Manganese in PDB 8jq5: Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Protein crystallography data
The structure of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose, PDB code: 8jq5
was solved by
H.Yoshida,
A.Yoshihara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.23 /
1.73
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.887,
139.445,
146.834,
90,
90,
90
|
R / Rfree (%)
|
13.9 /
18.7
|
Manganese Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Manganese atom in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
(pdb code 8jq5). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the
Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose, PDB code: 8jq5:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 1 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:35.8
occ:1.00
|
OD2
|
A:ASP328
|
2.2
|
29.6
|
1.0
|
OD2
|
A:ASP261
|
2.2
|
21.5
|
1.0
|
OE2
|
A:GLU228
|
2.3
|
21.3
|
1.0
|
O2
|
A:PSJ503
|
2.5
|
32.4
|
1.0
|
ND1
|
A:HIS288
|
2.5
|
31.3
|
1.0
|
O3
|
A:PSJ503
|
2.5
|
31.1
|
1.0
|
CD
|
A:GLU228
|
3.1
|
18.4
|
1.0
|
CG
|
A:ASP261
|
3.3
|
16.7
|
1.0
|
C2
|
A:PSJ503
|
3.3
|
33.5
|
1.0
|
CG
|
A:ASP328
|
3.3
|
22.5
|
1.0
|
OE1
|
A:GLU228
|
3.3
|
20.1
|
1.0
|
CE1
|
A:HIS288
|
3.3
|
40.5
|
1.0
|
C3
|
A:PSJ503
|
3.3
|
30.6
|
1.0
|
O
|
A:HOH601
|
3.5
|
33.2
|
1.0
|
CG
|
A:HIS288
|
3.6
|
32.2
|
1.0
|
CB
|
A:ASP328
|
3.7
|
20.8
|
1.0
|
CB
|
A:ASP261
|
3.7
|
16.8
|
1.0
|
C4
|
A:PSJ503
|
3.9
|
35.5
|
1.0
|
CE1
|
A:HIS264
|
3.9
|
24.1
|
1.0
|
CB
|
A:HIS288
|
4.0
|
27.9
|
1.0
|
MN
|
A:MN502
|
4.0
|
23.4
|
0.2
|
O4
|
A:PSJ503
|
4.0
|
32.1
|
1.0
|
NE2
|
A:HIS264
|
4.3
|
22.7
|
1.0
|
OD1
|
A:ASP261
|
4.4
|
17.0
|
1.0
|
OD1
|
A:ASP328
|
4.4
|
24.6
|
1.0
|
CG
|
A:GLU228
|
4.5
|
16.9
|
1.0
|
NE2
|
A:HIS288
|
4.6
|
41.3
|
1.0
|
CD2
|
A:HIS288
|
4.7
|
36.2
|
1.0
|
C1
|
A:PSJ503
|
4.7
|
29.6
|
1.0
|
ND1
|
A:HIS264
|
4.8
|
23.4
|
1.0
|
MN
|
A:MN502
|
4.9
|
35.0
|
0.8
|
O
|
A:HOH602
|
4.9
|
