Manganese in PDB 4m3c: Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Protein crystallography data
The structure of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds, PDB code: 4m3c
was solved by
S.Surya,
J.Abhilash,
K.Geethanandan,
C.Sadasivan,
M.Haridas,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.84 /
2.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.110,
78.630,
96.190,
96.00,
89.99,
100.37
|
R / Rfree (%)
|
21.1 /
28.9
|
Other elements in 4m3c:
The structure of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
(pdb code 4m3c). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds, PDB code: 4m3c:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 1 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn302
b:39.7
occ:1.00
|
O
|
A:HOH422
|
2.0
|
13.5
|
1.0
|
OD1
|
A:ASP128
|
2.1
|
17.7
|
1.0
|
OD1
|
A:ASP137
|
2.2
|
27.7
|
1.0
|
OE2
|
A:GLU126
|
2.3
|
19.8
|
1.0
|
NE2
|
A:HIS142
|
2.4
|
29.6
|
1.0
|
O
|
A:HOH401
|
3.1
|
15.7
|
1.0
|
CG
|
A:ASP137
|
3.2
|
26.3
|
1.0
|
CD2
|
A:HIS142
|
3.2
|
28.3
|
1.0
|
CG
|
A:ASP128
|
3.2
|
19.7
|
1.0
|
CD
|
A:GLU126
|
3.4
|
19.0
|
1.0
|
CE1
|
A:HIS142
|
3.4
|
28.7
|
1.0
|
OD2
|
A:ASP137
|
3.7
|
26.9
|
1.0
|
CB
|
A:ASP128
|
3.7
|
20.2
|
1.0
|
OG
|
A:SER152
|
3.7
|
22.1
|
1.0
|
OE1
|
A:GLU126
|
3.7
|
17.3
|
1.0
|
CB
|
A:ASP137
|
4.3
|
24.9
|
1.0
|
OD2
|
A:ASP128
|
4.3
|
18.8
|
1.0
|
O
|
A:HOH421
|
4.3
|
17.2
|
1.0
|
CA
|
A:CA301
|
4.3
|
18.3
|
1.0
|
CG
|
A:HIS142
|
4.5
|
26.6
|
1.0
|
CA
|
A:ASP137
|
4.5
|
25.4
|
1.0
|
O
|
A:ILE150
|
4.5
|
21.9
|
1.0
|
ND1
|
A:HIS142
|
4.5
|
28.1
|
1.0
|
CG
|
A:GLU126
|
4.7
|
19.3
|
1.0
|
CD
|
A:PRO138
|
4.7
|
24.8
|
1.0
|
CB
|
A:SER152
|
5.0
|
21.5
|
1.0
|
|
Manganese binding site 2 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 2 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn302
b:27.9
occ:1.00
|
OE2
|
B:GLU126
|
2.1
|
19.7
|
1.0
|
OD2
|
B:ASP128
|
2.1
|
21.1
|
1.0
|
OD1
|
B:ASP137
|
2.2
|
27.1
|
1.0
|
NE2
|
B:HIS142
|
2.3
|
20.6
|
1.0
|
O
|
B:HOH420
|
2.3
|
21.8
|
1.0
|
O
|
B:HOH435
|
2.4
|
22.4
|
1.0
|
CG
|
B:ASP128
|
3.1
|
21.4
|
1.0
|
CD
|
B:GLU126
|
3.1
|
20.7
|
1.0
|
CE1
|
B:HIS142
|
3.1
|
21.5
|
1.0
|
CG
|
B:ASP137
|
3.2
|
27.2
|
1.0
|
CD2
|
B:HIS142
|
3.3
|
20.6
|
1.0
|
CB
|
B:ASP128
|
3.4
|
21.6
|
1.0
|
OE1
|
B:GLU126
|
3.5
|
20.5
|
1.0
|
OD2
|
