Manganese in PDB 1v6n: Peanut Lectin with 9MER Peptide (Pviwssatg)
Protein crystallography data
The structure of Peanut Lectin with 9MER Peptide (Pviwssatg), PDB code: 1v6n
was solved by
S.Kundhavai Natchiar,
A.Arockia Jeyaprakash,
T.N.C.Ramya,
C.J.Thomas,
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)
|
20.00 /
3.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.150,
125.796,
84.737,
90.00,
116.19,
90.00
|
R / Rfree (%)
|
18.7 /
29.2
|
Other elements in 1v6n:
The structure of Peanut Lectin with 9MER Peptide (Pviwssatg) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Peanut Lectin with 9MER Peptide (Pviwssatg)
(pdb code 1v6n). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Peanut Lectin with 9MER Peptide (Pviwssatg), PDB code: 1v6n:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 1 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1238
b:0.0
occ:1.00
|
OE2
|
A:GLU121
|
2.1
|
4.5
|
1.0
|
OD1
|
A:ASP132
|
2.3
|
3.7
|
1.0
|
OD2
|
A:ASP123
|
2.3
|
0.0
|
1.0
|
CD
|
A:GLU121
|
2.9
|
4.5
|
1.0
|
OE1
|
A:GLU121
|
3.0
|
4.5
|
1.0
|
NE2
|
A:HIS137
|
3.1
|
0.0
|
1.0
|
CG
|
A:ASP132
|
3.3
|
3.7
|
1.0
|
CG
|
A:ASP123
|
3.4
|
0.0
|
1.0
|
OG
|
A:SER147
|
3.7
|
0.0
|
1.0
|
O
|
A:VAL145
|
3.8
|
0.0
|
1.0
|
OD2
|
A:ASP132
|
3.8
|
3.7
|
1.0
|
CB
|
A:ASP123
|
3.8
|
0.0
|
1.0
|
CE1
|
A:HIS137
|
3.9
|
0.0
|
1.0
|
CD2
|
A:HIS137
|
4.1
|
0.0
|
1.0
|
CG
|
A:GLU121
|
4.2
|
4.5
|
1.0
|
CB
|
A:ASP132
|
4.5
|
3.7
|
1.0
|
OD1
|
A:ASP123
|
4.5
|
0.0
|
1.0
|
CA
|
A:ASP132
|
4.6
|
0.0
|
1.0
|
CA
|
A:CA1237
|
4.7
|
0.0
|
1.0
|
OD1
|
A:ASP141
|
5.0
|
0.0
|
1.0
|
C
|
A:VAL145
|
5.0
|
0.0
|
1.0
|
CB
|
A:SER147
|
5.0
|
0.0
|
1.0
|
|
Manganese binding site 2 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 2 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn2238
b:0.0
occ:1.00
|
OD1
|
B:ASP132
|
2.1
|
0.0
|
1.0
|
OE2
|
B:GLU121
|
2.2
|
0.0
|
1.0
|
NE2
|
B:HIS137
|
2.5
|
0.0
|
1.0
|
OD2
|
B:ASP123
|
2.8
|
0.0
|
1.0
|
CD
|
B:GLU121
|
3.0
|
0.0
|
1.0
|
OG
|
B:SER147
|
3.1
|
0.0
|
1.0
|
CD2
|
B:HIS137
|
3.2
|
0.0
|
1.0
|
OE1
|
B:GLU121
|
3.3
|
0.0
|
1.0
|
CG
|
B:ASP132
|
3.3
|
0.0
|
1.0
|
CG
|
B:ASP123
|
3.7
|
0.0
|
1.0
|
CE1
|
B:HIS137
|
3.7
|
0.0
|
1.0
|
O
|
B:VAL145
|
3.7
|
0.0
|
1.0
|
CB
|
B:ASP123
|
3.8
|
0.0
|
1.0
|
OD2