35.6
|
1.0
|
CA
|
A:ASP261
|
5.0
|
16.7
|
1.0
|
|
Manganese binding site 2 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 2 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:35.0
occ:0.80
|
MN
|
A:MN502
|
0.0
|
35.0
|
0.8
|
OD1
|
A:ASP296
|
1.8
|
28.8
|
1.0
|
O
|
A:HOH601
|
1.8
|
33.2
|
1.0
|
MN
|
A:MN502
|
1.9
|
23.4
|
0.2
|
O
|
A:HOH602
|
2.4
|
35.6
|
1.0
|
CG
|
A:ASP296
|
2.4
|
26.3
|
1.0
|
OD1
|
A:ASP298
|
2.5
|
31.8
|
1.0
|
OD2
|
A:ASP296
|
2.5
|
31.3
|
1.0
|
NE2
|
A:HIS264
|
2.6
|
22.7
|
1.0
|
CD2
|
A:HIS264
|
3.1
|
21.4
|
1.0
|
CG
|
A:ASP298
|
3.2
|
23.5
|
1.0
|
OD2
|
A:ASP298
|
3.3
|
25.4
|
1.0
|
O2
|
A:PSJ503
|
3.7
|
32.4
|
1.0
|
O
|
A:HOH744
|
3.7
|
25.8
|
1.0
|
CE1
|
A:HIS264
|
3.8
|
24.1
|
1.0
|
OD2
|
A:ASP261
|
3.8
|
21.5
|
1.0
|
CB
|
A:ASP296
|
3.9
|
23.9
|
1.0
|
O1
|
A:PSJ503
|
3.9
|
28.2
|
1.0
|
OD1
|
A:ASP261
|
4.0
|
17.0
|
1.0
|
CG
|
A:ASP261
|
4.1
|
16.7
|
1.0
|
OG
|
A:SER290
|
4.2
|
18.7
|
1.0
|
CG
|
A:HIS264
|
4.4
|
21.1
|
1.0
|
O
|
A:ASP296
|
4.4
|
22.4
|
1.0
|
CA
|
A:ASP296
|
4.5
|
21.3
|
1.0
|
C2
|
A:PSJ503
|
4.5
|
33.5
|
1.0
|
C
|
A:ASP296
|
4.5
|
21.4
|
1.0
|
CB
|
A:ASP298
|
4.6
|
21.9
|
1.0
|
ND1
|
A:HIS264
|
4.7
|
23.4
|
1.0
|
C1
|
A:PSJ503
|
4.7
|
29.6
|
1.0
|
OD2
|
A:ASP328
|
4.8
|
29.6
|
1.0
|
N
|
A:ASP298
|
4.8
|
19.2
|
1.0
|
CA
|
A:ASP298
|
4.8
|
20.4
|
1.0
|
MN
|
A:MN501
|
4.9
|
35.8
|
1.0
|
O4
|
A:PSJ503
|
4.9
|
32.1
|
1.0
|
CA
|
A:GLY263
|
4.9
|
17.4
|
1.0
|
CB
|
A:SER290
|
5.0
|
18.7
|
1.0
|
C
|
A:GLY263
|
5.0
|
16.6
|
1.0
|
|
Manganese binding site 3 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 3 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:23.4
occ:0.20
|
MN
|
A:MN502
|
0.0
|
23.4
|
0.2
|
O
|
A:HOH602
|
1.8
|
35.6
|
1.0
|
NE2
|
A:HIS264
|
1.8
|
22.7
|
1.0
|
MN
|
A:MN502
|
1.9
|
35.0
|
0.8
|
O2
|
A:PSJ503
|
2.1
|
32.4
|
1.0
|
O1
|
A:PSJ503
|
2.2
|
28.2
|
1.0
|
O
|
A:HOH601
|
2.4
|
33.2
|
1.0
|
CE1
|
A:HIS264
|
2.5
|
24.1
|
1.0
|
OD2
|
A:ASP296
|
2.6
|
31.3
|
1.0
|
C2
|
A:PSJ503
|
2.8
|
33.5
|
1.0
|
C1
|
A:PSJ503
|
2.9
|
29.6
|
1.0
|
CD2
|
A:HIS264
|
3.1
|
21.4
|
1.0
|
CG
|
A:ASP296
|
3.3
|
26.3
|
1.0
|
OD1
|
A:ASP296
|
3.3
|
28.8
|
1.0
|
ND1
|
A:HIS264
|
3.8
|
23.4
|
1.0
|
OD2
|
A:ASP261
|
3.8
|
21.5
|
1.0
|
OD1
|
A:ASP298
|
3.9
|
31.8
|
1.0
|
O4
|
A:PSJ503
|
3.9
|
32.1
|
1.0
|
CG
|
A:HIS264
|
4.0
|
21.1
|
1.0
|
MN
|
A:MN501
|
4.0
|
35.8
|
1.0
|
OD2
|
A:ASP298
|
4.1
|
25.4
|
1.0
|
NZ
|
A:LYS230
|
4.2
|
22.7
|
1.0
|
CE
|
A:LYS230
|
4.2
|
22.1
|
1.0
|
C3
|
A:PSJ503
|
4.2
|
30.6
|
1.0
|
CG
|
A:ASP261
|
4.3
|
16.7
|
1.0
|
OD2
|
A:ASP328
|
4.3
|
29.6
|
1.0
|
CG
|
A:ASP298
|
4.4
|
23.5
|
1.0
|
OE2
|
A:GLU228
|
4.5
|
21.3
|
1.0
|
CG2
|
A:ILE61
|
4.5
|
45.1
|
1.0
|
OD1
|
A:ASP261
|
4.6
|
17.0
|
1.0
|
C4
|
A:PSJ503
|
4.7
|
35.5
|
1.0
|
CB
|
A:ASP296
|
4.7
|
23.9
|
1.0
|
CD
|
A:LYS230
|
4.8
|
21.4
|
1.0
|
O3
|
A:PSJ503
|
4.8
|
31.1
|
1.0
|
|
Manganese binding site 4 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 4 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:38.7
occ:1.00
|
OD2
|
B:ASP328
|
2.1
|
33.1
|
1.0
|
OE2
|
B:GLU228
|
2.2
|
21.0
|
1.0
|
OD2
|
B:ASP261
|
2.2
|
19.8
|
1.0
|
ND1
|
B:HIS288
|
2.4
|
38.2
|
1.0
|
O2
|
B:PSJ503
|
2.4
|
38.2
|
1.0
|
O3
|
B:PSJ503
|
2.5
|
29.3
|
1.0
|
CD
|
B:GLU228
|
3.1
|
19.1
|
1.0
|
CG
|
B:ASP328
|
3.2
|
25.3
|
1.0
|
CE1
|
B:HIS288
|
3.2
|
46.9
|
1.0
|
C2
|
B:PSJ503
|
3.2
|
31.1
|
1.0
|
C3
|
B:PSJ503
|
3.3
|
28.7
|
1.0
|
O
|
B:HOH606
|
3.3
|
32.2
|
1.0
|
CG
|
B:ASP261
|
3.3
|
17.7
|
1.0
|
OE1
|
B:GLU228
|
3.3
|
19.4
|
1.0
|
CG
|
B:HIS288
|
3.6
|
31.3
|
1.0
|
CB
|
B:ASP328
|
3.7
|
22.0
|
1.0
|
CB
|
B:ASP261
|
3.8
|
17.9
|
1.0
|
C4
|
B:PSJ503
|
3.9
|
34.4
|
1.0
|
CB
|
B:HIS288
|
3.9
|
28.4
|
1.0
|
CE1
|
B:HIS264
|
4.0
|
23.3
|
1.0
|
MN
|
B:MN502
|
4.0
|
25.5
|
0.2
|
O4
|
B:PSJ503
|
4.1
|
30.3
|
1.0
|
OD1
|
B:ASP328
|
4.3
|
28.2
|
1.0
|
NE2
|
B:HIS264
|
4.3
|
25.3
|
1.0
|
OD1
|
B:ASP261
|
4.4
|
19.1
