Atomistry » Manganese » PDB 1pj4-1r1o » 1qf3
Atomistry »
  Manganese »
    PDB 1pj4-1r1o »
      1qf3 »

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: Sat Oct 5 12:12:07 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy