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Sodium 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:

Potassium (K) 7 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms, PDB code: 6rjn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6rjn

Go back to Sodium Binding Sites List in 6rjn
Sodium binding site 1 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na612

b:37.3
occ:1.00
O A:ASN34 2.4 32.7 1.0
OD1 A:ASN28 2.4 39.0 1.0
O A:PRO36 2.4 42.5 1.0
O A:HOH788 2.4 34.3 1.0
O A:HOH943 2.5 33.9 1.0
O A:HOH917 2.6 35.1 1.0
CG A:ASN28 3.2 34.9 1.0
ND2 A:ASN28 3.3 36.3 1.0
C A:ASN34 3.5 31.1 1.0
C A:PRO36 3.5 30.2 1.0
O A:ALA35 3.9 31.7 1.0
C A:ALA35 4.0 32.9 1.0
O A:HOH945 4.1 36.4 1.0
O A:HOH818 4.1 32.2 1.0
CG A:LYS37 4.2 40.2 1.0
N A:PRO36 4.2 35.8 1.0
CA A:ASN34 4.2 41.7 1.0
N A:LYS37 4.3 39.4 1.0
CA A:LYS37 4.4 33.8 1.0
N A:ALA35 4.4 33.0 1.0
CB A:ASN34 4.5 40.7 1.0
CA A:PRO36 4.5 35.1 1.0
CA A:ALA35 4.5 34.7 1.0
NZ A:LYS37 4.5 51.4 1.0
CB A:ASN28 4.6 35.5 1.0
O D:HOH859 4.8 45.4 1.0
O A:ASN28 4.8 41.6 1.0
C A:ASN28 4.9 44.8 1.0
CB A:LYS37 4.9 34.7 1.0
CD A:PRO36 5.0 44.5 1.0

Sodium binding site 2 out of 4 in 6rjn

Go back to Sodium Binding Sites List in 6rjn
Sodium binding site 2 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na612

b:50.9
occ:1.00
O B:HOH762 2.2 35.2 1.0
OD1 B:ASN28 2.4 35.0 1.0
O B:ASN34 2.4 46.9 1.0
O B:HOH967 2.6 40.2 1.0
O B:PRO36 2.7 33.9 1.0
O B:HOH994 2.7 40.9 1.0
CG B:ASN28 3.3 42.6 1.0
C B:ASN34 3.6 47.6 1.0
ND2 B:ASN28 3.6 44.8 1.0
O B:HOH932 3.6 39.1 1.0
C B:PRO36 3.8 40.4 1.0
O B:ALA35 4.1 43.3 1.0
C B:ALA35 4.2 43.7 1.0
CG B:LYS37 4.3 40.8 1.0
NZ B:LYS37 4.3 59.9 1.0
CA B:ASN34 4.4 48.0 1.0
O B:HOH835 4.4 30.6 1.0
N B:ALA35 4.5 42.5 1.0
N B:PRO36 4.5 37.6 1.0
CB B:ASN34 4.5 45.4 1.0
CA B:ALA35 4.6 51.0 1.0
O B:ASN28 4.6 39.8 1.0
N B:LYS37 4.6 35.7 1.0
CA B:LYS37 4.7 36.9 1.0
C B:ASN28 4.7 33.4 1.0
CB B:ASN28 4.7 43.6 1.0
O C:HOH807 4.8 37.8 1.0
CA B:PRO36 4.8 41.1 1.0
CG B:ASN34 4.9 48.1 1.0
N B:ASN28 4.9 34.9 1.0

Sodium binding site 3 out of 4 in 6rjn

Go back to Sodium Binding Sites List in 6rjn
Sodium binding site 3 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na610

b:41.4
occ:1.00
O C:ASN34 2.3 38.7 1.0
O C:HOH935 2.4 46.2 1.0
OD1 C:ASN28 2.5 33.0 1.0
O C:HOH815 2.5 50.1 1.0
O C:HOH976 2.7 44.3 1.0
O C:PRO36 2.7 35.7 1.0
CG C:ASN28 3.5 32.5 1.0
C C:ASN34 3.5 35.1 1.0
ND2 C:ASN28 3.7 32.9 1.0
O C:HOH920 3.7 45.3 1.0
C C:PRO36 3.8 37.9 1.0
O C:HOH898 3.8 35.4 1.0
O C:ALA35 4.0 34.1 1.0
C C:ALA35 4.1 40.6 1.0
CA C:ASN34 4.3 44.4 1.0
CB C:ASN34 4.4 47.2 1.0
CG C:LYS37 4.4 37.7 1.0
NZ C:LYS37 4.4 50.6 1.0
N C:PRO36 4.4 39.5 1.0
N C:ALA35 4.5 34.4 1.0
CA C:ALA35 4.5 36.4 1.0
N C:LYS37 4.5 39.1 1.0
O C:HOH779 4.5 26.6 1.0
O B:HOH915 4.7 51.8 1.0
CA C:LYS37 4.7 29.2 1.0
CA C:PRO36 4.7 36.9 1.0
CG C:ASN34 4.8 41.3 1.0
C C:ASN28 4.8 41.0 1.0
CB C:ASN28 4.9 37.1 1.0
O C:ASN28 5.0 42.8 1.0

Sodium binding site 4 out of 4 in 6rjn

Go back to Sodium Binding Sites List in 6rjn
Sodium binding site 4 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
D:Na609

b:49.3
occ:1.00
O D:HOH750 2.2 47.7 1.0
O D:ASN34 2.3 40.4 1.0
O D:PRO36 2.4 37.3 1.0
O D:HOH961 2.5 40.4 1.0
OD1 D:ASN28 2.6 33.3 1.0
O D:HOH954 2.6 36.2 1.0
C D:PRO36 3.5 37.4 1.0
CG D:ASN28 3.5 40.9 1.0
C D:ASN34 3.5 40.0 1.0
O D:ALA35 3.5 39.7 1.0
ND2 D:ASN28 3.6 38.7 1.0
C D:ALA35 3.7 39.8 1.0
CG D:LYS37 3.9 38.6 1.0
NZ D:LYS37 4.0 59.0 1.0
N D:PRO36 4.2 42.8 1.0
O D:HOH956 4.2 33.4 1.0
N D:LYS37 4.3 33.8 1.0
CA D:ALA35 4.3 40.7 1.0
N D:ALA35 4.3 38.7 1.0
O D:HOH725 4.4 33.0 1.0
CA D:LYS37 4.4 31.4 1.0
CA D:PRO36 4.4 43.1 1.0
CA D:ASN34 4.4 42.4 1.0
O D:HOH968 4.6 47.7 1.0
CB D:ASN34 4.7 47.5 1.0
CB D:LYS37 4.8 36.1 1.0
CD D:PRO36 4.9 43.2 1.0
CB D:ASN28 4.9 36.6 1.0
CE D:LYS37 5.0 52.1 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: Tue Dec 15 12:54:58 2020

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