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Potassium in PDB 6rjn: Crystal Structure of A Fungal Catalase at 2.3 Angstroms

Enzymatic activity of Crystal Structure of A Fungal Catalase at 2.3 Angstroms

All present enzymatic activity of Crystal Structure of A Fungal Catalase at 2.3 Angstroms:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of A Fungal Catalase at 2.3 Angstroms, PDB code: 6rjn was solved by S.Gomez, S.Navas-Yuste, A.M.Payne, W.Rivera, M.Lopez-Estepa, C.Brangbour, D.Fulla, J.Juanhuix, F.J.Fernandez, M.C.Vega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.67 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 165.943, 173.690, 96.490, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 19.6

Other elements in 6rjn:

The structure of Crystal Structure of A Fungal Catalase at 2.3 Angstroms also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms (pdb code 6rjn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms, PDB code: 6rjn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 6rjn

Go back to Potassium Binding Sites List in 6rjn
Potassium binding site 1 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K611

b:51.6
occ:1.00
 O A:GLY208 2.4 23.6 1.0
O A:HOH880 2.4 28.3 1.0
O A:PRO142 2.4 25.9 1.0
O A:LYS292 2.6 23.8 1.0
O A:HOH801 2.7 22.6 1.0
C A:GLY208 3.4 25.4 1.0
NE2 A:GLN224 3.6 24.3 1.0
C A:PRO142 3.7 27.7 1.0
C A:LYS292 3.8 23.8 1.0
OE1 A:GLN224 3.9 26.2 1.0
CA A:GLY208 3.9 22.2 1.0
CD A:GLN224 4.0 22.6 1.0
O A:LEU290 4.2 28.1 1.0
CG2 A:ILE143 4.2 26.1 1.0
CA A:VAL293 4.4 22.7 1.0
CD1 A:LEU290 4.5 23.8 1.0
CA A:ILE143 4.5 32.4 1.0
N A:ILE143 4.5 30.8 1.0
N A:VAL293 4.5 18.7 1.0
N A:HIS209 4.6 27.5 1.0
CA A:PRO142 4.6 22.9 1.0
C A:LEU290 4.6 27.1 1.0
CA A:LEU290 4.7 22.5 1.0
CB A:PRO142 4.7 32.6 1.0
O A:ASP289 4.7 23.4 1.0
N A:LYS292 4.8 21.9 1.0
N A:GLY208 4.9 25.4 1.0
CG1 A:VAL293 4.9 27.6 1.0
O A:HOH888 4.9 32.1 1.0
CA A:LYS292 4.9 27.0 1.0

Potassium binding site 2 out of 7 in 6rjn

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Potassium binding site 2 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:51.9
occ:1.00
 O A:GLN377 2.8 22.9 1.0
O B:HOH832 2.8 20.4 1.0
O B:SER51 2.9 18.2 1.0
N B:PHE55 3.5 20.4 1.0
CB B:PHE55 3.5 29.9 1.0
CA A:MET378 3.6 24.6 1.0
CG A:MET378 3.6 29.3 1.0
OG B:SER51 3.6 30.5 1.0
C A:GLN377 3.6 23.6 1.0
CA B:PHE55 3.7 20.8 1.0
C B:SER51 3.8 25.9 1.0
CB C:PRO153 3.8 27.8 1.0
N A:MET378 4.0 29.8 1.0
CB A:MET378 4.1 27.0 1.0
CG A:GLN377 4.2 27.1 1.0
CG C:PRO153 4.2 30.4 1.0
CA B:SER51 4.2 24.1 1.0
CB B:HIS54 4.3 25.6 1.0
C B:HIS54 4.3 22.2 1.0
OE2 B:GLU58 4.4 35.6 1.0
CB B:SER51 4.5 23.7 1.0
CG B:PHE55 4.5 26.7 1.0
CD1 B:PHE55 4.6 21.8 1.0
ND1 B:HIS54 4.6 28.1 1.0
C A:MET378 4.8 27.4 1.0
CE1 C:HIS157 4.8 23.3 1.0
N A:ARG379 4.8 22.3 1.0
CB A:GLN377 4.9 29.4 1.0
CA B:HIS54 4.9 20.6 1.0
CA A:GLN377 4.9 24.6 1.0
CG B:HIS54 4.9 35.6 1.0
N B:LEU52 4.9 22.3 1.0

Potassium binding site 3 out of 7 in 6rjn

Go back to Potassium Binding Sites List in 6rjn
Potassium binding site 3 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K611

b:46.4
occ:1.00
 O B:LYS292 2.3 27.1 1.0
O B:HOH819 2.5 23.6 1.0
O B:GLY208 2.6 22.4 1.0
O B:HOH750 2.6 21.8 1.0
O B:PRO142 2.6 21.8 1.0
C B:LYS292 3.5 20.1 1.0
C B:GLY208 3.6 19.4 1.0
NE2 B:GLN224 3.6 25.6 1.0
C B:PRO142 3.8 27.0 1.0
O B:LEU290 4.1 21.7 1.0
CA B:GLY208 4.1 19.7 1.0
OE1 B:GLN224 4.1 29.6 1.0
CA B:VAL293 4.1 27.1 1.0
CD B:GLN224 4.1 27.0 1.0
N B:VAL293 4.2 25.0 1.0
CG2 B:ILE143 4.3 21.1 1.0
O B:ASP289 4.4 17.0 1.0
N B:LYS292 4.5 18.9 1.0
O B:HOH931 4.5 26.8 1.0
C B:LEU290 4.6 24.3 1.0
CA B:ILE143 4.6 21.6 1.0
CA B:LYS292 4.6 19.9 1.0
N B:ILE143 4.6 23.4 1.0
CA B:LEU290 4.7 25.3 1.0
CD1 B:LEU290 4.7 23.4 1.0
CA B:PRO142 4.8 26.3 1.0
N B:HIS209 4.8 21.9 1.0
CB B:PRO142 4.9 25.1 1.0
CG1 B:VAL293 4.9 24.0 1.0

Potassium binding site 4 out of 7 in 6rjn

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Potassium binding site 4 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K613

b:62.2
occ:1.00
 O B:HOH959 2.5 33.2 1.0
O C:SER150 2.6 26.0 1.0
O C:HOH805 2.8 25.6 1.0
OG B:SER51 3.0 30.5 1.0
CB B:SER51 3.4 23.7 1.0
C C:SER150 3.5 25.4 1.0
CA C:SER150 3.6 24.2 1.0
CB C:SER150 3.7 32.2 1.0
NE2 C:HIS154 4.0 25.1 1.0
CG C:PRO153 4.1 30.4 1.0
CD2 C:HIS154 4.1 29.4 1.0
CD C:PRO153 4.1 26.0 1.0
NE2 A:GLN377 4.2 29.4 1.0
CG A:GLN377 4.3 27.1 1.0
O B:HOH920 4.3 35.5 1.0
CD A:GLN377 4.7 28.4 1.0
N C:LYS151 4.7 24.6 1.0
O B:HOH905 4.8 30.5 1.0
CB C:PRO153 4.8 27.8 1.0
CD1 B:LEU48 4.9 27.8 1.0
CA B:SER51 4.9 24.1 1.0
OG C:SER150 4.9 37.5 1.0
O B:VAL18 5.0 29.1 1.0
N C:SER150 5.0 25.4 1.0

Potassium binding site 5 out of 7 in 6rjn

Go back to Potassium Binding Sites List in 6rjn
Potassium binding site 5 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K609

b:54.5
occ:1.00
 O C:LYS292 2.4 28.7 1.0
O C:HOH869 2.4 32.9 1.0
O C:PRO142 2.5 23.8 1.0
O C:GLY208 2.6 21.9 1.0
O C:HOH780 2.6 21.9 1.0
NE2 C:GLN224 3.5 26.6 1.0
C C:LYS292 3.6 29.4 1.0
C C:GLY208 3.6 25.1 1.0
C C:PRO142 3.7 20.4 1.0
OE1 C:GLN224 4.0 31.2 1.0
CD C:GLN224 4.1 28.7 1.0
CA C:GLY208 4.1 26.1 1.0
O C:LEU290 4.1 25.1 1.0
CA C:VAL293 4.2 29.7 1.0
CG2 C:ILE143 4.2 28.3 1.0
N C:VAL293 4.3 28.4 1.0
CA C:ILE143 4.5 24.2 1.0
O C:HOH855 4.5 30.6 1.0
N C:ILE143 4.5 21.3 1.0
O C:ASP289 4.5 21.9 1.0
N C:LYS292 4.5 25.7 1.0
C C:LEU290 4.6 24.8 1.0
CG1 C:VAL293 4.7 35.6 1.0
CA C:PRO142 4.7 30.8 1.0
CA C:LYS292 4.7 25.6 1.0
CB C:PRO142 4.7 30.0 1.0
CA C:LEU290 4.7 27.1 1.0
N C:HIS209 4.8 31.2 1.0
CD1 C:LEU290 4.8 23.9 1.0
O C:HOH728 4.9 27.1 1.0
CB C:VAL293 5.0 38.0 1.0
CB C:ILE143 5.0 26.7 1.0

Potassium binding site 6 out of 7 in 6rjn

Go back to Potassium Binding Sites List in 6rjn
Potassium binding site 6 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K611

b:57.5
occ:1.00
 O D:GLN377 2.6 27.6 1.0
O C:HOH772 2.7 24.1 1.0
O C:SER51 3.1 27.3 1.0
N C:PHE55 3.4 22.9 1.0
CB C:PHE55 3.4 26.6 1.0
C D:GLN377 3.5 25.5 1.0
CA D:MET378 3.6 32.1 1.0
CA C:PHE55 3.6 21.4 1.0
CG D:MET378 3.7 30.6 1.0
CB B:PRO153 3.8 24.2 1.0
N D:MET378 3.9 22.0 1.0
OG C:SER51 3.9 28.4 1.0
OE2 C:GLU58 4.0 26.5 1.0
CG B:PRO153 4.1 25.6 1.0
CB D:MET378 4.1 20.5 1.0
C C:SER51 4.1 25.7 1.0
CG D:GLN377 4.3 25.3 1.0
CB C:HIS54 4.3 27.7 1.0
C C:HIS54 4.3 20.0 1.0
CG C:PHE55 4.4 22.3 1.0
CD1 C:PHE55 4.4 20.9 1.0
CA C:SER51 4.6 29.2 1.0
CE1 B:HIS157 4.7 19.8 1.0
ND1 C:HIS54 4.7 30.3 1.0
C D:MET378 4.8 28.0 1.0
CA D:GLN377 4.8 25.6 1.0
CB D:GLN377 4.8 23.7 1.0
N D:ARG379 4.8 23.1 1.0
CA C:HIS54 4.8 22.2 1.0
CB C:SER51 4.9 22.9 1.0
CG C:HIS54 4.9 34.4 1.0
NE2 B:HIS157 5.0 27.3 1.0

Potassium binding site 7 out of 7 in 6rjn

Go back to Potassium Binding Sites List in 6rjn
Potassium binding site 7 out of 7 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K608

b:51.5
occ:1.00
 O D:LYS292 2.4 25.1 1.0
O D:HOH834 2.5 26.7 1.0
O D:GLY208 2.5 25.6 1.0
O D:HOH791 2.6 26.0 1.0
O D:PRO142 2.6 23.3 1.0
C D:GLY208 3.5 28.3 1.0
C D:LYS292 3.6 26.2 1.0
NE2 D:GLN224 3.7 24.8 1.0
C D:PRO142 3.8 22.6 1.0
CA D:GLY208 3.9 24.5 1.0
OE1 D:GLN224 3.9 32.3 1.0
CD D:GLN224 4.1 29.5 1.0
CA D:VAL293 4.2 25.8 1.0
CG2 D:ILE143 4.2 24.1 1.0
O D:LEU290 4.3 25.0 1.0
N D:VAL293 4.3 25.7 1.0
O D:ASP289 4.5 30.5 1.0
O D:HOH932 4.6 25.4 1.0
CG1 D:VAL293 4.6 36.9 1.0
CA D:ILE143 4.6 24.8 1.0
N D:LYS292 4.6 25.2 1.0
C D:LEU290 4.7 25.8 1.0
N D:ILE143 4.7 24.0 1.0
N D:HIS209 4.7 27.5 1.0
CB D:PRO142 4.7 25.1 1.0
CA D:LEU290 4.7 20.1 1.0
CA D:LYS292 4.7 28.2 1.0
CA D:PRO142 4.8 24.7 1.0
CD1 D:LEU290 4.8 23.0 1.0
O D:HOH792 4.9 30.6 1.0
CB D:VAL293 4.9 29.1 1.0
N D:GLY208 5.0 25.1 1.0

Reference:

S.Gomez, S.Navas-Yuste, A.M.Payne, W.Rivera, M.Lopez-Estepa, C.Brangbour, D.Fulla, J.Juanhuix, F.J.Fernandez, M.C.Vega. Peroxisomal Catalases From the Yeasts Pichia Pastoris and Kluyveromyces Lactis As Models For Oxidative Damage in Higher Eukaryotes. Free Radic. Biol. Med. V. 141 279 2019.
ISSN: ISSN 1873-4596
PubMed: 31238127
DOI: 10.1016/J.FREERADBIOMED.2019.06.025
Page generated: Mon Aug 12 17:28:15 2024

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