B:ASP137
|
3.6
|
27.7
|
1.0
|
O
|
B:HOH434
|
3.9
|
21.6
|
1.0
|
CA
|
B:CA301
|
4.2
|
23.3
|
1.0
|
OG
|
B:SER152
|
4.2
|
21.9
|
1.0
|
OD1
|
B:ASP128
|
4.2
|
22.3
|
1.0
|
ND1
|
B:HIS142
|
4.3
|
20.6
|
1.0
|
CB
|
B:ASP137
|
4.4
|
28.4
|
1.0
|
CG
|
B:HIS142
|
4.4
|
21.3
|
1.0
|
CG
|
B:GLU126
|
4.4
|
20.4
|
1.0
|
O
|
B:ILE150
|
4.6
|
22.3
|
1.0
|
CA
|
B:ASP137
|
4.8
|
29.5
|
1.0
|
CA
|
B:ASP128
|
4.9
|
23.0
|
1.0
|
CD
|
B:PRO138
|
5.0
|
27.8
|
1.0
|
|
Manganese binding site 3 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 3 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn302
b:36.1
occ:1.00
|
O
|
C:HOH429
|
1.9
|
15.9
|
1.0
|
OD2
|
C:ASP128
|
2.0
|
22.8
|
1.0
|
OE2
|
C:GLU126
|
2.2
|
20.5
|
1.0
|
OD1
|
C:ASP137
|
2.2
|
21.9
|
1.0
|
NE2
|
C:HIS142
|
2.4
|
24.3
|
1.0
|
O
|
C:HOH407
|
2.6
|
15.4
|
1.0
|
O
|
C:HOH423
|
3.0
|
24.4
|
1.0
|
CG
|
C:ASP128
|
3.2
|
23.2
|
1.0
|
CG
|
C:ASP137
|
3.2
|
22.7
|
1.0
|
CD
|
C:GLU126
|
3.3
|
20.1
|
1.0
|
CD2
|
C:HIS142
|
3.4
|
23.0
|
1.0
|
CE1
|
C:HIS142
|
3.4
|
23.2
|
1.0
|
OD2
|
C:ASP137
|
3.6
|
21.4
|
1.0
|
OE1
|
C:GLU126
|
3.6
|
20.9
|
1.0
|
CB
|
C:ASP128
|
3.7
|
21.1
|
1.0
|
OG
|
C:SER152
|
3.9
|
24.1
|
1.0
|
CA
|
C:CA301
|
4.1
|
38.2
|
1.0
|
OD1
|
C:ASP128
|
4.2
|
25.0
|
1.0
|
CB
|
C:ASP137
|
4.5
|
22.3
|
1.0
|
CG
|
C:GLU126
|
4.5
|
19.3
|
1.0
|
ND1
|
C:HIS142
|
4.6
|
23.8
|
1.0
|
O
|
C:ILE150
|
4.6
|
23.4
|
1.0
|
CG
|
C:HIS142
|
4.6
|
22.7
|
1.0
|
CA
|
C:ASP137
|
4.7
|
25.9
|
1.0
|
|
Manganese binding site 4 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 4 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn302
b:33.4
occ:1.00
|
OD2
|
D:ASP137
|
2.2
|
21.3
|
1.0
|
OD1
|
D:ASP128
|
2.2
|
18.6
|
1.0
|
OE2
|
D:GLU126
|
2.4
|
17.3
|
1.0
|
NE2
|
D:HIS142
|
2.4
|
19.4
|
1.0
|
O
|
D:HOH425
|
2.6
|
14.2
|
1.0
|
CG
|
D:ASP137
|
3.3
|
23.4
|
1.0
|
CD2
|
D:HIS142
|
3.3
|
19.1
|
1.0
|
CD
|
D:GLU126
|
3.3
|
19.2
|
1.0
|
CG
|
D:ASP128
|
3.4
|
19.7
|
1.0
|
CE1
|
D:HIS142
|
3.5
|
20.1
|
1.0
|
OE1
|
D:GLU126
|
3.6
|
20.2
|
1.0
|
OD1
|
D:ASP137
|
3.7
|
23.6
|
1.0
|
CB
|
D:ASP128
|
3.9
|
18.1
|
1.0
|
OG
|
D:SER152
|
3.9
|
18.5
|
1.0
|
O
|
D:HOH420
|
4.1
|
16.0
|
1.0
|
O
|
D:ILE150
|
4.3
|
27.6
|
1.0
|
CA
|
D:CA301
|
4.4
|
25.1
|
1.0
|
OD2
|
D:ASP128
|
4.4
|
19.5
|
1.0
|
CG
|
D:HIS142
|
4.5
|
18.7
|
1.0
|
CB
|
D:ASP137
|
4.5
|
24.4
|