|
1.0
|
NE2
|
B:HIS288
|
4.4
|
47.4
|
1.0
|
CG
|
B:GLU228
|
4.5
|
19.0
|
1.0
|
CD2
|
B:HIS288
|
4.6
|
35.7
|
1.0
|
C1
|
B:PSJ503
|
4.7
|
28.5
|
1.0
|
ND1
|
B:HIS264
|
4.8
|
23.7
|
1.0
|
MN
|
B:MN502
|
4.8
|
36.0
|
0.8
|
|
Manganese binding site 5 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 5 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:36.0
occ:0.80
|
MN
|
B:MN502
|
0.0
|
36.0
|
0.8
|
O
|
B:HOH606
|
1.8
|
32.2
|
1.0
|
OD1
|
B:ASP296
|
1.8
|
29.1
|
1.0
|
MN
|
B:MN502
|
1.9
|
25.5
|
0.2
|
OD1
|
B:ASP298
|
2.5
|
34.3
|
1.0
|
NE2
|
B:HIS264
|
2.6
|
25.3
|
1.0
|
CG
|
B:ASP296
|
2.6
|
27.9
|
1.0
|
OD2
|
B:ASP296
|
2.8
|
33.5
|
1.0
|
O
|
B:HOH604
|
2.8
|
34.5
|
1.0
|
CG
|
B:ASP298
|
3.1
|
24.7
|
1.0
|
OD2
|
B:ASP298
|
3.1
|
23.7
|
1.0
|
CD2
|
B:HIS264
|
3.2
|
22.0
|
1.0
|
O
|
B:HOH745
|
3.6
|
21.5
|
1.0
|
O2
|
B:PSJ503
|
3.7
|
38.2
|
1.0
|
O1
|
B:PSJ503
|
3.8
|
30.8
|
1.0
|
OD2
|
B:ASP261
|
3.8
|
19.8
|
1.0
|
CE1
|
B:HIS264
|
3.8
|
23.3
|
1.0
|
OD1
|
B:ASP261
|
3.9
|
19.1
|
1.0
|
CB
|
B:ASP296
|
4.1
|
24.7
|
1.0
|
CG
|
B:ASP261
|
4.1
|
17.7
|
1.0
|
OG
|
B:SER290
|
4.2
|
17.7
|
1.0
|
CG
|
B:HIS264
|
4.4
|
20.8
|
1.0
|
O
|
B:ASP296
|
4.5
|
23.2
|
1.0
|
C2
|
B:PSJ503
|
4.5
|
31.1
|
1.0
|
CB
|
B:ASP298
|
4.5
|
22.2
|
1.0
|
C
|
B:ASP296
|
4.6
|
21.6
|
1.0
|
C1
|
B:PSJ503
|
4.6
|
28.5
|
1.0
|
CA
|
B:ASP296
|
4.6
|
23.8
|
1.0
|
ND1
|
B:HIS264
|
4.7
|
23.7
|
1.0
|
CA
|
B:ASP298
|
4.8
|
19.8
|
1.0
|
OD2
|
B:ASP328
|
4.8
|
33.1
|
1.0
|
N
|
B:ASP298
|
4.8
|
18.8
|
1.0
|
O4
|
B:PSJ503
|
4.8
|
30.3
|
1.0
|
MN
|
B:MN501
|
4.8
|
38.7
|
1.0
|
CB
|
B:SER290
|
4.9
|
18.4
|
1.0
|
CA
|
B:GLY263
|
4.9
|
16.1
|
1.0
|
|
Manganese binding site 6 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 6 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:25.5
occ:0.20
|
MN
|
B:MN502
|
0.0
|
25.5
|
0.2
|
NE2
|
B:HIS264
|
1.8
|
25.3
|
1.0
|
MN
|
B:MN502
|
1.9
|
36.0
|
0.8
|
O1
|
B:PSJ503
|
2.1
|
30.8
|
1.0
|
O2
|
B:PSJ503
|
2.1
|
38.2
|
1.0
|
O
|
B:HOH604
|
2.2
|
34.5
|
1.0
|
O
|
B:HOH606
|
2.3
|
32.2
|
1.0
|
CE1
|
B:HIS264
|
2.5
|
23.3
|
1.0
|
OD2
|
B:ASP296
|
2.7
|
33.5
|
1.0
|
C2
|
B:PSJ503
|
2.8
|
31.1
|
1.0
|
C1
|
B:PSJ503
|
2.9
|
28.5
|
1.0
|
CD2
|
B:HIS264
|
3.0
|
22.0
|
1.0
|
OD1
|
B:ASP296
|
3.1
|
29.1
|
1.0
|
CG
|
B:ASP296
|
3.3
|
27.9
|
1.0
|
ND1
|
B:HIS264
|
3.7
|
23.7
|
1.0
|
OD2
|
B:ASP261
|
3.7
|
19.8
|
1.0
|
OD1
|
B:ASP298
|
3.8
|
34.3
|
1.0
|
O4
|
B:PSJ503
|
3.9
|
30.3
|
1.0
|
CG
|
B:HIS264
|
4.0
|
20.8
|
1.0
|
OD2
|
B:ASP298
|
4.0
|
23.7
|
1.0
|
MN
|
B:MN501
|
4.0
|
38.7
|
1.0
|
NZ
|
B:LYS230
|
4.1
|
20.4
|
1.0
|
CE
|
B:LYS230
|
4.2
|
21.8
|
1.0
|
CG
|
B:ASP261
|
4.2
|
17.7
|
1.0
|
C3
|
B:PSJ503
|
4.2
|
28.7
|
1.0
|
CG
|
B:ASP298
|
4.3
|
24.7
|
1.0
|
OD2
|
B:ASP328
|
4.4
|
33.1
|
1.0
|
OE2
|
B:GLU228
|
4.5
|
21.0
|
1.0
|
OD1
|
B:ASP261
|
4.5
|
19.1
|
1.0
|
CG2
|
B:ILE61
|
4.6
|
44.1
|
1.0
|
C4
|
B:PSJ503
|
4.6
|
34.4
|
1.0
|
CB
|
B:ASP296
|
4.7
|
24.7
|
1.0
|
CD
|
B:LYS230
|
4.7
|
20.4
|
1.0
|
O3
|
B:PSJ503
|
4.9
|
29.3
|
1.0
|
|
Manganese binding site 7 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 7 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn501
b:40.9
occ:1.00
|
OD2
|
C:ASP261
|
2.2
|
18.9
|
1.0
|
OE2
|
C:GLU228
|
2.2
|
24.6
|
1.0
|
OD2
|
C:ASP328
|
2.3
|
35.1
|
1.0
|
ND1
|
C:HIS288
|
2.4
|
31.6
|
1.0
|
O3
|
C:PSJ503
|
2.6
|
39.0
|
0.5
|
O2
|
C:PSJ503
|
2.7
|
38.7
|
0.5
|
O2
|
C:PSV504
|
2.7
|
27.1
|
0.5
|
O3
|
C:PSV504
|
2.8
|
28.6
|
0.5
|
CD
|
C:GLU228
|
3.1
|
19.6
|
1.0
|
CE1
|
C:HIS288
|
3.2
|
37.8
|
1.0
|
CG
|
C:ASP261
|
3.2
|
17.1
|
1.0
|
CG
|
C:ASP328
|
3.3
|
26.6
|
1.0
|
OE1
|
C:GLU228
|
3.3
|
20.8
|
1.0
|
O
|
C:HOH605
|
3.4
|
30.4
|
1.0
|
C2
|
C:PSJ503
|
3.5
|
36.5
|
0.5
|
CG
|
C:HIS288
|
3.5
|
30.4
|
1.0
|
C3
|
C:PSJ503
|
3.5
|
37.4
|
0.5
|
CB
|
C:ASP261
|
3.7
|
18.2
|
1.0
|
CB
|
C:ASP328
|
3.7
|
23.3
|
1.0
|
C2
|
C:PSV504
|
3.7
|
28.2
|
0.5
|
C3
|
C:PSV504
|
3.8
|
28.6
|
0.5
|
CB
|
C:HIS288
|
3.8
|
26.5
|
1.0
|
CE1
|
C:HIS264
|
4.0
|
23.8
|
1.0
|
O5
|
C:PSV504
|
4.1
|
29.4
|
0.5
|
C4
|
C:PSJ503
|
4.1
|
39.0
|
0.5
|
MN
|
C:MN502
|
4.2
|
24.1
|
0.2
|
O4
|
C:PSJ503
|
4.3
|
35.5
|
0.5
|
OD1
|
C:ASP261
|
4.3
|
19.2
|
1.0
|
CG
|
C:GLU228
|
4.4
|
18.3
|
1.0
|
OD1
|
C:ASP328
|
4.4
|
27.6
|
1.0
|
NE2
|
C:HIS288
|
4.4
|
41.3
|
1.0
|
NE2
|
C:HIS264
|
4.5
|
23.5
|
1.0
|
CD2
|
C:HIS288
|
4.6
|
34.7
|
1.0
|
C5
|
C:PSV504
|
4.7
|
28.8
|
0.5
|
ND1
|
C:HIS264
|
4.8
|
20.4
|
1.0
|
C4
|
C:PSV504
|
4.9
|
29.2
|
0.5
|
CA
|
C:ASP261
|
4.9
|
17.3
|
1.0
|
C1
|
C:PSJ503
|
4.9
|
33.2
|
0.5
|
MN
|
C:MN502
|
5.0
|
29.4
|
0.8
|
|
Manganese binding site 8 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 8 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn502
b:29.4
occ:0.80
|
MN
|
C:MN502
|
0.0
|
29.4
|
0.8
|
OD1
|
C:ASP296
|
1.8
|
26.2
|
1.0
|
O
|
C:HOH605
|
1.9
|
30.4
|
1.0
|
MN
|
C:MN502
|
1.9
|
24.1
|
0.2
|
NE2
|
C:HIS264
|
2.3
|
23.5
|
1.0
|
OD1
|
C:ASP298
|
2.4
|
36.5
|
1.0
|
CG
|
C:ASP296
|
2.5
|
26.4
|
1.0
|
OD2
|
C:ASP296
|
2.6
|
33.8
|
1.0
|
O
|
C:HOH602
|
2.6
|
41.3
|
1.0
|
CD2
|
C:HIS264
|
3.1
|
21.7
|
1.0
|
CG
|
C:ASP298
|
3.2
|
25.4
|
1.0
|
OD2
|
C:ASP298
|
3.2
|
25.1
|
1.0
|
CE1
|
C:HIS264
|
3.5
|
23.8
|
1.0
|
O2
|
C:PSV504
|
3.7
|
27.1
|
0.5
|
O
|
C:HOH731
|
3.8
|
23.3
|
1.0
|
OD2
|
C:ASP261
|
3.9
|
18.9
|
1.0
|
OD1
|
C:ASP261
|
3.9
|
19.2
|
1.0
|
CB
|
C:ASP296
|
3.9
|
26.9
|
1.0
|
O2
|
C:PSJ503
|
3.9
|
38.7
|
0.5
|
O1
|
C:PSJ503
|
4.0
|
34.8
|
0.5
|
O1
|
C:PSV504
|
4.0
|
22.9
|
0.5
|
CG
|
C:ASP261
|
4.2
|
17.1
|
1.0
|
OG
|
C:SER290
|
4.3
|
17.5
|
1.0
|
CG
|
C:HIS264
|
4.3
|
18.7
|
1.0
|
O
|
C:ASP296
|
4.4
|
22.3
|
1.0
|
ND1
|
C:HIS264
|
4.5
|
20.4
|
1.0
|
CB
|
C:ASP298
|
4.5
|
22.6
|
1.0
|
CA
|
C:ASP296
|
4.6
|
24.7
|
1.0
|
C
|
C:ASP296
|
4.6
|
24.1
|
1.0
|
C2
|
C:PSV504
|
4.7
|
28.2
|
0.5
|
C2
|
C:PSJ503
|
4.7
|
36.5
|
0.5
|
CA
|
C:ASP298
|
4.8
|
20.6
|
1.0
|
C1
|
C:PSV504
|
4.9
|
27.8
|
0.5
|
OD2
|
C:ASP328
|
4.9
|
35.1
|
1.0
|
N
|
C:ASP298
|
4.9
|
19.6
|
1.0
|
O5
|
C:PSV504
|
4.9
|
29.4
|
0.5
|
C1
|
C:PSJ503
|
4.9
|
33.2
|
0.5
|
CA
|
C:GLY263
|
4.9
|
17.1
|
1.0
|
MN
|
C:MN501
|
5.0
|
40.9
|
1.0
|
C
|
C:GLY263
|
5.0
|
16.6
|
1.0
|
|
Manganese binding site 9 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 9 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn502
b:24.1
occ:0.20
|
MN
|
C:MN502
|
0.0
|
24.1
|
0.2
|
MN
|
C:MN502
|
1.9
|
29.4
|
0.8
|
NE2
|
C:HIS264
|
2.0
|
23.5
|
1.0
|
O
|
C:HOH602
|
2.0
|
41.3
|
1.0
|
O2
|
C:PSV504
|
2.2
|
27.1
|
0.5
|
O1
|
C:PSJ503
|
2.2
|
34.8
|
0.5
|
O
|
C:HOH605
|
2.2
|
30.4
|
1.0
|
O1
|
C:PSV504
|
2.3
|
22.9
|
0.5
|
O2
|
C:PSJ503
|
2.3
|
38.7
|
0.5
|
CE1
|
C:HIS264
|
2.5
|
23.8
|
1.0
|
OD2
|
C:ASP296
|
2.6
|
33.8
|
1.0
|
C2
|
C:PSJ503
|
2.9
|
36.5
|
0.5
|
C2
|
C:PSV504
|
3.1
|
28.2
|
0.5
|
C1
|
C:PSJ503
|
3.1
|
33.2
|
0.5
|
C1
|
C:PSV504
|
3.1
|
27.8
|
0.5
|
CD2
|
C:HIS264
|
3.3
|
21.7
|
1.0
|
OD1
|
C:ASP296
|
3.3
|
26.2
|
1.0
|
CG
|
C:ASP296
|
3.3
|
26.4
|
1.0
|
O5
|
C:PSV504
|
3.7
|
29.4
|
0.5
|
ND1
|
C:HIS264
|
3.7
|
20.4
|
1.0
|
OD1
|
C:ASP298
|
3.8
|
36.5
|
1.0
|
OD2
|
C:ASP261
|
3.9
|
18.9
|
1.0
|
OD2
|
C:ASP298
|
4.0
|
25.1
|
1.0
|
O4
|
C:PSJ503
|
4.0
|
35.5
|
0.5
|
NZ
|
C:LYS230
|
4.0
|
23.4
|
1.0
|
CG
|
C:HIS264
|
4.1
|
18.7
|
1.0
|
CE
|
C:LYS230
|
4.2
|
23.6
|
1.0
|
MN
|
C:MN501
|
4.2
|
40.9
|
1.0
|
CG
|
C:ASP298
|
4.3
|
25.4
|
1.0
|
C3
|
C:PSJ503
|
4.3
|
37.4
|
0.5
|
C3
|
C:PSV504
|
4.4
|
28.6
|
0.5
|
OD2
|
C:ASP328
|
4.4
|
35.1
|
1.0
|
CG
|
C:ASP261
|
4.4
|
17.1
|
1.0
|
OE2
|
C:GLU228
|
4.5
|
24.6
|
1.0
|
OD1
|
C:ASP261
|
4.7
|
19.2
|
1.0
|
C4
|
C:PSJ503
|
4.8
|
39.0
|
0.5
|
CB
|
C:ASP296
|
4.8
|
26.9
|
1.0
|
CD
|
C:LYS230
|
4.8
|
21.9
|
1.0
|
O3
|
C:PSV504
|
4.8
|
28.6
|
0.5
|
O3
|
C:PSJ503
|
4.9
|
39.0
|
0.5
|
|
Manganese binding site 10 out
of 12 in 8jq5
Go back to
Manganese Binding Sites List in 8jq5
