Iron in PDB 5bv2: Crystal Structure of E. Coli Hpii Catalase Variant

All present enzymatic activity of Crystal Structure of E. Coli Hpii Catalase Variant:
1.11.1.6;

The structure of Crystal Structure of E. Coli Hpii Catalase Variant, PDB code: 5bv2 was solved by J.Wang, I.V.Lomkalin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.789, 171.331, 122.484, 90.00, 121.55, 90.00
R / Rfree (%)	8.2 / 13.2

The structure of Crystal Structure of E. Coli Hpii Catalase Variant also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Crystal Structure of E. Coli Hpii Catalase Variant (pdb code 5bv2). 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 E. Coli Hpii Catalase Variant, PDB code: 5bv2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of E. Coli Hpii Catalase Variant


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 E. Coli Hpii Catalase Variant within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe801 b:9.8 occ:1.00 FE P:HDD801 0.0 9.8 1.0 ND P:HDD801 2.0 8.8 1.0 OH P:TYR415 2.0 10.5 1.0 NA P:HDD801 2.0 8.6 1.0 NC P:HDD801 2.1 8.6 1.0 NB P:HDD801 2.1 9.4 1.0 HO2 P:GOL802 2.4 18.0 1.0 O2 P:GOL802 2.5 23.2 1.0 HH P:TYR415 2.6 10.2 0.0 C4D P:HDD801 3.0 8.8 1.0 CZ P:TYR415 3.0 9.1 1.0 C1D P:HDD801 3.0 9.3 1.0 C1A P:HDD801 3.0 7.7 1.0 C4A P:HDD801 3.1 8.3 1.0 C4C P:HDD801 3.1 9.1 1.0 C4B P:HDD801 3.1 8.7 1.0 C1C P:HDD801 3.1 8.4 1.0 C1B P:HDD801 3.1 9.4 1.0 HE P:ARG411 3.3 8.2 1.0 CHA P:HDD801 3.4 8.1 1.0 CHD P:HDD801 3.4 8.4 1.0 CHC P:HDD801 3.4 7.7 1.0 CHB P:HDD801 3.5 8.3 1.0 HE2 P:TYR415 3.5 8.6 1.0 H11 P:GOL802 3.6 17.1 1.0 HH21 P:ARG411 3.6 9.2 1.0 CE2 P:TYR415 3.7 8.8 1.0 C2 P:GOL802 3.9 26.3 1.0 CE1 P:TYR415 3.9 9.0 1.0 HE1 P:TYR415 4.0 8.8 1.0 HG22 P:VAL127 4.0 9.1 1.0 C1 P:GOL802 4.2 18.9 1.0 NE P:ARG411 4.2 8.2 1.0 HZ P:PHE214 4.2 11.2 1.0 NH2 P:ARG411 4.3 9.4 1.0 HG23 P:VAL127 4.3 9.0 1.0 HD2 P:HIS128 4.3 9.2 1.0 C2A P:HDD801 4.3 8.1 1.0 C3A P:HDD801 4.3 7.7 1.0 HE2 P:HIS128 4.3 10.9 1.0 C3C P:HDD801 4.4 9.4 1.0 C2D P:HDD801 4.4 10.6 1.0 C3B P:HDD801 4.4 9.1 1.0 C3D P:HDD801 4.4 10.6 1.0 H12 P:GOL802 4.4 20.0 1.0 C2B P:HDD801 4.4 9.1 1.0 C2C P:HDD801 4.4 8.7 1.0 HHA P:HDD801 4.4 8.1 1.0 H2 P:GOL802 4.5 20.6 1.0 HHD P:HDD801 4.5 8.6 1.0 HHC P:HDD801 4.5 7.6 1.0 HG2 P:ARG411 4.5 8.3 1.0 HHB P:HDD801 4.5 8.5 1.0 CG2 P:VAL127 4.6 9.1 1.0 CZ P:ARG411 4.6 8.6 1.0 CZ P:PHE214 4.6 10.1 1.0 CD2 P:HIS128 4.7 9.3 1.0 NE2 P:HIS128 4.7 10.5 1.0 HG11 P:VAL199 4.7 9.0 1.0 H32 P:GOL802 4.8 24.1 1.0 HH22 P:ARG411 4.9 8.9 1.0 CD2 P:TYR415 4.9 8.2 1.0 HG21 P:VAL127 4.9 9.0 1.0 C3 P:GOL802 4.9 34.0 1.0 HG12 P:VAL199 5.0 9.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of E. Coli Hpii Catalase Variant