1.0
|
ND1
|
D:HIS142
|
4.6
|
20.1
|
1.0
|
CG
|
D:GLU126
|
4.7
|
18.6
|
1.0
|
CA
|
D:ASP137
|
4.8
|
26.1
|
1.0
|
CG2
|
D:THR155
|
4.9
|
19.9
|
1.0
|
CB
|
D:SER152
|
5.0
|
21.6
|
1.0
|
|
Manganese binding site 5 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 5 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn302
b:35.1
occ:1.00
|
OD1
|
E:ASP128
|
1.9
|
22.7
|
1.0
|
O
|
E:HOH428
|
2.2
|
18.8
|
1.0
|
O
|
E:HOH426
|
2.4
|
14.4
|
1.0
|
OD1
|
E:ASP137
|
2.4
|
23.2
|
1.0
|
OE2
|
E:GLU126
|
2.6
|
25.5
|
1.0
|
NE2
|
E:HIS142
|
2.6
|
25.1
|
1.0
|
CG
|
E:ASP128
|
3.0
|
22.3
|
1.0
|
CG
|
E:ASP137
|
3.2
|
22.9
|
1.0
|
CD2
|
E:HIS142
|
3.4
|
25.4
|
1.0
|
CD
|
E:GLU126
|
3.4
|
26.1
|
1.0
|
OD2
|
E:ASP137
|
3.5
|
22.9
|
1.0
|
OE1
|
E:GLU126
|
3.5
|
26.5
|
1.0
|
CB
|
E:ASP128
|
3.6
|
21.3
|
1.0
|
CE1
|
E:HIS142
|
3.6
|
24.0
|
1.0
|
O
|
E:HOH411
|
3.7
|
30.6
|
1.0
|
OG
|
E:SER152
|
4.0
|
23.0
|
1.0
|
OD2
|
E:ASP128
|
4.0
|
22.9
|
1.0
|
CA
|
E:CA301
|
4.1
|
31.4
|
1.0
|
CB
|
E:ASP137
|
4.4
|
23.0
|
1.0
|
O
|
E:ILE150
|
4.6
|
23.6
|
1.0
|
CG
|
E:HIS142
|
4.7
|
24.9
|
1.0
|
ND1
|
E:HIS142
|
4.7
|
24.4
|
1.0
|
CA
|
E:ASP137
|
4.7
|
25.6
|
1.0
|
CG
|
E:GLU126
|
4.9
|
22.9
|
1.0
|
CD
|
E:PRO138
|
4.9
|
28.9
|
1.0
|
|
Manganese binding site 6 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 6 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn302
b:31.0
occ:1.00
|
OD2
|
F:ASP128
|
2.1
|
26.1
|
1.0
|
O
|
F:HOH430
|
2.1
|
22.6
|
1.0
|
OE2
|
F:GLU126
|
2.1
|
18.8
|
1.0
|
NE2
|
F:HIS142
|
2.2
|
20.0
|
1.0
|
OD1
|
F:ASP137
|
2.3
|
28.8
|
1.0
|
O
|
F:HOH415
|
2.4
|
20.9
|
1.0
|
CD
|
F:GLU126
|
3.0
|
19.5
|
1.0
|
CG
|
F:ASP128
|
3.0
|
25.0
|
1.0
|
CD2
|
F:HIS142
|
3.1
|
20.3
|
1.0
|
OE1
|
F:GLU126
|
3.2
|
20.8
|
1.0
|
CE1
|
F:HIS142
|
3.3
|
20.2
|
1.0
|
CG
|
F:ASP137
|
3.3
|
27.1
|
1.0
|
CB
|
F:ASP128
|
3.4
|
23.3
|
1.0
|
OD2
|
F:ASP137
|
3.7
|
25.5
|
1.0
|
O
|
F:HOH411
|
3.9
|
24.1
|
1.0
|
CA
|
F:CA301
|
4.0
|
28.8
|
1.0
|
OD1
|
F:ASP128
|
4.1
|
27.0
|
1.0
|
OG
|
F:SER152
|
4.2
|
19.4
|
1.0
|
CG
|
F:HIS142
|
4.4
|
19.4
|
1.0
|
ND1
|
F:HIS142
|
4.4
|
19.1
|
1.0
|
CG
|
F:GLU126
|
4.4
|
19.5
|
1.0
|
CB
|
F:ASP137
|
4.6
|
26.3
|
1.0
|
O
|
F:ILE150
|
4.8
|
29.3
|
1.0
|
CA
|
F:ASP128
|
4.9
|
22.8
|
1.0
|
CA
|
F:ASP137
|
4.9
|
27.9
|
1.0
|
|
Manganese binding site 7 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 7 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn302
b:30.4
occ:1.00
|
OD2
|
G:ASP128
|
2.0
|
21.4
|
1.0
|
NE2
|
G:HIS142
|
2.1
|
23.4
|
1.0
|
OE2
|
G:GLU126
|
2.2
|
20.9
|
1.0
|
O
|
G:HOH433
|
2.3
|
10.6
|
1.0
|
OD1
|
G:ASP137
|
2.4
|
23.5
|
1.0
|
O
|
G:HOH432
|
2.6
|
23.6
|
1.0
|
CE1
|
G:HIS142
|
3.1
|
24.2
|
1.0
|
CG
|
G:ASP128
|
3.1
|
22.3
|
1.0
|
CD2
|
G:HIS142
|
3.1
|
21.9
|
1.0
|
CG
|
G:ASP137
|
3.2
|
23.1
|
1.0
|
CD
|
G:GLU126
|
3.3
|
20.9
|
1.0
|
OD2
|
G:ASP137
|
3.6
|
22.9
|
1.0
|
CB
|
G:ASP128
|
3.6
|
22.9
|
1.0
|
OE1
|
G:GLU126
|
3.7
|
19.3
|
1.0
|
O
|
G:HOH431
|
4.0
|
16.4
|
1.0
|
CA
|
G:CA301
|
4.0
|
22.2
|
1.0
|
OD1
|
G:ASP128
|
4.2
|
22.6
|
1.0
|
ND1
|
G:HIS142
|
4.2
|
22.6
|
1.0
|
OG
|
G:SER152
|
4.3
|
23.8
|
1.0
|
CG
|
G:HIS142
|
4.3
|
21.8
|
1.0
|
CB
|
G:ASP137
|
4.3
|
25.9
|
1.0
|
CG
|
G:GLU126
|
4.6
|
19.9
|
1.0
|
CA
|
G:ASP137
|
4.7
|
27.6
|
1.0
|
O
|
G:ILE150
|
4.8
|
26.7
|
1.0
|
CD
|
G:PRO138
|
5.0
|
30.0
|
1.0
|
|
Manganese binding site 8 out
of 8 in 4m3c
Go back to
Manganese Binding Sites List in 4m3c
Manganese binding site 8 out
of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn302
b:41.1
occ:1.00
|
OD1
|
H:ASP128
|
1.9
|
21.4
|
1.0
|
NE2
|
H:HIS142
|
2.1
|
21.2
|
1.0
|
OE2
|
H:GLU126
|
2.1
|
18.4
|
1.0
|
OD2
|
H:ASP137
|
2.4
|
31.2
|
1.0
|
O
|
H:HOH433
|
2.4
|
13.6
|
1.0
|
CD2
|
H:HIS142
|
3.1
|
20.3
|
1.0
|
CG
|
H:ASP128
|
3.1
|
21.1
|
1.0
|
CE1
|
H:HIS142
|
3.1
|
21.8
|
1.0
|
CG
|
H:ASP137
|
3.1
|
30.2
|
1.0
|
CD
|
H:GLU126
|
3.2
|
19.3
|
1.0
|
OD1
|
H:ASP137
|
3.4
|
33.6
|
1.0
|
OE1
|
H:GLU126
|
3.6
|
18.7
|
1.0
|
CB
|
H:ASP128
|
3.6
|
20.7
|
1.0
|
O
|
H:HOH411
|
4.0
|
16.1
|
1.0
|
OG
|
H:SER152
|
4.1
|
18.8
|
1.0
|
OD2
|
H:ASP128
|
4.1
|
20.4
|
1.0
|
CA
|
H:CA301
|
4.1
|
23.8
|
1.0
|
O
|
H:HOH410
|
4.2
|
15.4
|
1.0
|
ND1
|
H:HIS142
|
4.2
|
20.7
|
1.0
|
CG
|
H:HIS142
|
4.2
|
20.1
|
1.0
|
CB
|
H:ASP137
|
4.4
|
27.1
|
1.0
|
CG
|
H:GLU126
|
4.5
|
18.3
|
1.0
|
O
|
H:ILE150
|
4.7
|
22.8
|
1.0
|
CD
|
H:PRO138
|
4.7
|
26.6
|
1.0
|
CA
|
H:ASP137
|
4.7
|
28.2
|
1.0
|
|
Reference:
S.Surya,
J.Abhilash,
K.Geethanandan,
C.Sadasivan,
M.Haridas.
Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds To Be Published.
Page generated: Sat Oct 5 20:17:58 2024
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