|
B:ASP132
|
3.8
|
0.0
|
1.0
|
CG
|
B:GLU121
|
4.3
|
0.0
|
1.0
|
CB
|
B:SER147
|
4.3
|
0.0
|
1.0
|
CG2
|
B:THR150
|
4.4
|
25.7
|
1.0
|
CB
|
B:ASP132
|
4.5
|
0.0
|
1.0
|
CG
|
B:HIS137
|
4.5
|
0.0
|
1.0
|
OD1
|
B:ASP141
|
4.7
|
0.0
|
1.0
|
ND1
|
B:HIS137
|
4.7
|
0.0
|
1.0
|
CD
|
B:PRO133
|
4.7
|
21.8
|
1.0
|
CA
|
B:ASP132
|
4.7
|
0.0
|
1.0
|
N
|
B:SER147
|
4.8
|
0.0
|
1.0
|
OD1
|
B:ASP123
|
4.8
|
0.0
|
1.0
|
C
|
B:VAL145
|
4.9
|
0.0
|
1.0
|
|
Manganese binding site 3 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 3 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn3238
b:0.0
occ:1.00
|
OD2
|
C:ASP123
|
2.3
|
0.0
|
1.0
|
OD1
|
C:ASP132
|
2.4
|
0.0
|
1.0
|
OE2
|
C:GLU121
|
2.6
|
0.0
|
1.0
|
OE1
|
C:GLU121
|
2.9
|
0.0
|
1.0
|
NE2
|
C:HIS137
|
3.0
|
3.9
|
1.0
|
OD2
|
C:ASP132
|
3.0
|
0.0
|
1.0
|
CG
|
C:ASP132
|
3.0
|
0.0
|
1.0
|
CD
|
C:GLU121
|
3.1
|
0.0
|
1.0
|
CG
|
C:ASP123
|
3.5
|
0.0
|
1.0
|
O
|
C:VAL145
|
3.6
|
0.0
|
1.0
|
CE1
|
C:HIS137
|
3.7
|
3.9
|
1.0
|
CA
|
C:CA3237
|
3.8
|
0.0
|
1.0
|
CD2
|
C:HIS137
|
4.1
|
3.9
|
1.0
|
OD1
|
C:ASP123
|
4.3
|
0.0
|
1.0
|
CB
|
C:ASP123
|
4.4
|
0.0
|
1.0
|
CB
|
C:ASP132
|
4.5
|
0.0
|
1.0
|
OG
|
C:SER147
|
4.6
|
48.2
|
1.0
|
CG
|
C:GLU121
|
4.6
|
0.0
|
1.0
|
C
|
C:VAL145
|
4.6
|
0.0
|
1.0
|
CB
|
C:VAL145
|
4.9
|
12.2
|
1.0
|
ND1
|
C:HIS137
|
4.9
|
3.9
|
1.0
|
CA
|
C:ASP132
|
5.0
|
0.0
|
1.0
|
|
Manganese binding site 4 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 4 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn4238
b:0.0
occ:1.00
|
OD1
|
D:ASP132
|
2.1
|
25.2
|
1.0
|
OE2
|
D:GLU121
|
2.2
|
0.5
|
1.0
|
OD2
|
D:ASP123
|
2.6
|
0.0
|
1.0
|
NE2
|
D:HIS137
|
2.8
|
0.0
|
1.0
|
CG
|
D:ASP132
|
3.2
|
25.2
|
1.0
|
CD
|
D:GLU121
|
3.3
|
0.5
|
1.0
|
CG
|
D:ASP123
|
3.4
|
0.0
|
1.0
|
CD2
|
D:HIS137
|
3.6
|
0.0
|
1.0
|
OG
|
D:SER147
|
3.6
|
33.7
|
1.0
|
OE1
|
D:GLU121
|
3.7
|
0.5
|
1.0
|
CB
|
D:ASP123
|
3.8
|
0.0
|
1.0
|
O
|
D:VAL145
|
3.8
|
0.0
|
1.0
|
CE1
|
D:HIS137
|
3.9
|
0.0
|
1.0
|
OD2
|
D:ASP132
|
3.9
|
25.2
|
1.0
|
CB
|
D:ASP132
|
4.3
|
25.2
|
1.0
|
OD1
|
D:ASP123
|
4.5
|
0.0
|
1.0
|
CG
|
D:GLU121
|
4.6
|
0.5
|
1.0
|
CD
|
D:PRO133
|
4.6
|
0.0
|
1.0
|
CA
|
D:ASP132
|
4.7
|
23.4
|
1.0
|
CB
|
D:SER147
|
4.8
|
33.7
|
1.0
|
CG
|
D:HIS137
|
4.9
|
0.0
|
1.0
|
ND1
|
D:HIS137