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 E. Coli Hpii Catalase Variant within 5.0Å range: probe atom residue distance (Å) B Occ Q:Fe801 b:10.1 occ:1.00 FE Q:HDD801 0.0 10.1 1.0 ND Q:HDD801 2.0 9.1 1.0 OH Q:TYR415 2.0 9.1 1.0 NA Q:HDD801 2.1 9.6 1.0 NB Q:HDD801 2.1 9.6 1.0 NC Q:HDD801 2.1 9.8 1.0 O2 Q:GOL802 2.5 22.7 1.0 HH Q:TYR415 2.6 8.8 0.0 HO2 Q:GOL802 2.9 16.8 1.0 CZ Q:TYR415 3.0 8.3 1.0 C1D Q:HDD801 3.0 8.9 1.0 C4D Q:HDD801 3.0 9.5 1.0 C4C Q:HDD801 3.1 9.0 1.0 C1A Q:HDD801 3.1 8.8 1.0 C4A Q:HDD801 3.1 8.7 1.0 C4B Q:HDD801 3.1 9.8 1.0 C1B Q:HDD801 3.1 9.9 1.0 C1C Q:HDD801 3.1 9.5 1.0 HE Q:ARG411 3.3 8.2 1.0 CHD Q:HDD801 3.4 8.6 1.0 CHA Q:HDD801 3.4 8.6 1.0 CHB Q:HDD801 3.4 8.8 1.0 CHC Q:HDD801 3.5 8.9 1.0 HE2 Q:TYR415 3.5 8.2 1.0 HH21 Q:ARG411 3.6 8.8 1.0 CE2 Q:TYR415 3.6 8.3 1.0 H32 Q:GOL802 3.7 17.1 1.0 C2 Q:GOL802 3.7 22.4 1.0 H2 Q:GOL802 3.9 21.2 1.0 CE1 Q:TYR415 3.9 8.2 1.0 HE1 Q:TYR415 4.0 8.1 1.0 HG22 Q:VAL127 4.1 9.7 1.0 NE Q:ARG411 4.2 8.1 1.0 C3 Q:GOL802 4.2 20.2 1.0 HZ Q:PHE214 4.2 12.6 1.0 NH2 Q:ARG411 4.3 8.9 1.0 HG23 Q:VAL127 4.3 9.4 1.0 C3D Q:HDD801 4.3 11.2 1.0 C2D Q:HDD801 4.3 10.9 1.0 C2A Q:HDD801 4.3 8.0 1.0 HD2 Q:HIS128 4.3 9.5 1.0 C3C Q:HDD801 4.4 9.9 1.0 C3A Q:HDD801 4.4 8.4 1.0 HE2 Q:HIS128 4.4 11.0 1.0 C3B Q:HDD801 4.4 9.8 1.0 C2B Q:HDD801 4.4 9.7 1.0 C2C Q:HDD801 4.4 9.4 1.0 HHD Q:HDD801 4.5 8.7 1.0 HHA Q:HDD801 4.5 8.5 1.0 HHB Q:HDD801 4.5 8.8 1.0 HG2 Q:ARG411 4.5 9.1 1.0 HHC Q:HDD801 4.5 8.9 1.0 H31 Q:GOL802 4.5 20.1 1.0 CG2 Q:VAL127 4.6 9.6 1.0 CZ Q:ARG411 4.7 8.4 1.0 CZ Q:PHE214 4.7 11.7 1.0 NE2 Q:HIS128 4.7 10.5 1.0 HG11 Q:VAL199 4.7 8.2 1.0 CD2 Q:HIS128 4.7 9.2 1.0 CD2 Q:TYR415 4.9 8.4 1.0 C1 Q:GOL802 4.9 28.4 1.0 HH22 Q:ARG411 4.9 8.6 1.0 H11 Q:GOL802 4.9 25.2 1.0 HG12 Q:VAL199 5.0 8.0 1.0 HG21 Q:VAL127 5.0 9.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of E. Coli Hpii Catalase Variant


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 E. Coli Hpii Catalase Variant within 5.0Å range: probe atom residue distance (Å) B Occ R:Fe801 b:10.4 occ:1.00 FE R:HDD801 0.0 10.4 1.0 ND R:HDD801 2.0 9.7 1.0 OH R:TYR415 2.0 10.7 1.0 NA R:HDD801 2.0 9.8 1.0 NC R:HDD801 2.1 10.6 1.0 NB R:HDD801 2.1 9.7 1.0 O2 R:GOL802 2.3 20.2 0.8 HO2 R:GOL802 2.5 17.2 0.8 HH R:TYR415 2.5 10.6 0.0 CZ R:TYR415 3.0 8.8 1.0 C1D R:HDD801 3.0 10.1 1.0 C4D R:HDD801 3.0 9.6 1.0 C4A R:HDD801 3.0 10.9 1.0 C1A R:HDD801 3.0 9.0 1.0 C4C R:HDD801 3.1 10.2 1.0 C1B R:HDD801 3.1 10.2 1.0 C1C R:HDD801 3.1 10.5 1.0 C4B R:HDD801 3.1 10.8 1.0 HE R:ARG411 3.3 9.4 1.0 CHD R:HDD801 3.4 10.3 1.0 CHA R:HDD801 3.4 8.7 1.0 CHB R:HDD801 3.4 10.3 1.0 CHC R:HDD801 3.5 9.9 1.0 HE2 R:TYR415 3.5 8.9 1.0 HH21 R:ARG411 3.6 9.8 1.0 C2 R:GOL802 3.6 21.3 0.8 H11 R:GOL802 3.6 16.4 0.8 CE2 R:TYR415 3.7 9.1 1.0 CE1 R:TYR415 3.9 9.6 1.0 HE1 R:TYR415 3.9 9.3 1.0 C1 R:GOL802 4.0 18.1 0.8 HG22 R:VAL127 4.0 9.0 1.0 H12 R:GOL802 4.1 17.6 0.8 NE R:ARG411 4.2 9.7 1.0 HZ R:PHE214 4.2 12.7 1.0 H2 R:GOL802 4.2 18.6 0.8 NH2 R:ARG411 4.3 10.1 1.0 HG23 R:VAL127 4.3 8.8 1.0 HD2 R:HIS128 4.3 10.2 1.0 C2A R:HDD801 4.3 9.0 1.0 C3C R:HDD801 4.3 10.2 1.0 C3A R:HDD801 4.3 9.7 1.0 C2D R:HDD801 4.4 12.5 1.0 HE2 R:HIS128 4.4 12.0 1.0 C3D R:HDD801 4.4 12.2 1.0 C3B R:HDD801 4.4 10.6 1.0 C2B R:HDD801 4.4 10.2 1.0 C2C R:HDD801 4.4 10.1 1.0 HHD R:HDD801 4.5 10.4 1.0 HHA R:HDD801 4.5 8.7 1.0 HHB R:HDD801 4.5 10.3 1.0 HG2 R:ARG411 4.5 9.2 1.0 HHC R:HDD801 4.5 9.6 1.0 H32 R:GOL802 4.6 22.0 0.8 CG2 R:VAL127 4.6 9.0 1.0 CZ R:ARG411 4.6 9.6 1.0 C3 R:GOL802 4.6 27.0 0.8 CZ R:PHE214 4.7 11.6 1.0 HG11 R:VAL199 4.7 9.3 1.0 CD2 R:HIS128 4.7 10.3 1.0 NE2 R:HIS128 4.7 11.3 1.0 H31 R:GOL802 4.8 23.7 0.8 CD2 R:TYR415 4.9 9.3 1.0 HH22 R:ARG411 4.9 10.0 1.0 HG21 R:VAL127 4.9 8.7 1.0 HG12 R:VAL199 5.0 9.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of E. Coli Hpii Catalase Variant


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 E. Coli Hpii Catalase Variant within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe801 b:9.8 occ:1.00 FE S:HDD801 0.0 9.8 1.0 ND S:HDD801 2.0 8.9 1.0 OH S:TYR415 2.0 10.3 1.0 NA S:HDD801 2.0 9.4 1.0 NC S:HDD801 2.1 9.6 1.0 NB S:HDD801 2.1 9.8 1.0 HO2 S:GOL802 2.3 15.4 0.8 O2 S:GOL802 2.4 17.7 0.8 HH S:TYR415 2.6 9.5 0.0 CZ S:TYR415 3.0 8.5 1.0 C1D S:HDD801 3.0 9.0 1.0 C4D S:HDD801 3.0 8.9 1.0 C1A S:HDD801 3.0 8.3 1.0 C4C S:HDD801 3.0 8.5 1.0 C4A S:HDD801 3.1 8.1 1.0 C1C S:HDD801 3.1 9.4 1.0 C4B S:HDD801 3.1 9.1 1.0 C1B S:HDD801 3.1 9.1 1.0 HE S:ARG411 3.3 8.2 1.0 H32 S:GOL802 3.4 15.2 0.8 CHD S:HDD801 3.4 8.5 1.0 CHA S:HDD801 3.4 8.7 1.0 CHC S:HDD801 3.4 9.4 1.0 CHB S:HDD801 3.4 8.8 1.0 C2 S:GOL802 3.5 19.0 0.8 HE2 S:TYR415 3.5 8.7 1.0 H2 S:GOL802 3.6 18.2 0.8 HH21 S:ARG411 3.6 7.7 1.0 CE2 S:TYR415 3.7 9.0 1.0 CE1 S:TYR415 3.9 8.3 1.0 C3 S:GOL802 3.9 17.9 0.8 HE1 S:TYR415 3.9 8.1 1.0 HG22 S:VAL127 4.1 8.7 1.0 NE S:ARG411 4.2 8.4 1.0 HZ S:PHE214 4.2 11.6 1.0 NH2 S:ARG411 4.3 7.6 1.0 HG23 S:VAL127 4.3 8.4 1.0 HD2 S:HIS128 4.3 9.1 1.0 C2A S:HDD801 4.3 7.8 1.0 C3B S:HDD801 4.3 9.4 1.0 HE2 S:HIS128 4.3 11.0 1.0 C3A S:HDD801 4.4 7.6 1.0 C3C S:HDD801 4.4 9.0 1.0 C2D S:HDD801 4.4 11.1 1.0 C3D S:HDD801 4.4 11.6 1.0 C2C S:HDD801 4.4 9.3 1.0 C2B S:HDD801 4.4 9.2 1.0 H31 S:GOL802 4.4 17.7 0.8 HHD S:HDD801 4.5 8.4 1.0 HHA S:HDD801 4.5 8.6 1.0 HG2 S:ARG411 4.5 8.5 1.0 HHB S:HDD801 4.5 8.7 1.0 HHC S:HDD801 4.5 9.2 1.0 CG2 S:VAL127 4.6 8.5 1.0 CZ S:ARG411 4.6 8.4 1.0 CZ S:PHE214 4.7 10.7 1.0 CD2 S:HIS128 4.7 9.1 1.0 NE2 S:HIS128 4.7 10.4 1.0 HG11 S:VAL199 4.7 8.9 1.0 C1 S:GOL802 4.8 24.4 0.8 HH22 S:ARG411 4.9 7.6 1.0 CD2 S:TYR415 4.9 8.4 1.0 HG21 S:VAL127 5.0 8.4 1.0 HG12 S:VAL199 5.0 9.1 1.0 H11 S:GOL802 5.0 22.6 0.8

J.Wang, I.V.Lomkalin. Influence of Weak-Intensity Data, Ordered Water Molecules, and Hydrogen Atoms on the Refinement of A Large Protein Crystal Structure To Be Published.