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Manganese in PDB 1qdo: Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex

Protein crystallography data

The structure of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdo was solved by J.Bouckaert, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.410, 64.530, 126.960, 90.00, 93.21, 90.00
R / Rfree (%) 16.4 / 25.7

Other elements in 1qdo:

The structure of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex (pdb code 1qdo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1qdo

Go back to Manganese Binding Sites List in 1qdo
Manganese binding site 1 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn240

b:43.9
occ:1.00
OE2 A:GLU8 1.9 38.3 1.0
OD2 A:ASP10 2.2 15.8 1.0
OD1 A:ASP19 2.2 41.6 1.0
NE2 A:HIS24 2.6 17.3 1.0
CD A:GLU8 3.0 45.8 1.0
CG A:ASP19 3.2 38.0 1.0
CG A:ASP10 3.3 27.9 1.0
OG A:SER34 3.4 15.3 1.0
OE1 A:GLU8 3.5 27.0 1.0
CD2 A:HIS24 3.5 17.4 1.0
OD2 A:ASP19 3.7 44.7 1.0
CE1 A:HIS24 3.7 15.2 1.0
CB A:ASP10 3.7 22.8 1.0
O A:VAL32 4.2 24.1 1.0
CG A:GLU8 4.3 38.1 1.0
OD1 A:ASP10 4.3 43.7 1.0
CB A:ASP19 4.4 16.6 1.0
CA A:ASP19 4.5 51.2 1.0
CG A:HIS24 4.7 31.3 1.0
ND1 A:HIS24 4.8 20.9 1.0
CB A:SER34 4.8 16.2 1.0

Manganese binding site 2 out of 4 in 1qdo

Go back to Manganese Binding Sites List in 1qdo
Manganese binding site 2 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn242

b:42.3
occ:1.00
OE2 B:GLU8 2.0 37.9 1.0
OD2 B:ASP10 2.0 25.0 1.0
O B:HOH1242 2.1 23.4 1.0
OD1 B:ASP19 2.2 45.5 1.0
NE2 B:HIS24 2.5 15.7 1.0
CG B:ASP10 3.1 36.8 1.0
CG B:ASP19 3.1 33.0 1.0
CD B:GLU8 3.2 34.9 1.0
CD2 B:HIS24 3.4 28.9 1.0
OD2 B:ASP19 3.5 32.4 1.0
CE1 B:HIS24 3.5 27.6 1.0
CB B:ASP10 3.5 20.8 1.0
O B:HOH1240 3.6 16.4 1.0
OE1 B:GLU8 3.9 18.2 1.0
OG B:SER34 4.2 32.0 1.0
OD1 B:ASP10 4.2 46.8 1.0
CG B:GLU8 4.3 29.7 1.0
CB B:ASP19 4.4 21.4 1.0
CA B:CA243 4.5 39.4 1.0
CG B:HIS24 4.6 31.6 1.0
CA B:ASP19 4.6 46.0 1.0
ND1 B:HIS24 4.6 16.2 1.0
O B:VAL32 4.7 28.4 1.0

Manganese binding site 3 out of 4 in 1qdo

Go back to Manganese Binding Sites List in 1qdo
Manganese binding site 3 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn244

b:42.8
occ:1.00
OE2 C:GLU8 1.8 30.5 1.0
OD2 C:ASP10 2.0 10.3 1.0
OD1 C:ASP19 2.0 44.5 1.0
NE2 C:HIS24 2.5 23.1 1.0
CD C:GLU8 3.0 39.6 1.0
CG C:ASP19 3.2 42.0 1.0
CG C:ASP10 3.3 23.0 1.0
CE1 C:HIS24 3.4 14.3 1.0
OG C:SER34 3.4 30.8 1.0
OE1 C:GLU8 3.6 29.4 1.0
CD2 C:HIS24 3.6 21.4 1.0
OD2 C:ASP19 3.7 41.1 1.0
CB C:ASP10 3.9 10.3 1.0
O C:VAL32 4.0 26.6 1.0
CG C:GLU8 4.3 37.0 1.0
OD1 C:ASP10 4.3 36.0 1.0
CB C:ASP19 4.4 32.1 1.0
CA C:ASP19 4.6 48.5 1.0
ND1 C:HIS24 4.6 28.4 1.0
CG C:HIS24 4.7 32.8 1.0
CB C:SER34 4.8 12.3 1.0
CA C:CA245 4.9 47.0 1.0

Manganese binding site 4 out of 4 in 1qdo

Go back to Manganese Binding Sites List in 1qdo
Manganese binding site 4 out of 4 in the Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Man(APLHA1-3)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn246

b:48.0
occ:1.00
O D:HOH3243 1.8 29.3 1.0
OD2 D:ASP10 1.9 20.2 1.0
OD1 D:ASP19 2.1 33.1 1.0
OE2 D:GLU8 2.1 31.7 1.0
NE2 D:HIS24 2.6 13.1 1.0
CG D:ASP10 3.0 37.2 1.0
CG D:ASP19 3.0 37.5 1.0
CD D:GLU8 3.3 28.8 1.0
OD2 D:ASP19 3.4 42.0 1.0
CB D:ASP10 3.5 30.3 1.0
CE1 D:HIS24 3.5 13.1 1.0
CD2 D:HIS24 3.7 27.0 1.0
OE1 D:GLU8 4.0 14.7 1.0
OD1 D:ASP10 4.0 53.8 1.0
OG D:SER34 4.1 23.2 1.0
CB D:ASP19 4.4 28.9 1.0
CG D:GLU8 4.4 29.4 1.0
CA D:CA247 4.4 42.8 1.0
O D:VAL32 4.6 23.2 1.0
ND1 D:HIS24 4.7 18.9 1.0
CA D:ASP19 4.7 40.3 1.0
CG D:HIS24 4.8 32.8 1.0
CA D:ASP10 4.9 15.0 1.0

Reference:

J.Bouckaert, T.W.Hamelryck, L.Wyns, R.Loris. The Crystal Structures of Man(ALPHA1-3)Man(ALPHA1-O)Me and Man(ALPHA1-6)Man(ALPHA1-O)Me in Complex with Concanavalin A. J.Biol.Chem. V. 274 29188 1999.
ISSN: ISSN 0021-9258
PubMed: 10506175
DOI: 10.1074/JBC.274.41.29188
Page generated: Tue Dec 15 03:54:40 2020

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