Manganese in PDB 5tg3: Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man

The structure of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man, PDB code: 5tg3 was solved by M.Q.Santiago, J.L.A.Correia, V.R.Pinto-Junior, V.J.S.Osterne, R.I.Pereira, J.C.Silva-Filho, C.F.Lossio, B.A.M.Rocha, P.Delatorre, A.H.B.Neco, D.A.Araripe, K.S.Nascimento, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.85 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.460, 85.180, 174.580, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.9

The structure of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Calcium	(Ca)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Manganese atom in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man (pdb code 5tg3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man, PDB code: 5tg3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:14.0 occ:1.00 OE2 A:GLU8 2.1 15.3 1.0 O A:HOH466 2.2 16.6 1.0 OD2 A:ASP10 2.2 14.1 1.0 NE2 A:HIS24 2.3 12.9 1.0 OD1 A:ASP19 2.3 16.5 1.0 O A:HOH442 2.3 16.0 1.0 CD A:GLU8 3.2 14.7 1.0 CG A:ASP19 3.2 19.1 1.0 CD2 A:HIS24 3.2 14.8 1.0 CE1 A:HIS24 3.2 13.6 1.0 CG A:ASP10 3.3 16.6 1.0 OE1 A:GLU8 3.5 16.4 1.0 OD2 A:ASP19 3.6 15.1 1.0 CB A:ASP10 3.7 13.9 1.0 O A:HOH482 3.9 24.9 1.0 O A:HOH419 4.2 16.5 1.0 CA A:CA301 4.2 11.6 1.0 O A:HOH565 4.2 25.5 1.0 OG A:SER34 4.3 17.1 1.0 ND1 A:HIS24 4.3 16.4 1.0 OD1 A:ASP10 4.4 11.1 1.0 CG A:HIS24 4.4 15.0 1.0 CB A:ASP19 4.4 16.7 1.0 CG A:GLU8 4.5 16.3 1.0 CA A:ASP19 4.7 14.3 1.0 O A:VAL32 4.7 18.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:83.6 occ:1.00 OD2 B:ASP10 2.1 21.4 1.0 OD1 B:ASP19 2.2 22.2 1.0 OE2 B:GLU8 2.2 20.4 1.0 NE2 B:HIS24 2.3 21.2 1.0 O B:HOH454 2.3 16.2 1.0 O B:HOH443 2.4 19.0 1.0 CG B:ASP10 3.2 22.3 1.0 CG B:ASP19 3.2 26.7 1.0 CD B:GLU8 3.2 22.1 1.0 CE1 B:HIS24 3.2 23.6 1.0 CD2 B:HIS24 3.3 22.1 1.0 OE1 B:GLU8 3.5 23.2 1.0 CB B:ASP10 3.6 21.1 1.0 OD2 B:ASP19 3.6 20.3 1.0 O B:HOH496 3.9 19.9 1.0 O B:HOH497 3.9 33.4 1.0 CA B:CA301 4.2 25.4 1.0 OG B:SER34 4.2 20.3 1.0 O B:HOH552 4.2 27.6 1.0 OD1 B:ASP10 4.3 18.3 1.0 ND1 B:HIS24 4.4 20.1 1.0 CB B:ASP19 4.4 25.1 1.0 CG B:HIS24 4.4 20.2 1.0 CG B:GLU8 4.6 17.0 1.0 CA B:ASP19 4.7 24.6 1.0 O B:VAL32 4.8 27.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:18.2 occ:1.00 OD2 C:ASP10 2.0 21.0 1.0 OE2 C:GLU8 2.3 19.0 1.0 O C:HOH418 2.3 24.8 1.0 NE2 C:HIS24 2.3 23.7 1.0 OD1 C:ASP19 2.4 17.8 1.0 O C:HOH458 2.4 22.4 1.0 CG C:ASP10 3.1 19.3 1.0 CG C:ASP19 3.2 26.3 1.0 CD C:GLU8 3.2 21.8 1.0 CD2 C:HIS24 3.2 17.3 1.0 CE1 C:HIS24 3.3 21.9 1.0 OE1 C:GLU8 3.5 21.1 1.0 CB C:ASP10 3.5 17.6 1.0 OD2 C:ASP19 3.6 24.2 1.0 O C:HOH483 3.8 22.3 1.0 O C:HOH437 4.1 29.0 1.0 OD1 C:ASP10 4.2 19.3 1.0 CA C:CA301 4.3 18.9 1.0 OG C:SER34 4.3 20.4 1.0 O C:HOH503 4.4 30.6 1.0 CB C:ASP19 4.4 19.7 1.0 CG C:HIS24 4.4 21.3 1.0 ND1 C:HIS24 4.4 18.0 1.0 CG C:GLU8 4.6 16.2 1.0 O C:VAL32 4.7 25.4 1.0 CA C:ASP19 4.8 22.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:21.2 occ:1.00 OD2 D:ASP10 2.0 20.3 1.0 O D:HOH409 2.3 19.7 1.0 NE2 D:HIS24 2.3 22.5 1.0 O D:HOH441 2.3 26.6 1.0 OE2 D:GLU8 2.4 21.7 1.0 OD1 D:ASP19 2.4 25.1 1.0 CG D:ASP10 3.1 19.4 1.0 CE1 D:HIS24 3.1 22.6 1.0 CG D:ASP19 3.2 25.3 1.0 CD D:GLU8 3.3 27.0 1.0 CD2 D:HIS24 3.4 21.6 1.0 OD2 D:ASP19 3.5 28.0 1.0 CB D:ASP10 3.5 19.0 1.0 OE1 D:GLU8 3.6 22.5 1.0 O D:HOH424 4.1 26.1 1.0 O D:HOH423 4.1 31.1 1.0 OD1 D:ASP10 4.2 21.5 1.0 ND1 D:HIS24 4.3 23.1 1.0 CA D:CA301 4.3 24.1 1.0 OG D:SER34 4.3 21.4 1.0 CB D:ASP19 4.4 22.3 1.0 CG D:HIS24 4.4 24.9 1.0 O D:VAL32 4.6 23.8 1.0 O D:HOH503 4.6 31.5 1.0 CG D:GLU8 4.7 21.5 1.0 CA D:ASP19 4.7 23.1 1.0

V.R.Pinto-Junior, V.J.Osterne, M.Q.Santiago, J.L.Correia, F.N.Pereira-Junior, R.B.Leal, M.G.Pereira, L.S.Chicas, C.S.Nagano, B.A.Rocha, J.C.Silva-Filho, W.P.Ferreira, C.R.Rocha, K.S.Nascimento, A.M.Assreuy, B.S.Cavada. Structural Studies of A Vasorelaxant Lectin From Dioclea Reflexa Hook Seeds: Crystal Structure, Molecular Docking and Dynamics. Int. J. Biol. Macromol. V. 98 12 2017.
ISSN: ISSN 1879-0003
PubMed: 28130130
DOI: 10.1016/J.IJBIOMAC.2017.01.092