|
4.9
|
0.0
|
1.0
|
C
|
D:VAL145
|
5.0
|
0.0
|
1.0
|
|
Manganese binding site 5 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 5 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn5238
b:0.0
occ:1.00
|
OD1
|
E:ASP132
|
2.4
|
6.6
|
1.0
|
OD2
|
E:ASP123
|
2.4
|
3.9
|
1.0
|
OE2
|
E:GLU121
|
2.5
|
0.0
|
1.0
|
NE2
|
E:HIS137
|
2.6
|
0.0
|
1.0
|
OE1
|
E:GLU121
|
2.9
|
0.0
|
1.0
|
CD
|
E:GLU121
|
3.0
|
0.0
|
1.0
|
CG
|
E:ASP132
|
3.4
|
6.6
|
1.0
|
CE1
|
E:HIS137
|
3.5
|
0.0
|
1.0
|
O
|
E:VAL145
|
3.5
|
0.0
|
1.0
|
CG
|
E:ASP123
|
3.5
|
3.9
|
1.0
|
CD2
|
E:HIS137
|
3.5
|
0.0
|
1.0
|
OG
|
E:SER147
|
3.6
|
0.0
|
1.0
|
OD2
|
E:ASP132
|
3.7
|
6.6
|
1.0
|
CB
|
E:ASP123
|
4.1
|
3.9
|
1.0
|
CA
|
E:CA5237
|
4.3
|
0.0
|
1.0
|
CG
|
E:GLU121
|
4.4
|
0.0
|
1.0
|
OD1
|
E:ASP123
|
4.5
|
3.9
|
1.0
|
ND1
|
E:HIS137
|
4.6
|
0.0
|
1.0
|
C
|
E:VAL145
|
4.7
|
0.0
|
1.0
|
CG
|
E:HIS137
|
4.7
|
0.0
|
1.0
|
CB
|
E:ASP132
|
4.7
|
6.6
|
1.0
|
CB
|
E:SER147
|
4.9
|
0.0
|
1.0
|
CA
|
E:ASP132
|
4.9
|
7.1
|
1.0
|
CD
|
E:PRO133
|
5.0
|
16.1
|
1.0
|
|
Manganese binding site 6 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 6 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn6238
b:0.0
occ:1.00
|
OE2
|
F:GLU121
|
2.1
|
0.0
|
1.0
|
OD1
|
F:ASP132
|
2.2
|
0.0
|
1.0
|
OD2
|
F:ASP123
|
2.4
|
15.9
|
1.0
|
NE2
|
F:HIS137
|
3.0
|
0.0
|
1.0
|
CD
|
F:GLU121
|
3.1
|
0.0
|
1.0
|
CG
|
F:ASP132
|
3.1
|
0.0
|
1.0
|
CG
|
F:ASP123
|
3.3
|
15.9
|
1.0
|
OE1
|
F:GLU121
|
3.4
|
0.0
|
1.0
|
OD2
|
F:ASP132
|
3.4
|
0.0
|
1.0
|
CB
|
F:ASP123
|
3.5
|
15.9
|
1.0
|
CE1
|
F:HIS137
|
3.8
|
0.0
|
1.0
|
O
|
F:VAL145
|
3.8
|
0.0
|
1.0
|
CD2
|
F:HIS137
|
4.0
|
0.0
|
1.0
|
OG
|
F:SER147
|
4.0
|
0.0
|
1.0
|
OD1
|
F:ASP123
|
4.3
|
15.9
|
1.0
|
CG
|
F:GLU121
|
4.4
|
0.0
|
1.0
|
CB
|
F:ASP132
|
4.4
|
0.0
|
1.0
|
CA
|
F:CA6237
|
4.7
|
0.0
|
1.0
|
CA
|
F:ASP132
|
4.7
|
0.0
|
1.0
|
CD
|
F:PRO133
|
4.8
|
0.0
|
1.0
|
C
|
F:VAL145
|
5.0
|
0.0
|
1.0
|
ND1
|
F:HIS137
|
5.0
|
0.0
|
1.0
|
CA
|
F:ASP123
|
5.0
|
0.0
|
1.0
|
|
Manganese binding site 7 out
of 8 in 1v6n
Go back to
Manganese Binding Sites List in 1v6n
Manganese binding site 7 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn7238
b:0.0
occ:1.00
|
OD1
|
G:ASP132
|
2.1
|
0.0
|
1.0
|
OE2
|
G:GLU121
|
2.3
|
0.0
|
1.0
|
OD2
|
