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:
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 Oct 8 13:14:20 2024
|