Manganese in PDB 1qf3: Peanut Lectin Complexed with Methyl-Beta-Galactose
Protein crystallography data
The structure of Peanut Lectin Complexed with Methyl-Beta-Galactose, PDB code: 1qf3
was solved by
R.Ravishankar,
K.Suguna,
A.Surolia,
M.Vijayan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.80
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.953,
126.683,
77.284,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
24.7
|
Other elements in 1qf3:
The structure of Peanut Lectin Complexed with Methyl-Beta-Galactose also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Peanut Lectin Complexed with Methyl-Beta-Galactose
(pdb code 1qf3). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Peanut Lectin Complexed with Methyl-Beta-Galactose, PDB code: 1qf3:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1qf3
Go back to
Manganese Binding Sites List in 1qf3
Manganese binding site 1 out
of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn238
b:36.0
occ:1.00
|
OD1
|
A:ASP132
|
2.0
|
11.6
|
1.0
|
O
|
A:HOH527
|
2.0
|
16.1
|
1.0
|
O
|
A:HOH528
|
2.1
|
2.0
|
1.0
|
OD2
|
A:ASP123
|
2.3
|
2.0
|
1.0
|
NE2
|
A:HIS137
|
2.3
|
20.8
|
1.0
|
OE2
|
A:GLU121
|
2.5
|
9.1
|
1.0
|
CG
|
A:ASP132
|
2.8
|
8.2
|
1.0
|
CG
|
A:ASP123
|
3.1
|
2.2
|
1.0
|
OD2
|
A:ASP132
|
3.1
|
13.2
|
1.0
|
CE1
|
A:HIS137
|
3.2
|
18.9
|
1.0
|
CD2
|
A:HIS137
|
3.4
|
19.5
|
1.0
|
CD
|
A:GLU121
|
3.5
|
10.2
|
1.0
|
CB
|
A:ASP123
|
3.5
|
2.0
|
1.0
|
OE1
|
A:GLU121
|
3.8
|
12.8
|
1.0
|
CA
|
A:CA437
|
3.8
|
3.6
|
1.0
|
O
|
A:HOH525
|
3.8
|
5.3
|
1.0
|
OD1
|
A:ASP123
|
4.1
|
8.6
|
1.0
|
CB
|
A:ASP132
|
4.1
|
7.0
|
1.0
|
ND1
|
A:HIS137
|
4.4
|
18.5
|
1.0
|
OG
|
A:SER147
|
4.4
|
4.4
|
1.0
|
O
|
A:VAL145
|
4.5
|
11.8
|
1.0
|
CD
|
A:PRO133
|
4.5
|
21.6
|
1.0
|
CG
|
A:HIS137
|
4.5
|
15.8
|
1.0
|
CA
|
A:ASP132
|
4.5
|
30.7
|
1.0
|
O
|
A:HOH447
|
4.6
|
15.2
|
1.0
|
CG
|
A:GLU121
|
4.8
|
7.5
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1qf3
Go back to
Manganese Binding Sites List in 1qf3
Manganese binding site 2 out
of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn238
b:44.8
occ:1.00
|
OD2
|
B:ASP123
|
1.8
|
32.1
|
1.0
|
NE2
|
B:HIS137
|
2.1
|
7.6
|
1.0
|
CG
|
B:ASP123
|
2.3
|
25.4
|
1.0
|
OD1
|
B:ASP132
|
2.4
|
7.0
|
1.0
|
O
|
B:HOH554
|
2.5
|
2.0
|
1.0
|
OE2
|
B:GLU121
|
2.5
|
12.7
|
1.0
|
O
|
B:HOH553
|
2.6
|
2.0
|
1.0
|
CE1
|
B:HIS137
|
2.8
|
5.7
|
1.0
|
CB
|
B:ASP123
|
2.8
|
21.5
|
1.0
|
CG
|
B:ASP132
|
3.0
|
6.8
|
1.0
|
OD2
|
B:ASP132
|
3.1
|
4.9
|
1.0
|
OD1
|
B:ASP123
|
3.1
|
27.0
|
1.0
|
CD2
|
B:HIS137
|
3.2
|
4.3
|
1.0
|
CA
|
B:CA237
|
3.6
|
2.0
|
1.0
|
CD
|
B:GLU121
|
3.6
|
9.8
|
1.0
|
O
|
B:HOH551
|
3.8
|
2.0
|
1.0
|
ND1
|
B:HIS137
|
4.0
|
10.9
|
1.0
|
OE1
|
B:GLU121
|
4.1
|
16.5
|
1.0
|
CG
|
B:HIS137
|
4.2
|
10.9
|
1.0
|
CB
|
B:ASP132
|
4.2
|
2.0
|
1.0
|
CA
|
B:ASP123
|
4.3
|