G:ASP123
|
2.4
|
0.0
|
1.0
|
NE2
|
G:HIS137
|
2.9
|
5.0
|
1.0
|
CG
|
G:ASP132
|
2.9
|
0.0
|
1.0
|
OD2
|
G:ASP132
|
3.1
|
0.0
|
1.0
|
CD
|
G:GLU121
|
3.1
|
0.0
|
1.0
|
OE1
|
G:GLU121
|
3.2
|
0.0
|
1.0
|
CE1
|
G:HIS137
|
3.4
|
5.0
|
1.0
|
CG
|
G:ASP123
|
3.4
|
0.0
|
1.0
|
O
|
G:VAL145
|
3.4
|
0.0
|
1.0
|
CB
|
G:ASP123
|
3.9
|
0.0
|
1.0
|
CD2
|
G:HIS137
|
4.1
|
5.0
|
1.0
|
OG
|
G:SER147
|
4.3
|
2.9
|
1.0
|
CB
|
G:ASP132
|
4.4
|
0.0
|
1.0
|
OD1
|
G:ASP123
|
4.5
|
0.0
|
1.0
|
CG
|
G:GLU121
|
4.5
|
0.0
|
1.0
|
C
|
G:VAL145
|
4.7
|
0.0
|
1.0
|
ND1
|
G:HIS137
|
4.7
|
5.0
|
1.0
|
CA
|
G:CA7237
|
4.7
|
0.0
|
1.0
|
CA
|
G:ASP132
|
4.9
|
0.0
|
1.0
|
O
|
G:TYR130
|
4.9
|
1.9
|
1.0
|
|
Manganese binding site 8 out
of 8 in 1v6n
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Manganese Binding Sites List in 1v6n
Manganese binding site 8 out
of 8 in the Peanut Lectin with 9MER Peptide (Pviwssatg)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Peanut Lectin with 9MER Peptide (Pviwssatg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn8238
b:0.0
occ:1.00
|
OE2
|
H:GLU121
|
2.2
|
0.0
|
1.0
|
OD1
|
H:ASP132
|
2.5
|
5.9
|
1.0
|
NE2
|
H:HIS137
|
2.7
|
0.0
|
1.0
|
OD2
|
H:ASP123
|
2.8
|
0.2
|
1.0
|
CD
|
H:GLU121
|
3.1
|
0.0
|
1.0
|
OE1
|
H:GLU121
|
3.4
|
0.0
|
1.0
|
CG
|
H:ASP132
|
3.5
|
5.9
|
1.0
|
CE1
|
H:HIS137
|
3.5
|
0.0
|
1.0
|
CG
|
H:ASP123
|
3.6
|
0.2
|
1.0
|
CD2
|
H:HIS137
|
3.7
|
0.0
|
1.0
|
CB
|
H:ASP123
|
3.7
|
0.2
|
1.0
|
OD2
|
H:ASP132
|
4.0
|
5.9
|
1.0
|
O
|
H:VAL145
|
4.1
|
0.0
|
1.0
|
CA
|
H:CA8237
|
4.2
|
0.0
|
1.0
|
OG
|
H:SER147
|
4.3
|
8.2
|
1.0
|
CG
|
H:GLU121
|
4.5
|
0.0
|
1.0
|
ND1
|
H:HIS137
|
4.7
|
0.0
|
1.0
|
OD1
|
H:ASP123
|
4.7
|
0.2
|
1.0
|
CD
|
H:PRO133
|
4.7
|
0.0
|
1.0
|
CB
|
H:ASP132
|
4.7
|
5.9
|
1.0
|
CG
|
H:HIS137
|
4.8
|
0.0
|
1.0
|
CB
|
H:SER147
|
4.9
|
8.2
|
1.0
|
|
Reference:
S.Kundhavai Natchiar,
A.Arockia Jeyaprakash,
T.N.Ramya,
C.J.Thomas,
K.Suguna,
A.Surolia,
M.Vijayan.
Structural Plasticity of Peanut Lectin: An X-Ray Analysis Involving Variation in pH, Ligand Binding and Crystal Structure. Acta Crystallogr.,Sect.D V. 60 211 2004.
ISSN: ISSN 0907-4449
PubMed: 14747696
DOI: 10.1107/S090744490302849X
Page generated: Sat Oct 5 12:43:38 2024
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