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Manganese in PDB 1ciw: Peanut Lectin Complexed with N-Acetyllactosamine

Protein crystallography data

The structure of Peanut Lectin Complexed with N-Acetyllactosamine, PDB code: 1ciw 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 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 129.380, 126.922, 76.065, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 1ciw:

The structure of Peanut Lectin Complexed with N-Acetyllactosamine 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 N-Acetyllactosamine (pdb code 1ciw). 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 N-Acetyllactosamine, PDB code: 1ciw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1ciw

Go back to Manganese Binding Sites List in 1ciw
Manganese binding site 1 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:40.5
occ:1.00
OD2 A:ASP123 1.9 14.0 1.0
O A:HOH509 2.0 17.4 1.0
OE2 A:GLU121 2.0 18.9 1.0
O A:HOH510 2.1 15.4 1.0
OD1 A:ASP132 2.3 25.8 1.0
NE2 A:HIS137 2.5 23.0 1.0
CG A:ASP123 2.8 8.4 1.0
CB A:ASP123 3.1 7.9 1.0
CD A:GLU121 3.1 17.3 1.0
CG A:ASP132 3.2 29.9 1.0
CE1 A:HIS137 3.4 21.8 1.0
CD2 A:HIS137 3.4 19.6 1.0
OD2 A:ASP132 3.5 27.4 1.0
OE1 A:GLU121 3.5 17.3 1.0
O A:HOH507 3.7 27.5 1.0
OD1 A:ASP123 3.9 12.5 1.0
CA A:CA237 3.9 17.6 1.0
CG A:GLU121 4.4 18.6 1.0
OG A:SER147 4.4 13.4 1.0
ND1 A:HIS137 4.5 21.4 1.0
O A:VAL145 4.5 18.5 1.0
CB A:ASP132 4.6 28.1 1.0
CG A:HIS137 4.6 16.4 1.0
CA A:ASP123 4.6 11.4 1.0
CD A:PRO133 4.9 34.4 1.0
CA A:ASP132 5.0 27.7 1.0

Manganese binding site 2 out of 4 in 1ciw

Go back to Manganese Binding Sites List in 1ciw
Manganese binding site 2 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:41.1
occ:1.00
O B:HOH533 1.8 46.9 1.0
OE2 B:GLU121 2.0 21.6 1.0
O B:HOH532 2.2 22.4 1.0
OD1 B:ASP132 2.2 24.6 1.0
OD2 B:ASP123 2.3 11.0 1.0
NE2 B:HIS137 2.6 15.8 1.0
CD B:GLU121 3.1 18.8 1.0
CG B:ASP132 3.3 21.3 1.0
CG B:ASP123 3.3 15.1 1.0
OE1 B:GLU121 3.4 22.4 1.0
CD2 B:HIS137 3.5 13.4 1.0
CE1 B:HIS137 3.6 11.4 1.0
CB B:ASP123 3.6 9.4 1.0
OD2 B:ASP132 3.7 22.2 1.0
OG B:SER147 3.8 16.3 1.0
O B:VAL145 4.1 16.3 1.0
O B:HOH407 4.1 21.2 1.0
O B:HOH530 4.3 27.8 1.0
CA B:CA237 4.4 11.9 1.0
CG B:GLU121 4.4 14.8 1.0
OD1 B:ASP123 4.4 15.6 1.0
CB B:ASP132 4.5 14.8 1.0
CG B:HIS137 4.6 12.6 1.0
ND1 B:HIS137 4.7 17.1 1.0
CD B:PRO133 4.7 19.5 1.0
CA B:ASP132 4.8 29.3 1.0

Manganese binding site 3 out of 4 in 1ciw

Go back to Manganese Binding Sites List in 1ciw
Manganese binding site 3 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:44.7
occ:1.00
O C:HOH499 1.9 22.1 1.0
O C:HOH498 1.9 6.8 1.0
OD2 C:ASP123 2.0 30.3 1.0
OD1 C:ASP132 2.0 28.7 1.0
OE2 C:GLU121 2.3 17.2 1.0
NE2 C:HIS137 2.4 22.5 1.0
CG C:ASP123 3.0 24.0 1.0
CG C:ASP132 3.0 26.5 1.0
OD2 C:ASP132 3.3 17.7 1.0
CB C:ASP123 3.4 15.0 1.0
CE1 C:HIS137 3.4 22.4 1.0
CD2 C:HIS137 3.4 22.7 1.0
CD C:GLU121 3.4 15.9 1.0
O C:HOH496 3.7 12.7 1.0
OE1 C:GLU121 3.8 15.8 1.0
OD1 C:ASP123 4.0 27.6 1.0
CA C:CA237 4.0 21.2 1.0
CB C:ASP132 4.2 19.5 1.0
O C:HOH479 4.3 46.2 1.0
OG C:SER147 4.4 29.1 1.0
O C:VAL145 4.5 24.5 1.0
ND1 C:HIS137 4.5 25.3 1.0
CG C:HIS137 4.5 21.1 1.0
CD C:PRO133 4.6 34.1 1.0
CA C:ASP132 4.6 29.2 1.0
CG C:GLU121 4.7 13.9 1.0
CA C:ASP123 4.9 6.1 1.0

Manganese binding site 4 out of 4 in 1ciw

Go back to Manganese Binding Sites List in 1ciw
Manganese binding site 4 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:36.5
occ:1.00
NE2 D:HIS137 2.1 12.8 1.0
OE2 D:GLU121 2.2 15.1 1.0
OD2 D:ASP123 2.2 23.5 1.0
OD1 D:ASP132 2.2 25.1 1.0
O D:HOH493 2.3 16.4 1.0
O D:HOH492 2.4 19.4 1.0
CG D:ASP123 3.0 19.2 1.0
CD2 D:HIS137 3.1 11.6 1.0
CE1 D:HIS137 3.1 13.3 1.0
CG D:ASP132 3.1 27.9 1.0
CB D:ASP123 3.2 14.8 1.0
CD D:GLU121 3.3 17.0 1.0
OD2 D:ASP132 3.5 23.9 1.0
OE1 D:GLU121 3.8 15.9 1.0
CA D:CA237 4.0 20.4 1.0
OD1 D:ASP123 4.1 19.2 1.0
ND1 D:HIS137 4.2 15.1 1.0
CG D:HIS137 4.2 11.5 1.0
OG D:SER147 4.2 15.4 1.0
O D:HOH490 4.3 21.0 1.0
CB D:ASP132 4.4 20.8 1.0
CD D:PRO133 4.5 31.2 1.0
CG D:GLU121 4.6 13.8 1.0
O D:VAL145 4.6 12.3 1.0
CA D:ASP132 4.7 27.8 1.0
CA D:ASP123 4.7 10.9 1.0
O D:HOH463 4.9 28.8 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 10:01:44 2024

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