11.6
|
1.0
|
O
|
B:TYR125
|
4.5
|
4.5
|
1.0
|
CD
|
B:PRO133
|
4.7
|
33.6
|
1.0
|
O
|
B:HOH445
|
4.7
|
12.6
|
1.0
|
CG
|
B:GLU121
|
4.8
|
15.3
|
1.0
|
CA
|
B:ASP132
|
4.8
|
30.0
|
1.0
|
OG
|
B:SER147
|
4.9
|
25.3
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1qf3
Go back to
Manganese Binding Sites List in 1qf3
Manganese binding site 3 out
of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn238
b:38.8
occ:1.00
|
O
|
C:HOH519
|
1.8
|
41.6
|
1.0
|
OD1
|
C:ASP132
|
2.2
|
29.0
|
1.0
|
OE2
|
C:GLU121
|
2.2
|
17.1
|
1.0
|
OD2
|
C:ASP123
|
2.3
|
20.9
|
1.0
|
NE2
|
C:HIS137
|
2.4
|
20.0
|
1.0
|
O
|
C:HOH518
|
2.5
|
10.2
|
1.0
|
CG
|
C:ASP132
|
3.0
|
34.3
|
1.0
|
CG
|
C:ASP123
|
3.2
|
11.5
|
1.0
|
CD
|
C:GLU121
|
3.3
|
16.6
|
1.0
|
OD2
|
C:ASP132
|
3.3
|
28.7
|
1.0
|
CE1
|
C:HIS137
|
3.3
|
18.3
|
1.0
|
CD2
|
C:HIS137
|
3.3
|
14.8
|
1.0
|
CB
|
C:ASP123
|
3.5
|
8.2
|
1.0
|
OE1
|
C:GLU121
|
3.7
|
13.2
|
1.0
|
OD1
|
C:ASP123
|
4.1
|
17.3
|
1.0
|
O
|
C:HOH516
|
4.2
|
2.0
|
1.0
|
OG
|
C:SER147
|
4.2
|
16.8
|
1.0
|
CA
|
C:CA237
|
4.2
|
14.3
|
1.0
|
CB
|
C:ASP132
|
4.3
|
28.0
|
1.0
|
O
|
C:HOH455
|
4.3
|
22.4
|
1.0
|
O
|
C:VAL145
|
4.4
|
14.7
|
1.0
|
ND1
|
C:HIS137
|
4.4
|
20.2
|
1.0
|
CG
|
C:HIS137
|
4.5
|
17.8
|
1.0
|
CD
|
C:PRO133
|
4.6
|
11.2
|
1.0
|
CG
|
C:GLU121
|
4.6
|
18.0
|
1.0
|
CA
|
C:ASP132
|
4.7
|
19.2
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1qf3
Go back to
Manganese Binding Sites List in 1qf3
Manganese binding site 4 out
of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn238
b:37.2
occ:1.00
|
OE2
|
D:GLU121
|
2.0
|
2.9
|
1.0
|
O
|
D:HOH526
|
2.1
|
8.7
|
1.0
|
O
|
D:HOH525
|
2.2
|
24.9
|
1.0
|
NE2
|
D:HIS137
|
2.3
|
2.1
|
1.0
|
OD1
|
D:ASP132
|
2.4
|
13.1
|
1.0
|
OD2
|
D:ASP123
|
2.5
|
20.7
|
1.0
|
CD
|
D:GLU121
|
3.1
|
3.7
|
1.0
|
CD2
|
D:HIS137
|
3.2
|
2.1
|
1.0
|
CG
|
D:ASP132
|
3.3
|
13.9
|
1.0
|
CE1
|
D:HIS137
|
3.3
|
10.3
|
1.0
|
CG
|
D:ASP123
|
3.4
|
13.1
|
1.0
|
OE1
|
D:GLU121
|
3.5
|
2.0
|
1.0
|
CB
|
D:ASP123
|
3.6
|
2.0
|
1.0
|
OD2
|
D:ASP132
|
3.7
|
7.8
|
1.0
|
OG
|
D:SER147
|
3.9
|
9.1
|
1.0
|
O
|
D:HOH523
|
4.3
|
31.0
|
1.0
|
O
|
D:VAL145
|
4.4
|
7.7
|
1.0
|
CG
|
D:GLU121
|
4.4
|
2.0
|
1.0
|
CG
|
D:HIS137
|
4.4
|
8.4
|
1.0
|
ND1
|
D:HIS137
|
4.4
|
19.4
|
1.0
|
OD1
|
D:ASP123
|
4.4
|
13.4
|
1.0
|
CA
|
D:CA237
|
4.5
|
13.4
|
1.0
|
CB
|
D:ASP132
|
4.5
|
10.5
|
1.0
|
CD
|
D:PRO133
|
4.6
|
36.3
|
1.0
|
O
|
D:HOH478
|
4.8
|
26.3
|
1.0
|
CA
|
D:ASP132
|
4.8
|
13.8
|
1.0
|
|
Reference:
R.Ravishankar,
K.Suguna,
A.Surolia,
M.Vijayan.
Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N-Acetyllactosamine and A Comparative Study of Carbohydrate Binding in Gal/Galnac-Specific Legume Lectins. Acta Crystallogr.,Sect.D V. 55 1375 1999.
ISSN: ISSN 0907-4449
PubMed: 10417405
DOI: 10.1107/S0907444999006587
Page generated: Sat Oct 5 12:12:07 2024
|