Manganese binding site 10 out
of 12 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allulose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn501
b:37.2
occ:1.00
|
OD2
|
D:ASP261
|
2.2
|
18.9
|
1.0
|
OD2
|
D:ASP328
|
2.2
|
30.4
|
1.0
|
OE2
|
D:GLU228
|
2.3
|
22.7
|
1.0
|
O3
|
D:PSJ503
|
2.4
|
37.5
|
0.5
|
O2
|
D:PSV504
|
2.6
|
28.1
|
0.5
|
ND1
|
D:HIS288
|
2.6
|
32.6
|
1.0
|
O2
|
D:PSJ503
|
2.6
|
34.8
|
0.5
|
O3
|
D:PSV504
|
2.6
|
27.3
|
0.5
|
CD
|
D:GLU228
|
3.1
|
19.2
|
1.0
|
OE1
|
D:GLU228
|
3.2
|
19.7
|
1.0
|
CG
|
D:ASP328
|
3.3
|
24.0
|
1.0
|
CG
|
D:ASP261
|
3.3
|
17.7
|
1.0
|
C3
|
D:PSJ503
|
3.3
|
31.9
|
0.5
|
C2
|
D:PSJ503
|
3.3
|
31.2
|
0.5
|
O
|
D:HOH617
|
3.3
|
26.3
|
1.0
|
CE1
|
D:HIS288
|
3.4
|
39.3
|
1.0
|
C2
|
D:PSV504
|
3.5
|
28.0
|
0.5
|
C3
|
D:PSV504
|
3.6
|
26.5
|
0.5
|
CG
|
D:HIS288
|
3.6
|
30.3
|
1.0
|
CB
|
D:ASP328
|
3.7
|
20.6
|
1.0
|
CB
|
D:ASP261
|
3.7
|
19.0
|
1.0
|
C4
|
D:PSJ503
|
3.9
|
33.5
|
0.5
|
CE1
|
D:HIS264
|
3.9
|
25.1
|
1.0
|
CB
|
D:HIS288
|
4.0
|
26.4
|
1.0
|
O5
|
D:PSV504
|
4.0
|
31.6
|
0.5
|
O4
|
D:PSJ503
|
4.0
|
26.1
|
0.5
|
MN
|
D:MN502
|
4.1
|
24.4
|
0.2
|
NE2
|
D:HIS264
|
4.4
|
24.7
|
1.0
|
OD1
|
D:ASP261
|
4.4
|
16.8
|
1.0
|
OD1
|
D:ASP328
|
4.4
|
24.0
|
1.0
|
C5
|
D:PSV504
|
4.4
|
29.4
|
0.5
|
CG
|
D:GLU228
|
4.5
|
18.0
|
1.0
|
NE2
|
D:HIS288
|
4.6
|
41.0
|
1.0
|
C4
|
D:PSV504
|
4.6
|
27.6
|
0.5
|
CD2
|
D:HIS288
|
4.7
|
36.2
|
1.0
|
ND1
|
D:HIS264
|
4.8
|
23.1
|
1.0
|
C1
|
D:PSJ503
|
4.8
|
29.0
|
0.5
|
C1
|
D:PSV504
|
4.9
|
27.1
|
0.5
|
CA
|
D:ASP261
|
5.0
|
17.1
|
1.0
|
|
Reference:
H.Yoshida,
N.Yamamoto,
L.H.Kurahara,
K.Izumori,
A.Yoshihara.
X-Ray Structure and Characterization of A Probiotic Lactobacillus Rhamnosus Probio-M9 L-Rhamnose Isomerase. Appl.Microbiol.Biotechnol. V. 108 249 2024.
ISSN: ESSN 1432-0614
PubMed: 38430263
DOI: 10.1007/S00253-024-13075-9
Page generated: Sun Oct 6 13:20:47 2024
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