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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:

Calcium (Ca) 4 atoms

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: Tue Dec 15 03:54:40 2020

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