.0
NC E:HDD760 2.1 20.4 1.0
NB E:HDD760 2.1 24.7 1.0
NA E:HDD760 2.1 15.8 1.0
C1D E:HDD760 2.8 23.3 1.0
CHD E:HDD760 2.9 25.7 1.0
C4D E:HDD760 2.9 28.1 1.0
CHA E:HDD760 2.9 23.6 1.0
CZ E:TYR415 3.0 31.9 1.0
C4C E:HDD760 3.0 24.2 1.0
C1A E:HDD760 3.0 14.6 1.0
C4B E:HDD760 3.0 34.1 1.0
CHC E:HDD760 3.1 29.9 1.0
C1C E:HDD760 3.1 28.0 1.0
C1B E:HDD760 3.1 23.6 1.0
C4A E:HDD760 3.1 21.0 1.0
CHB E:HDD760 3.5 23.1 1.0
CE1 E:TYR415 3.6 31.5 1.0
CE2 E:TYR415 3.9 35.6 1.0
NE E:ARG411 4.1 31.3 1.0
C2D E:HDD760 4.1 21.8 1.0
C3C E:HDD760 4.2 24.4 1.0
C3D E:HDD760 4.3 25.2 1.0
C3B E:HDD760 4.3 38.3 1.0
NH2 E:ARG411 4.3 37.4 1.0
C2A E:HDD760 4.3 19.2 1.0
C2B E:HDD760 4.3 34.4 1.0
C2C E:HDD760 4.4 28.1 1.0
NE2 A:HIS128 4.4 38.1 1.0
C3A E:HDD760 4.4 10.8 1.0
CD2 A:HIS128 4.5 38.1 1.0
CG2 A:VAL127 4.6 33.6 1.0
CZ E:ARG411 4.7 33.7 1.0
O A:HOH320 4.7 37.9 1.0
CZ A:PHE214 4.8 39.8 1.0
O1D E:HDD760 4.9 29.7 1.0
CD1 E:TYR415 4.9 30.7 1.0
CMD E:HDD760 4.9 12.7 1.0
OND E:HDD760 5.0 20.7 1.0

Iron binding site 2 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 2 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From 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 Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe760

b:24.9
occ:1.00
FE F:HDD760 0.0 24.9 1.0
ND F:HDD760 1.9 20.7 1.0
NB F:HDD760 2.1 22.1 1.0
NC F:HDD760 2.1 22.5 1.0
NA F:HDD760 2.1 14.7 1.0
OH F:TYR415 2.2 22.4 1.0
C4D F:HDD760 2.9 30.7 1.0
C1D F:HDD760 2.9 22.9 1.0
CZ F:TYR415 3.0 30.5 1.0
CHA F:HDD760 3.0 25.1 1.0
C4B F:HDD760 3.0 31.5 1.0
CHC F:HDD760 3.0 31.5 1.0
CHD F:HDD760 3.0 23.4 1.0
C1A F:HDD760 3.1 26.6 1.0
C1B F:HDD760 3.1 27.4 1.0
C1C F:HDD760 3.1 30.3 1.0
C4C F:HDD760 3.1 27.4 1.0
C4A F:HDD760 3.1 12.3 1.0
CE1 F:TYR415 3.5 31.5 1.0
CHB F:HDD760 3.6 14.9 1.0
CE2 F:TYR415 3.9 34.9 1.0
NE F:ARG411 4.1 31.7 1.0
NH2 F:ARG411 4.2 36.0 1.0
C3B F:HDD760 4.2 31.0 1.0
C2B F:HDD760 4.3 27.3 1.0
C2D F:HDD760 4.3 27.0 1.0
C3D F:HDD760 4.3 32.7 1.0
C3C F:HDD760 4.3 19.6 1.0
C2C F:HDD760 4.3 20.2 1.0
C2A F:HDD760 4.4 18.0 1.0
C3A F:HDD760 4.4 14.7 1.0
CG2 B:VAL127 4.4 32.5 1.0
CD2 B:HIS128 4.5 38.4 1.0
NE2 B:HIS128 4.5 37.7 1.0
CZ B:PHE214 4.6 38.9 1.0
CZ F:ARG411 4.6 33.7 1.0
CD1 F:TYR415 4.7 30.5 1.0
CE1 B:PHE214 4.8 38.1 1.0

Iron binding site 3 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 3 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From 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 Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe760

b:32.2
occ:1.00
FE G:HDD760 0.0 32.2 1.0
ND G:HDD760 1.9 38.0 1.0
OH G:TYR415 2.0 22.5 1.0
NB G:HDD760 2.1 34.6 1.0
NC G:HDD760 2.1 35.3 1.0
NA G:HDD760 2.1 35.8 1.0
C4D G:HDD760 2.9 37.2 1.0
C1D G:HDD760 3.0 34.1 1.0
CHA G:HDD760 3.0 35.9 1.0
CZ G:TYR415 3.0 30.0 1.0
C4B G:HDD760 3.0 41.6 1.0
C1A G:HDD760 3.0 33.5 1.0
C4C G:HDD760 3.1 29.9 1.0
CHC G:HDD760 3.1 37.4 1.0
C1C G:HDD760 3.1 35.6 1.0
CHD G:HDD760 3.1 27.0 1.0
C1B G:HDD760 3.1 37.4 1.0
C4A G:HDD760 3.1 32.8 1.0
CHB G:HDD760 3.5 33.8 1.0
CE1 G:TYR415 3.6 31.0 1.0
NE G:ARG411 4.0 31.4 1.0
CE2 G:TYR415 4.0 35.6 1.0
C3C G:HDD760 4.2 30.2 1.0
C2D G:HDD760 4.3 37.1 1.0
C3B G:HDD760 4.3 43.5 1.0
C3D G:HDD760 4.3 40.0 1.0
C2B G:HDD760 4.3 42.7 1.0
C2C G:HDD760 4.3 32.7 1.0
C2A G:HDD760 4.3 29.9 1.0
C3A G:HDD760 4.4 32.6 1.0
CZ C:PHE214 4.4 40.4 1.0
NH2 G:ARG411 4.5 36.5 1.0
CZ G:ARG411 4.7 34.2 1.0
NE2 C:HIS128 4.7 37.6 1.0
CD2 C:HIS128 4.8 39.0 1.0
CG2 C:VAL127 4.8 32.4 1.0
CD G:ARG411 4.8 28.6 1.0
CG G:ARG411 4.8 30.8 1.0
OND G:HDD760 4.9 40.7 1.0
CE1 C:PHE214 4.9 39.0 1.0
CD1 G:TYR415 4.9 30.8 1.0

Iron binding site 4 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 4 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From 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 Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe760

b:35.9
occ:1.00
FE H:HDD760 0.0 35.9 1.0
OH H:TYR415 1.7 21.3 1.0
ND H:HDD760 1.9 38.4 1.0
NC H:HDD760 2.1 44.8 1.0
NB H:HDD760 2.1 45.3 1.0
NA H:HDD760 2.1 40.9 1.0
CZ H:TYR415 2.8 31.0 1.0
C4D H:HDD760 2.9 40.6 1.0
C1D H:HDD760 2.9 39.9 1.0
CHA H:HDD760 2.9 44.4 1.0
C1A H:HDD760 3.0 43.8 1.0
C1C H:HDD760 3.0 44.4 1.0
C4B H:HDD760 3.0 47.9 1.0
CHC H:HDD760 3.0 48.8 1.0
C4C H:HDD760 3.1 44.0 1.0
CHD H:HDD760 3.1 41.1 1.0
C1B H:HDD760 3.2 47.8 1.0
C4A H:HDD760 3.2 35.1 1.0
CE1 H:TYR415 3.4 31.8 1.0
CHB H:HDD760 3.6 38.7 1.0
CE2 H:TYR415 3.8 35.1 1.0
NE H:ARG411 4.1 32.2 1.0
NH2 H:ARG411 4.2 36.5 1.0
C3C H:HDD760 4.2 41.4 1.0
C2D H:HDD760 4.3 41.2 1.0
C2C H:HDD760 4.3 43.9 1.0
C3D H:HDD760 4.3 38.0 1.0
C3B H:HDD760 4.3 47.8 1.0
C2A H:HDD760 4.3 43.0 1.0
C2B H:HDD760 4.4 49.8 1.0
C3A H:HDD760 4.5 45.0 1.0
NE2 D:HIS128 4.5 36.8 1.0
CD2 D:HIS128 4.5 38.6 1.0
CG2 D:VAL127 4.5 33.0 1.0
CZ H:ARG411 4.6 33.8 1.0
CZ D:PHE214 4.6 38.8 1.0
CD1 H:TYR415 4.7 30.8 1.0
CE1 D:PHE214 4.9 38.6 1.0

Iron binding site 5 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 5 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe760

b:44.2
occ:1.00
FE M:HDD760 0.0 44.2 1.0
OH M:TYR415 1.7 23.8 1.0
ND M:HDD760 1.9 51.0 1.0
NA M:HDD760 2.1 50.1 1.0
NC M:HDD760 2.1 50.5 1.0
NB M:HDD760 2.1 59.6 1.0
CZ M:TYR415 2.9 31.6 1.0
C4D M:HDD760 2.9 50.4 1.0
C1D M:HDD760 2.9 49.3 1.0
CHA M:HDD760 2.9 49.8 1.0
C1A M:HDD760 3.0 49.0 1.0
CHD M:HDD760 3.0 46.5 1.0
C4C M:HDD760 3.0 53.5 1.0
C1C M:HDD760 3.1 56.4 1.0
C4B M:HDD760 3.1 61.7 1.0
CHC M:HDD760 3.1 58.6 1.0
C4A M:HDD760 3.1 48.5 1.0
C1B M:HDD760 3.2 62.3 1.0
CE1 M:TYR415 3.5 32.2 1.0
CHB M:HDD760 3.5 56.8 1.0
CE2 M:TYR415 3.9 35.4 1.0
C3D M:HDD760 4.3 53.0 1.0
C2D M:HDD760 4.3 51.0 1.0
NE M:ARG411 4.3 32.1 1.0
C3C M:HDD760 4.3 59.7 1.0
C2A M:HDD760 4.3 40.0 1.0
C2C M:HDD760 4.3 57.5 1.0
C3B M:HDD760 4.4 64.0 1.0
C3A M:HDD760 4.4 40.7 1.0
C2B M:HDD760 4.4 66.5 1.0
NE2 I:HIS128 4.4 37.3 1.0
CD2 I:HIS128 4.4 39.1 1.0
CG2 I:VAL127 4.5 33.4 1.0
CZ I:PHE214 4.6 39.9 1.0
NH2 M:ARG411 4.8 37.5 1.0
CZ M:ARG411 4.8 35.3 1.0
CD1 M:TYR415 4.8 31.4 1.0
CE1 I:PHE214 4.9 38.8 1.0
CD M:ARG411 4.9 29.1 1.0

Iron binding site 6 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 6 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe760

b:38.8
occ:1.00
FE N:HDD760 0.0 38.8 1.0
ND N:HDD760 1.9 42.8 1.0
OH N:TYR415 2.0 23.7 1.0
NB N:HDD760 2.1 33.6 1.0
NC N:HDD760 2.1 37.9 1.0
NA N:HDD760 2.1 40.7 1.0
C1D N:HDD760 2.8 46.1 1.0
C4D N:HDD760 2.9 42.4 1.0
CHD N:HDD760 2.9 44.2 1.0
CZ N:TYR415 3.0 31.2 1.0
CHA N:HDD760 3.0 34.2 1.0
C4C N:HDD760 3.0 38.5 1.0
C4B N:HDD760 3.0 40.0 1.0
C1A N:HDD760 3.1 37.1 1.0
C1C N:HDD760 3.1 37.1 1.0
CHC N:HDD760 3.1 36.6 1.0
C4A N:HDD760 3.1 37.4 1.0
C1B N:HDD760 3.1 34.5 1.0
CE1 N:TYR415 3.5 32.0 1.0
CHB N:HDD760 3.5 39.1 1.0
NE N:ARG411 3.9 30.6 1.0
CE2 N:TYR415 4.1 34.9 1.0
NH2 N:ARG411 4.1 37.1 1.0
C2D N:HDD760 4.2 47.6 1.0
C3D N:HDD760 4.2 43.2 1.0
C3C N:HDD760 4.2 37.5 1.0
C3B N:HDD760 4.3 40.7 1.0
C2C N:HDD760 4.3 41.7 1.0
C2A N:HDD760 4.3 37.1 1.0
C2B N:HDD760 4.3 37.2 1.0
C3A N:HDD760 4.4 32.5 1.0
NE2 J:HIS128 4.5 38.0 1.0
CZ N:ARG411 4.5 34.7 1.0
CD2 J:HIS128 4.5 39.3 1.0
CG2 J:VAL127 4.7 34.0 1.0
CZ J:PHE214 4.7 39.5 1.0
CD1 N:TYR415 4.8 30.5 1.0
O1D N:HDD760 4.9 44.0 1.0
CD N:ARG411 5.0 28.9 1.0

