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Chlorine in PDB 4qom: Bacillus Pumilus Catalase with Pyrogallol Bound

Enzymatic activity of Bacillus Pumilus Catalase with Pyrogallol Bound

All present enzymatic activity of Bacillus Pumilus Catalase with Pyrogallol Bound:
1.11.1.6;

Protein crystallography data

The structure of Bacillus Pumilus Catalase with Pyrogallol Bound, PDB code: 4qom was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.29 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.853, 109.424, 103.368, 90.00, 92.21, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 4qom:

The structure of Bacillus Pumilus Catalase with Pyrogallol Bound also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bacillus Pumilus Catalase with Pyrogallol Bound (pdb code 4qom). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Bacillus Pumilus Catalase with Pyrogallol Bound, PDB code: 4qom:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4qom

Go back to Chlorine Binding Sites List in 4qom
Chlorine binding site 1 out of 6 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:23.3
occ:1.00
 NH2 B:ARG48 3.3 13.8 1.0
NH2 A:ARG48 3.3 14.1 1.0
O D:HOH802 3.4 25.5 1.0
NE A:ARG48 3.5 14.1 1.0
NE B:ARG48 3.6 12.1 1.0
O C:HOH946 3.6 26.9 1.0
CZ A:ARG48 3.8 14.0 1.0
CZ B:ARG48 3.9 13.1 1.0
CA D:HIS346 4.1 16.4 1.0
N D:HIS346 4.1 15.9 1.0
CB D:HIS346 4.2 18.8 1.0
CA C:HIS346 4.2 16.1 1.0
N C:HIS346 4.3 15.2 1.0
CB C:HIS346 4.3 18.2 1.0
C D:ARG345 4.4 15.6 1.0
O D:ARG345 4.5 16.0 1.0
C C:ARG345 4.6 15.2 1.0
O C:ARG345 4.7 14.6 1.0
CD A:ARG48 4.7 14.2 1.0
CD B:ARG48 4.7 12.1 1.0
CB D:ARG345 4.8 14.8 1.0
CB C:ARG345 4.9 15.4 1.0

Chlorine binding site 2 out of 6 in 4qom

Go back to Chlorine Binding Sites List in 4qom
Chlorine binding site 2 out of 6 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:19.7
occ:1.00
 O B:HOH639 3.1 17.6 1.0
O C:HOH696 3.2 25.8 1.0
N A:ASN367 3.3 17.3 1.0
O A:HOH613 3.3 15.3 1.0
CB A:ASN366 3.7 18.9 1.0
CE C:LYS42 3.7 17.4 1.0
CB A:ASN367 3.9 16.8 1.0
CA A:ASN367 3.9 17.0 1.0
N A:GLN368 4.1 15.6 1.0
CD C:LYS42 4.1 17.0 1.0
CG C:LYS42 4.1 17.4 1.0
C A:ASN367 4.2 17.4 1.0
CD2 C:LEU9 4.2 26.0 0.5
CG A:ASN366 4.3 19.5 1.0
C A:ASN366 4.3 18.1 1.0
CD1 C:LEU9 4.4 25.3 0.5
CA A:ASN366 4.4 17.6 1.0
CG A:GLN368 4.4 18.3 1.0
CD1 C:LEU9 4.5 29.4 0.5
CE1 C:HIS38 4.5 21.6 1.0
CD2 C:LEU9 4.5 29.9 0.5
NZ C:LYS42 4.5 19.3 1.0
O B:HOH615 4.6 19.1 1.0
OD1 A:ASN366 4.6 18.5 1.0
OD1 A:ASN367 4.6 20.1 1.0
CG A:ASN367 4.7 17.8 1.0
CG C:LEU9 4.7 29.2 0.5
OD1 C:ASN20 4.7 19.9 1.0
CG C:LEU9 4.7 26.1 0.5
NE2 A:GLN368 4.9 21.1 1.0
O A:ASN367 5.0 16.0 1.0

Chlorine binding site 3 out of 6 in 4qom

Go back to Chlorine Binding Sites List in 4qom
Chlorine binding site 3 out of 6 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:19.1
occ:1.00
 O D:HOH840 3.1 27.1 1.0
O A:HOH606 3.1 17.6 1.0
O B:HOH682 3.2 17.1 1.0
N B:ASN367 3.3 16.6 1.0
CB B:ASN366 3.7 18.4 1.0
CE D:LYS42 3.7 16.9 1.0
CB B:ASN367 3.9 17.1 1.0
CA B:ASN367 3.9 16.8 1.0
CD D:LYS42 4.1 17.3 1.0
CG D:LYS42 4.1 16.6 1.0
N B:GLN368 4.1 17.2 1.0
C B:ASN367 4.2 18.3 1.0
C B:ASN366 4.3 17.9 1.0
CG B:ASN366 4.3 17.8 1.0
CG B:GLN368 4.3 19.0 1.0
CA B:ASN366 4.4 17.0 1.0
NZ D:LYS42 4.5 16.8 1.0
CD1 D:LEU9 4.5 31.4 1.0
OD1 B:ASN366 4.5 16.6 1.0
CD2 D:LEU9 4.5 34.8 1.0
CE1 D:HIS38 4.6 25.0 1.0
O A:HOH641 4.6 19.6 1.0
OD1 B:ASN367 4.7 19.8 1.0
CG B:ASN367 4.7 18.4 1.0
CG D:LEU9 4.7 32.4 1.0
OD1 D:ASN20 4.8 19.1 1.0
NE2 B:GLN368 4.9 19.8 1.0
O B:ASN367 5.0 17.9 1.0

Chlorine binding site 4 out of 6 in 4qom

Go back to Chlorine Binding Sites List in 4qom
Chlorine binding site 4 out of 6 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl505

b:23.5
occ:1.00
 NH2 C:ARG48 3.2 17.1 1.0
NH2 D:ARG48 3.2 17.1 1.0
NE C:ARG48 3.4 15.2 1.0
NE D:ARG48 3.5 15.1 1.0
O B:HOH831 3.6 28.1 1.0
O A:HOH884 3.7 26.1 1.0
CZ D:ARG48 3.8 15.4 1.0
CZ C:ARG48 3.8 15.8 1.0
N A:HIS346 4.1 17.9 1.0
CA A:HIS346 4.1 17.9 1.0
CA B:HIS346 4.2 15.8 1.0
CB A:HIS346 4.2 19.6 1.0
N B:HIS346 4.2 14.7 1.0
CB B:HIS346 4.2 17.0 1.0
C A:ARG345 4.4 18.0 1.0
C B:ARG345 4.5 15.8 1.0
O A:ARG345 4.6 17.5 1.0
O B:ARG345 4.7 17.7 1.0
CD C:ARG48 4.7 14.6 1.0
CD D:ARG48 4.7 14.7 1.0
CB A:ARG345 4.7 18.2 1.0
CB B:ARG345 4.9 15.0 1.0

Chlorine binding site 5 out of 6 in 4qom

Go back to Chlorine Binding Sites List in 4qom
Chlorine binding site 5 out of 6 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl506

b:19.9
occ:1.00
 O A:HOH677 3.1 26.3 1.0
O D:HOH682 3.2 18.9 1.0
O C:HOH619 3.2 16.8 1.0
N C:ASN367 3.3 15.4 1.0
CB C:ASN366 3.7 16.4 1.0
CE A:LYS42 3.7 15.6 1.0
CB C:ASN367 3.8 17.1 1.0
CA C:ASN367 3.9 16.4 1.0
CD A:LYS42 4.0 16.0 1.0
N C:GLN368 4.1 15.1 1.0
CG A:LYS42 4.1 16.2 1.0
C C:ASN367 4.2 15.6 1.0
CG C:ASN366 4.3 17.1 1.0
CG C:GLN368 4.4 15.7 1.0
C C:ASN366 4.4 16.9 1.0
CA C:ASN366 4.4 16.4 1.0
NZ A:LYS42 4.4 16.8 1.0
CD1 A:LEU9 4.5 30.4 1.0
CE1 A:HIS38 4.5 18.8 1.0
CD2 A:LEU9 4.6 35.1 1.0
OD1 C:ASN366 4.6 17.0 1.0
O D:HOH626 4.6 18.4 1.0
OD1 C:ASN367 4.7 18.8 1.0
CG C:ASN367 4.7 16.8 1.0
OD1 A:ASN20 4.7 16.6 1.0
CG A:LEU9 4.7 31.7 1.0
NE2 C:GLN368 4.9 18.2 1.0
O C:ASN367 4.9 16.4 1.0

Chlorine binding site 6 out of 6 in 4qom

Go back to Chlorine Binding Sites List in 4qom
Chlorine binding site 6 out of 6 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl505

b:18.2
occ:1.00
 O B:HOH643 3.1 27.1 1.0
O D:HOH679 3.2 17.4 1.0
O C:HOH605 3.2 16.0 1.0
N D:ASN367 3.3 15.8 1.0
CB D:ASN366 3.7 16.8 1.0
CE B:LYS42 3.8 13.4 1.0
CB D:ASN367 3.8 16.0 1.0
CA D:ASN367 3.9 15.8 1.0
CD B:LYS42 4.1 13.5 1.0
N D:GLN368 4.1 15.1 1.0
CG B:LYS42 4.1 13.7 1.0
C D:ASN367 4.2 15.1 1.0
CG D:ASN366 4.3 16.7 1.0
C D:ASN366 4.3 16.6 1.0
CA D:ASN366 4.4 17.2 1.0
CG D:GLN368 4.4 17.9 1.0
O C:HOH638 4.5 16.5 1.0
NZ B:LYS42 4.5 13.7 1.0
CD1 B:LEU9 4.5 27.1 1.0
OD1 D:ASN366 4.5 17.7 1.0
CD2 B:LEU9 4.6 30.4 1.0
CE1 B:HIS38 4.6 19.2 1.0
OD1 D:ASN367 4.6 19.9 1.0
CG D:ASN367 4.7 16.3 1.0
CG B:LEU9 4.7 26.1 1.0
OD1 B:ASN20 4.8 17.3 1.0
O D:ASN367 4.9 17.2 1.0
NE2 D:GLN368 4.9 20.0 1.0

Reference:

P.C.Loewen, J.Villanueva, J.Switala, L.J.Donald, A.Ivancich. Unprecedented Access of Phenolic Substrates to the Heme Active Site of A Catalase: Substrate Binding and Peroxidase-Like Reactivity of Bacillus Pumilus Catalase Monitored By X-Ray Crystallography and Epr Spectroscopy. Proteins 2015.
ISSN: ESSN 1097-0134
PubMed: 25663126
DOI: 10.1002/PROT.24777
Page generated: Fri Jul 26 00:40:29 2024

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