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:
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
Go back to
Potassium Binding Sites List in 6rjn
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
Go back to
Potassium Binding Sites List in 6rjn
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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