Iron binding site 7 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 7 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe760

b:53.5
occ:1.00
FE O:HDD760 0.0 53.5 1.0
OH O:TYR415 1.8 23.0 1.0
ND O:HDD760 1.9 53.8 1.0
NC O:HDD760 2.1 45.6 1.0
NA O:HDD760 2.1 52.8 1.0
NB O:HDD760 2.1 57.4 1.0
C4D O:HDD760 2.9 53.8 1.0
CZ O:TYR415 2.9 31.9 1.0
C1D O:HDD760 2.9 55.1 1.0
CHA O:HDD760 2.9 53.5 1.0
CHD O:HDD760 3.0 48.9 1.0
C1A O:HDD760 3.0 55.6 1.0
C4B O:HDD760 3.0 52.5 1.0
C4C O:HDD760 3.1 47.3 1.0
CHC O:HDD760 3.1 45.9 1.0
C1C O:HDD760 3.1 45.4 1.0
C1B O:HDD760 3.2 60.4 1.0
C4A O:HDD760 3.2 54.5 1.0
CE1 O:TYR415 3.4 31.8 1.0
CHB O:HDD760 3.6 57.8 1.0
CE2 O:TYR415 4.0 35.5 1.0
NE O:ARG411 4.1 33.1 1.0
NE2 K:HIS128 4.1 37.3 1.0
CD2 K:HIS128 4.2 39.2 1.0
C2D O:HDD760 4.2 59.0 1.0
C3D O:HDD760 4.2 57.6 1.0
NH2 O:ARG411 4.3 36.5 1.0
C3B O:HDD760 4.3 57.0 1.0
C3C O:HDD760 4.3 42.6 1.0
C2C O:HDD760 4.3 44.4 1.0
C2B O:HDD760 4.4 60.1 1.0
C2A O:HDD760 4.4 51.1 1.0
C3A O:HDD760 4.4 54.1 1.0
CG2 K:VAL127 4.6 33.2 1.0
CZ O:ARG411 4.7 35.7 1.0
CZ K:PHE214 4.7 39.8 1.0
CD1 O:TYR415 4.8 30.3 1.0
OND O:HDD760 5.0 61.5 1.0

Iron binding site 8 out of 8 in 1ye9

Go back to Iron Binding Sites List in 1ye9
Iron binding site 8 out of 8 in the Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Proteolytically Truncated Catalase Hpii From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe760

b:30.6
occ:1.00
FE P:HDD760 0.0 30.6 1.0
ND P:HDD760 2.0 19.1 1.0
OH P:TYR415 2.1 24.1 1.0
NA P:HDD760 2.1 17.0 1.0
NB P:HDD760 2.1 21.7 1.0
NC P:HDD760 2.1 24.5 1.0
C1D P:HDD760 3.0 23.2 1.0
C1A P:HDD760 3.0 19.1 1.0
CZ P:TYR415 3.0 31.4 1.0
C4D P:HDD760 3.0 24.4 1.0
CHD P:HDD760 3.0 21.8 1.0
CHA P:HDD760 3.0 28.3 1.0
C4C P:HDD760 3.0 29.2 1.0
C4B P:HDD760 3.1 33.7 1.0
C4A P:HDD760 3.1 24.4 1.0
C1C P:HDD760 3.1 26.5 1.0
CHC P:HDD760 3.1 23.5 1.0
C1B P:HDD760 3.1 28.7 1.0
CE1 P:TYR415 3.5 32.4 1.0
CHB P:HDD760 3.5 26.9 1.0
CE2 P:TYR415 4.0 35.5 1.0
NE P:ARG411 4.1 31.7 1.0
C2A P:HDD760 4.2 21.0 1.0
C3C P:HDD760 4.2 29.4 1.0
C3B P:HDD760 4.3 31.9 1.0
C3A P:HDD760 4.3 25.6 1.0
C2D P:HDD760 4.3 28.6 1.0
C3D P:HDD760 4.3 30.9 1.0
C2C P:HDD760 4.4 32.2 1.0
C2B P:HDD760 4.4 31.9 1.0
NH2 P:ARG411 4.4 36.6 1.0
CZ L:PHE214 4.5 40.2 1.0
NE2 L:HIS128 4.6 37.0 1.0
CZ P:ARG411 4.7 33.9 1.0
CD2 L:HIS128 4.8 38.4 1.0
CD1 P:TYR415 4.8 31.9 1.0
CG2 L:VAL127 4.8 33.5 1.0
CE1 L:PHE214 4.9 39.0 1.0
CG P:ARG411 5.0 31.0 1.0

Reference:

P.Chelikani, X.Carpena, R.Perez-Luque, L.J.Donald, H.W.Duckworth, J.Switala, I.Fita, P.C.Loewen. Characterization of A Large Subunit Catalase Truncated By Proteolytic Cleavage(,) Biochemistry V. 44 5597 2005.
ISSN: ISSN 0006-2960
PubMed: 15823018
DOI: 10.1021/BI047277M
Page generated: Sat Aug 3 17:37:02 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy