Calcium in PDB 1o9i: Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Enzymatic activity of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
All present enzymatic activity of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution:
1.11.1.6;
Protein crystallography data
The structure of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution, PDB code: 1o9i
was solved by
V.V.Barynin,
M.M.Whittaker,
J.W.Whittaker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.33
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.490,
95.270,
105.000,
90.00,
106.55,
90.00
|
R / Rfree (%)
|
11.5 /
14.5
|
Other elements in 1o9i:
The structure of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
(pdb code 1o9i). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution, PDB code: 1o9i:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1o9i
Go back to
Calcium Binding Sites List in 1o9i
Calcium binding site 1 out
of 6 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca269
b:23.1
occ:1.00
|
OD1
|
F:ASN218
|
2.1
|
22.5
|
1.0
|
O
|
F:GLY222
|
2.3
|
20.4
|
1.0
|
OD1
|
A:ASP57
|
2.4
|
19.6
|
1.0
|
O
|
F:SER220
|
2.4
|
20.2
|
1.0
|
OD2
|
A:ASP57
|
2.4
|
20.5
|
1.0
|
OD1
|
A:ASP61
|
2.5
|
18.1
|
1.0
|
O
|
F:HOH2198
|
2.7
|
29.7
|
1.0
|
CG
|
A:ASP57
|
2.8
|
17.9
|
1.0
|
OD2
|
A:ASP61
|
3.0
|
20.3
|
1.0
|
CG
|
A:ASP61
|
3.1
|
17.6
|
1.0
|
CG
|
F:ASN218
|
3.3
|
21.3
|
1.0
|
C
|
F:GLY222
|
3.4
|
19.9
|
1.0
|
C
|
F:SER220
|
3.5
|
17.2
|
1.0
|
OG
|
F:SER225
|
3.7
|
20.4
|
1.0
|
N
|
F:GLY222
|
3.9
|
19.5
|
1.0
|
CA
|
F:GLY222
|
4.1
|
19.9
|
1.0
|
ND2
|
F:ASN218
|
4.2
|
23.0
|
1.0
|
N
|
F:SER220
|
4.2
|
16.9
|
1.0
|
CA
|
F:SER220
|
4.2
|
16.9
|
1.0
|
CB
|
F:SER220
|
4.2
|
17.1
|
1.0
|
CB
|
A:ASP57
|
4.2
|
15.3
|
1.0
|
CB
|
F:ASN218
|
4.4
|
17.7
|
1.0
|
CA
|
F:ASN218
|
4.4
|
16.8
|
1.0
|
N
|
F:ASP223
|
4.4
|
20.9
|
1.0
|
C
|
F:ASP221
|
4.4
|
18.8
|
1.0
|
N
|
F:ASP221
|
4.5
|
17.5
|
1.0
|
O
|
A:ASP57
|
4.5
|
15.9
|
1.0
|
CA
|
F:ASP223
|
4.6
|
21.9
|
1.0
|
CB
|
A:ASP61
|
4.6
|
14.6
|
1.0
|
O
|
A:HOH2052
|
4.6
|
22.6
|
1.0
|
C
|
F:ASN218
|
4.7
|
17.1
|
1.0
|
O
|
F:HOH2192
|
4.7
|
30.9
|
1.0
|
CA
|
F:ASP221
|
4.7
|
17.2
|
1.0
|
OH
|
F:TYR241
|
4.7
|
21.4
|
1.0
|
CB
|
F:SER225
|
4.8
|
18.8
|
1.0
|
C
|
A:ASP57
|
4.9
|
15.7
|
1.0
|
N
|
F:PHE219
|
4.9
|
16.2
|
1.0
|
OG
|
F:SER220
|
4.9
|
17.7
|
1.0
|
N
|
F:SER225
|
4.9
|
17.7
|
1.0
|
CA
|
A:ASP57
|
5.0
|
15.2
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1o9i
Go back to
Calcium Binding Sites List in 1o9i
Calcium binding site 2 out
of 6 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca269
b:21.9
occ:1.00
|
OD1
|
C:ASN218
|
2.1
|
22.2
|
1.0
|
O
|
C:SER220
|
2.4
|
19.2
|
1.0
|
O
|
C:GLY222
|
2.4
|
18.8
|
1.0
|
OD2
|
B:ASP57
|
2.4
|
18.3
|
1.0
|
OD1
|
B:ASP57
|
2.4
|
18.5
|
1.0
|
OD1
|
B:ASP61
|
2.4
|
17.5
|
1.0
|
O
|
C:HOH2197
|
2.7
|
29.7
|
1.0
|
CG
|
B:ASP57
|
2.8
|
16.9
|
1.0
|
OD2
|
B:ASP61
|
3.1
|
21.8
|
1.0
|
CG
|
B:ASP61
|
3.1
|
16.3
|
1.0
|
CG
|
C:ASN218
|
3.3
|
20.7
|
1.0
|
C
|
C:GLY222
|
3.4
|
18.7
|
1.0
|
C
|
C:SER220
|
3.5
|
17.7
|
1.0
|
OG
|
C:SER225
|
3.8
|
19.6
|
1.0
|
N
|
C:GLY222
|
3.9
|
17.8
|
1.0
|
CA
|
C:GLY222
|
4.1
|
18.1
|
1.0
|
N
|
C:SER220
|
4.1
|
16.1
|
1.0
|
ND2
|
C:ASN218
|
4.1
|
23.2
|
1.0
|
CA
|
C:SER220
|
4.2
|
16.6
|
1.0
|
CB
|
B:ASP57
|
4.2
|
14.6
|
1.0
|
CB
|
C:SER220
|
4.3
|
17.1
|
1.0
|
CB
|
C:ASN218
|
4.3
|
17.3
|
1.0
|
C
|
C:ASP221
|
4.4
|
17.9
|
1.0
|
CA
|
C:ASN218
|
4.4
|
17.1
|
1.0
|
N
|
C:ASP223
|
4.5
|
21.3
|
1.0
|
N
|
C:ASP221
|
4.5
|
17.5
|
1.0
|
O
|
B:ASP57
|
4.5
|
15.2
|
1.0
|
CA
|
C:ASP223
|
4.6
|
22.2
|
1.0
|
O
|
C:HOH2190
|
4.6
|
32.1
|
1.0
|
CB
|
B:ASP61
|
4.6
|
14.5
|
1.0
|
C
|
C:ASN218
|
4.6
|
16.7
|
1.0
|
O
|
B:HOH2050
|
4.6
|
19.6
|
1.0
|
CA
|
C:ASP221
|
4.7
|
16.8
|
1.0
|
OH
|
C:TYR241
|
4.7
|
21.3
|
1.0
|
CB
|
C:SER225
|
4.7
|
17.8
|
1.0
|
OG
|
C:SER220
|
4.9
|
17.2
|
1.0
|
O
|
C:ASP221
|
4.9
|
20.1
|
1.0
|
N
|
C:PHE219
|
4.9
|
16.0
|
1.0
|
C
|
B:ASP57
|
4.9
|
14.6
|
1.0
|
N
|
C:SER225
|
5.0
|
17.4
|
1.0
|
CA
|
B:ASP57
|
5.0
|
14.8
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1o9i
Go back to
Calcium Binding Sites List in 1o9i
Calcium binding site 3 out
of 6 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca269
b:26.0
occ:1.00
|
OD1
|
B:ASN218
|
2.1
|
27.3
|
1.0
|
O
|
B:SER220
|
2.3
|
22.6
|
1.0
|
O
|
B:GLY222
|
2.4
|
23.0
|
1.0
|
OD1
|
C:ASP57
|
2.4
|
21.2
|
1.0
|
OD1
|
C:ASP61
|
2.4
|
19.8
|
1.0
|
OD2
|
C:ASP57
|
2.4
|
22.8
|
1.0
|
CG
|
C:ASP57
|
2.8
|
20.5
|
1.0
|
O
|
B:HOH2194
|
2.9
|
33.0
|
1.0
|
OD2
|
C:ASP61
|
3.1
|
21.5
|
1.0
|
CG
|
C:ASP61
|
3.2
|
19.5
|
1.0
|
CG
|
B:ASN218
|
3.3
|
24.1
|
1.0
|
C
|
B:SER220
|
3.4
|
20.2
|
1.0
|
C
|
B:GLY222
|
3.4
|
23.3
|
1.0
|
OG
|
B:SER225
|
3.8
|
22.9
|
1.0
|
N
|
B:GLY222
|
3.9
|
22.2
|
1.0
|
CA
|
B:GLY222
|
4.1
|
22.5
|
1.0
|
ND2
|
B:ASN218
|
4.1
|
26.5
|
1.0
|
N
|
B:SER220
|
4.1
|
19.3
|
1.0
|
CA
|
B:SER220
|
4.2
|
19.5
|
1.0
|
CB
|
B:SER220
|
4.2
|
19.1
|
1.0
|
CB
|
C:ASP57
|
4.3
|
18.2
|
1.0
|
C
|
B:ASP221
|
4.3
|
21.9
|
1.0
|
CB
|
B:ASN218
|
4.4
|
20.8
|
1.0
|
CA
|
B:ASN218
|
4.4
|
21.0
|
1.0
|
N
|
B:ASP221
|
4.4
|
21.2
|
1.0
|
N
|
B:ASP223
|
4.4
|
24.0
|
1.0
|
O
|
C:ASP57
|
4.5
|
17.5
|
1.0
|
O
|
B:HOH2190
|
4.5
|
35.4
|
1.0
|
O
|
C:HOH2065
|
4.6
|
22.2
|
1.0
|
CA
|
B:ASP223
|
4.6
|
25.1
|
1.0
|
C
|
B:ASN218
|
4.6
|
20.6
|
1.0
|
CA
|
B:ASP221
|
4.6
|
21.6
|
1.0
|
CB
|
C:ASP61
|
4.7
|
17.3
|
1.0
|
OH
|
B:TYR241
|
4.8
|
23.2
|
1.0
|
CB
|
B:SER225
|
4.8
|
21.9
|
1.0
|
N
|
B:PHE219
|
4.9
|
19.4
|
1.0
|
OG
|
B:SER220
|
4.9
|
19.9
|
1.0
|
O
|
B:ASP221
|
4.9
|
22.6
|
1.0
|
C
|
C:ASP57
|
4.9
|
16.8
|
1.0
|
CA
|
C:ASP57
|
5.0
|
17.4
|
1.0
|
N
|
B:SER225
|
5.0
|
21.4
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1o9i
Go back to
Calcium Binding Sites List in 1o9i
Calcium binding site 4 out
of 6 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca269
b:25.4
occ:1.00
|
OD1
|
E:ASN218
|
2.0
|
25.3
|
1.0
|
OD1
|
D:ASP57
|
2.3
|
22.7
|
1.0
|
O
|
E:SER220
|
2.4
|
22.4
|
1.0
|
OD1
|
D:ASP61
|
2.4
|
19.8
|
1.0
|
O
|
E:GLY222
|
2.5
|
22.9
|
1.0
|
OD2
|
D:ASP57
|
2.5
|
21.4
|
1.0
|
CG
|
D:ASP57
|
2.8
|
19.3
|
1.0
|
O
|
D:HOH2065
|
2.8
|
32.9
|
1.0
|
OD2
|
D:ASP61
|
3.0
|
20.0
|
1.0
|
CG
|
D:ASP61
|
3.1
|
17.3
|
1.0
|
CG
|
E:ASN218
|
3.3
|
21.7
|
1.0
|
C
|
E:SER220
|
3.5
|
19.3
|
1.0
|
C
|
E:GLY222
|
3.5
|
22.5
|
1.0
|
OG
|
E:SER225
|
3.7
|
23.0
|
1.0
|
N
|
E:GLY222
|
3.9
|
20.0
|
1.0
|
ND2
|
E:ASN218
|
4.1
|
25.9
|
1.0
|
N
|
E:SER220
|
4.2
|
17.5
|
1.0
|
CA
|
E:GLY222
|
4.2
|
20.7
|
1.0
|
CB
|
E:ASN218
|
4.2
|
20.1
|
1.0
|
CA
|
E:SER220
|
4.2
|
17.9
|
1.0
|
CB
|
D:ASP57
|
4.3
|
15.7
|
1.0
|
CA
|
E:ASN218
|
4.3
|
18.4
|
1.0
|
CB
|
E:SER220
|
4.3
|
17.7
|
1.0
|
C
|
E:ASP221
|
4.4
|
20.2
|
1.0
|
N
|
E:ASP221
|
4.5
|
19.5
|
1.0
|
N
|
E:ASP223
|
4.5
|
23.3
|
1.0
|
O
|
D:ASP57
|
4.5
|
16.5
|
1.0
|
O
|
D:HOH2064
|
4.6
|
25.0
|
1.0
|
C
|
E:ASN218
|
4.6
|
18.4
|
1.0
|
CB
|
D:ASP61
|
4.6
|
15.7
|
1.0
|
O
|
E:HOH2196
|
4.7
|
32.9
|
1.0
|
OH
|
E:TYR241
|
4.7
|
24.4
|
1.0
|
CB
|
E:SER225
|
4.7
|
20.7
|
1.0
|
CA
|
E:ASP221
|
4.7
|
19.6
|
1.0
|
CA
|
E:ASP223
|
4.7
|
24.7
|
1.0
|
N
|
E:PHE219
|
4.9
|
17.0
|
1.0
|
C
|
D:ASP57
|
4.9
|
15.4
|
1.0
|
OG
|
E:SER220
|
4.9
|
18.3
|
1.0
|
CA
|
D:ASP57
|
5.0
|
15.9
|
1.0
|
N
|
E:SER225
|
5.0
|
19.8
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1o9i
Go back to
Calcium Binding Sites List in 1o9i
Calcium binding site 5 out
of 6 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca269
b:22.6
occ:1.00
|
OD1
|
D:ASN218
|
2.1
|
25.2
|
1.0
|
O
|
D:SER220
|
2.3
|
21.1
|
1.0
|
O
|
D:GLY222
|
2.4
|
21.8
|
1.0
|
OD2
|
E:ASP57
|
2.4
|
21.0
|
1.0
|
OD1
|
E:ASP57
|
2.4
|
20.1
|
1.0
|
OD1
|
E:ASP61
|
2.5
|
19.2
|
1.0
|
O
|
D:HOH2192
|
2.8
|
29.1
|
1.0
|
CG
|
E:ASP57
|
2.8
|
18.6
|
1.0
|
OD2
|
E:ASP61
|
3.0
|
22.5
|
1.0
|
CG
|
E:ASP61
|
3.1
|
18.4
|
1.0
|
CG
|
D:ASN218
|
3.3
|
21.4
|
1.0
|
C
|
D:GLY222
|
3.4
|
21.7
|
1.0
|
C
|
D:SER220
|
3.5
|
19.1
|
1.0
|
OG
|
D:SER225
|
3.7
|
20.3
|
1.0
|
N
|
D:GLY222
|
4.0
|
19.9
|
1.0
|
N
|
D:SER220
|
4.2
|
18.7
|
1.0
|
CA
|
D:GLY222
|
4.2
|
20.9
|
1.0
|
ND2
|
D:ASN218
|
4.2
|
24.0
|
1.0
|
CA
|
D:SER220
|
4.2
|
18.4
|
1.0
|
CB
|
E:ASP57
|
4.3
|
16.8
|
1.0
|
CB
|
D:SER220
|
4.3
|
18.7
|
1.0
|
CB
|
D:ASN218
|
4.3
|
20.4
|
1.0
|
CA
|
D:ASN218
|
4.4
|
19.4
|
1.0
|
N
|
D:ASP223
|
4.4
|
23.0
|
1.0
|
C
|
D:ASP221
|
4.4
|
19.8
|
1.0
|
N
|
D:ASP221
|
4.4
|
19.2
|
1.0
|
CA
|
D:ASP223
|
4.5
|
23.5
|
1.0
|
O
|
E:ASP57
|
4.5
|
16.4
|
1.0
|
O
|
E:HOH2066
|
4.5
|
21.2
|
1.0
|
O
|
D:HOH2186
|
4.6
|
31.6
|
1.0
|
CB
|
E:ASP61
|
4.6
|
17.3
|
1.0
|
C
|
D:ASN218
|
4.7
|
19.8
|
1.0
|
CB
|
D:SER225
|
4.7
|
19.8
|
1.0
|
CA
|
D:ASP221
|
4.7
|
19.2
|
1.0
|
OH
|
D:TYR241
|
4.7
|
21.7
|
1.0
|
N
|
D:PHE219
|
4.9
|
18.5
|
1.0
|
C
|
E:ASP57
|
4.9
|
15.6
|
1.0
|
OG
|
D:SER220
|
4.9
|
18.4
|
1.0
|
O
|
D:ASP221
|
5.0
|
22.8
|
1.0
|
N
|
D:SER225
|
5.0
|
19.6
|
1.0
|
CA
|
E:ASP57
|
5.0
|
15.8
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1o9i
Go back to
Calcium Binding Sites List in 1o9i
Calcium binding site 6 out
of 6 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca269
b:25.7
occ:1.00
|
OD1
|
A:ASN218
|
2.1
|
24.5
|
1.0
|
O
|
A:SER220
|
2.3
|
20.8
|
1.0
|
OD1
|
F:ASP61
|
2.4
|
19.0
|
1.0
|
OD1
|
F:ASP57
|
2.4
|
20.9
|
1.0
|
O
|
A:GLY222
|
2.4
|
22.5
|
1.0
|
OD2
|
F:ASP57
|
2.5
|
21.5
|
1.0
|
O
|
F:HOH2067
|
2.7
|
35.1
|
1.0
|
CG
|
F:ASP57
|
2.8
|
19.1
|
1.0
|
OD2
|
F:ASP61
|
3.0
|
21.6
|
1.0
|
CG
|
F:ASP61
|
3.1
|
17.7
|
1.0
|
CG
|
A:ASN218
|
3.3
|
21.8
|
1.0
|
C
|
A:SER220
|
3.4
|
18.6
|
1.0
|
C
|
A:GLY222
|
3.5
|
21.8
|
1.0
|
OG
|
A:SER225
|
3.8
|
21.7
|
1.0
|
N
|
A:GLY222
|
3.9
|
20.4
|
1.0
|
N
|
A:SER220
|
4.1
|
17.7
|
1.0
|
CA
|
A:SER220
|
4.1
|
18.1
|
1.0
|
CA
|
A:GLY222
|
4.2
|
21.1
|
1.0
|
ND2
|
A:ASN218
|
4.2
|
24.9
|
1.0
|
CB
|
A:SER220
|
4.2
|
18.4
|
1.0
|
CB
|
F:ASP57
|
4.3
|
16.6
|
1.0
|
CB
|
A:ASN218
|
4.3
|
19.7
|
1.0
|
CA
|
A:ASN218
|
4.4
|
19.0
|
1.0
|
C
|
A:ASP221
|
4.4
|
20.9
|
1.0
|
N
|
A:ASP221
|
4.4
|
19.5
|
1.0
|
N
|
A:ASP223
|
4.4
|
23.1
|
1.0
|
O
|
A:HOH2173
|
4.5
|
31.2
|
1.0
|
CA
|
A:ASP223
|
4.5
|
23.8
|
1.0
|
O
|
F:ASP57
|
4.6
|
16.7
|
1.0
|
CB
|
F:ASP61
|
4.6
|
15.9
|
1.0
|
C
|
A:ASN218
|
4.6
|
18.6
|
1.0
|
CA
|
A:ASP221
|
4.6
|
19.8
|
1.0
|
OH
|
A:TYR241
|
4.7
|
24.8
|
1.0
|
O
|
F:HOH2066
|
4.7
|
20.9
|
1.0
|
CB
|
A:SER225
|
4.7
|
21.1
|
1.0
|
N
|
A:PHE219
|
4.9
|
17.9
|
1.0
|
OG
|
A:SER220
|
4.9
|
18.8
|
1.0
|
C
|
F:ASP57
|
5.0
|
16.4
|
1.0
|
|
Reference:
M.M.Whittaker,
V.V.Barynin,
T.Igarashi,
J.W.Whittaker.
Outer Sphere Mutagenesis of Lactobacillus Plantarum Manganese Catalase Disrupts the Cluster Core. Mechanistic Implications. Eur.J.Biochem. V. 270 1102 2003.
ISSN: ISSN 0014-2956
PubMed: 12631270
DOI: 10.1046/J.1432-1033.2003.03459.X
Page generated: Thu Jul 11 13:17:42 2024
|