Manganese in PDB 5t7p: Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man

The structure of Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man, PDB code: 5t7p was solved by V.R.Pinto-Junior, M.Q.Santiago, V.J.S.Osterne, J.C.Silva-Filho, B.A.M.Rocha, P.Delatorre, 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)	33.28 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.770, 62.970, 66.740, 90.00, 94.27, 90.00
R / Rfree (%)	17 / 22.1

The structure of Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Manganese atom in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man (pdb code 5t7p). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man, PDB code: 5t7p:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed 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 Pisum Arvense Lectin (Pal) Complexed with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:19.3 occ:1.00 OD2 A:ASP121 2.1 14.1 1.0 NE2 A:HIS136 2.2 12.3 1.0 OD1 A:ASP129 2.2 17.8 1.0 OE1 A:GLU119 2.2 11.9 1.0 O A:HOH429 2.3 16.9 1.0 O A:HOH408 2.3 11.0 1.0 CE1 A:HIS136 3.1 15.3 1.0 CD A:GLU119 3.1 12.8 1.0 CG A:ASP129 3.1 18.4 1.0 CG A:ASP121 3.2 13.5 1.0 CD2 A:HIS136 3.2 16.0 1.0 OE2 A:GLU119 3.4 10.0 1.0 CB A:ASP121 3.6 13.3 1.0 OD2 A:ASP129 3.6 15.3 1.0 O A:HOH449 3.7 13.9 1.0 CA A:CA302 4.1 16.3 1.0 ND1 A:HIS136 4.2 19.1 1.0 OD1 A:ASP121 4.2 15.2 1.0 OG A:SER146 4.3 17.1 1.0 CG A:HIS136 4.3 16.0 1.0 CB A:ASP129 4.4 13.6 1.0 O A:ILE144 4.4 15.0 1.0 CD1 A:TRP128 4.5 15.9 1.0 CG A:GLU119 4.5 14.4 1.0 CD A:PRO130 4.5 15.2 1.0 NE1 A:TRP128 4.5 16.4 1.0 O A:HOH435 4.6 15.1 1.0 CA A:ASP129 4.7 16.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed 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 Pisum Arvense Lectin (Pal) Complexed with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:22.3 occ:1.00 O B:HOH467 2.1 15.0 1.0 OD2 B:ASP121 2.1 13.4 1.0 NE2 B:HIS136 2.2 20.0 1.0 OE1 B:GLU119 2.2 17.7 1.0 OD1 B:ASP129 2.3 17.4 1.0 O B:HOH414 2.4 17.5 1.0 CE1 B:HIS136 3.0 18.2 1.0 CG B:ASP121 3.2 16.2 1.0 CD B:GLU119 3.2 19.1 1.0 CD2 B:HIS136 3.2 18.7 1.0 CG B:ASP129 3.3 20.6 1.0 OE2 B:GLU119 3.5 15.1 1.0 CB B:ASP121 3.5 17.0 1.0 O B:HOH430 3.8 20.2 1.0 OD2 B:ASP129 3.8 19.3 1.0 CA B:CA302 4.1 19.1 1.0 ND1 B:HIS136 4.2 18.8 1.0 OG B:SER146 4.2 19.9 1.0 OD1 B:ASP121 4.3 14.8 1.0 CG B:HIS136 4.3 20.1 1.0 CB B:ASP129 4.4 18.4 1.0 O B:ILE144 4.5 20.0 1.0 CD B:PRO130 4.5 21.5 1.0 CG B:GLU119 4.6 18.0 1.0 NE1 B:TRP128 4.6 20.9 1.0 CD1 B:TRP128 4.6 21.5 1.0 O B:HOH452 4.6 19.4 1.0 CA B:ASP129 4.7 19.6 1.0

V.R.Pinto-Junior, M.Q.Santiago, C.B.Nobre, V.J.S.Osterne, R.B.Leal, J.B.Cajazeiras, C.F.Lossio, B.A.M.Rocha, M.G.Q.Martins, C.A.S.Nobre, M.T.L.Silva, K.S.Nascimento, B.S.Cavada. Crystal Structure of Pisum Arvense Seed Lectin (Pal) and Characterization of Its Interaction with Carbohydrates By Molecular Docking and Dynamics. Arch. Biochem. Biophys. V. 630 27 2017.
ISSN: ESSN 1096-0384
PubMed: 28754321
DOI: 10.1016/J.ABB.2017.07.013