Manganese in PDB 1lod: Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall

The structure of Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall, PDB code: 1lod was solved by Y.Bourne, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.400, 139.800, 62.700, 90.00, 91.00, 90.00
R / Rfree (%)	19.7 / n/a

The structure of Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall (pdb code 1lod). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall, PDB code: 1lod:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn229 b:41.5 occ:1.00 O A:HOH275 1.9 23.3 1.0 OD1 A:ASP129 2.2 18.1 1.0 OE2 A:GLU119 2.2 15.8 1.0 NE2 A:HIS136 2.2 18.5 1.0 OD2 A:ASP121 2.3 21.9 1.0 CD2 A:HIS136 3.2 11.5 1.0 CE1 A:HIS136 3.2 12.7 1.0 CD A:GLU119 3.2 12.8 1.0 CG A:ASP129 3.3 12.8 1.0 CG A:ASP121 3.3 17.0 1.0 OE1 A:GLU119 3.6 16.2 1.0 CB A:ASP121 3.8 14.5 1.0 OD2 A:ASP129 3.8 16.5 1.0 O A:HOH269 4.0 14.6 1.0 OG A:SER146 4.2 16.7 1.0 ND1 A:HIS136 4.3 15.4 1.0 OD1 A:ASP121 4.3 18.5 1.0 CG A:HIS136 4.3 12.9 1.0 CB A:ASP129 4.4 14.5 1.0 O A:HOH270 4.4 22.6 1.0 O A:ILE144 4.4 14.2 1.0 CG A:GLU119 4.4 13.6 1.0 CA A:CA228 4.5 28.1 1.0 CD A:PRO130 4.5 18.3 1.0 CD1 A:TRP128 4.6 14.5 1.0 NE1 A:TRP128 4.7 13.3 1.0 CA A:ASP129 4.7 16.4 1.0

Manganese binding site 2 out of 4 in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn459 b:37.8 occ:1.00 O C:HOH493 2.0 79.6 1.0 O C:HOH492 2.0 28.5 1.0 OE2 C:GLU119 2.3 21.6 1.0 OD1 C:ASP129 2.4 34.1 1.0 OD2 C:ASP121 2.5 30.3 1.0 NE2 C:HIS136 2.6 23.2 1.0 CD C:GLU119 3.1 21.7 1.0 OE1 C:GLU119 3.3 22.9 1.0 CD2 C:HIS136 3.3 22.8 1.0 CG C:ASP121 3.4 28.6 1.0 CG C:ASP129 3.5 32.6 1.0 CB C:ASP121 3.6 27.0 1.0 CE1 C:HIS136 3.7 21.9 1.0 OD2 C:ASP129 4.0 33.7 1.0 OG C:SER146 4.1 27.7 1.0 O C:HOH491 4.3 37.6 1.0 O C:ILE144 4.5 27.7 1.0 O C:HOH470 4.5 31.4 1.0 CG C:GLU119 4.5 20.8 1.0 CD C:PRO130 4.5 34.2 1.0 CB C:ASP129 4.5 32.3 1.0 OD1 C:ASP121 4.6 30.5 1.0 CG C:HIS136 4.6 22.2 1.0 ND1 C:HIS136 4.7 23.5 1.0 CA C:ASP129 4.8 31.7 1.0 CD1 C:TRP128 4.9 30.8 1.0 CA C:CA458 5.0 44.8 1.0

Manganese binding site 3 out of 4 in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn689 b:16.5 occ:1.00 O E:HOH701 2.0 17.9 1.0 O E:HOH715 2.0 43.7 1.0 OD2 E:ASP121 2.1 16.2 1.0 OE2 E:GLU119 2.3 24.0 1.0 OD1 E:ASP129 2.4 27.2 1.0 NE2 E:HIS136 2.7 24.2 1.0 CG E:ASP121 3.2 17.5 1.0 CD E:GLU119 3.3 24.1 1.0 CG E:ASP129 3.4 26.6 1.0 OE1 E:GLU119 3.5 24.4 1.0 CD2 E:HIS136 3.5 24.0 1.0 CE1 E:HIS136 3.7 21.7 1.0 CB E:ASP121 3.7 17.9 1.0 OD2 E:ASP129 3.9 25.5 1.0 OG E:SER146 4.1 21.8 1.0 O E:HOH714 4.1 41.6 1.0 OD1 E:ASP121 4.2 19.9 1.0 O E:HOH738 4.4 31.5 1.0 O E:ILE144 4.4 22.9 1.0 CB E:ASP129 4.5 26.1 1.0 CD E:PRO130 4.6 28.7 1.0 CD1 E:TRP128 4.6 21.3 1.0 CG E:GLU119 4.6 21.7 1.0 CG E:HIS136 4.6 23.5 1.0 CA E:ASP129 4.7 27.5 1.0 ND1 E:HIS136 4.7 23.0 1.0 CA E:CA688 4.7 29.9 1.0 NE1 E:TRP128 4.8 19.2 1.0

Manganese binding site 4 out of 4 in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn919 b:11.1 occ:1.00 O G:HOH953 2.0 22.6 1.0 O G:HOH952 2.0 22.1 1.0 OD2 G:ASP121 2.3 23.6 1.0 OD1 G:ASP129 2.3 26.8 1.0 OE2 G:GLU119 2.3 20.0 1.0 NE2 G:HIS136 2.4 20.8 1.0 CD G:GLU119 3.2 18.5 1.0 CD2 G:HIS136 3.3 18.7 1.0 CG G:ASP129 3.3 24.1 1.0 CG G:ASP121 3.3 19.5 1.0 OE1 G:GLU119 3.3 18.8 1.0 CE1 G:HIS136 3.4 17.9 1.0 CB G:ASP121 3.8 18.2 1.0 OD2 G:ASP129 3.8 22.2 1.0 O G:HOH951 4.0 19.5 1.0 OG G:SER146 4.2 17.9 1.0 O G:HOH930 4.3 24.3 1.0 OD1 G:ASP121 4.3 21.1 1.0 CB G:ASP129 4.4 24.2 1.0 O G:ILE144 4.4 19.4 1.0 CA G:CA918 4.4 22.9 1.0 CG G:HIS136 4.4 18.6 1.0 CD1 G:TRP128 4.5 20.9 1.0 ND1 G:HIS136 4.5 19.9 1.0 NE1 G:TRP128 4.6 20.5 1.0 CG G:GLU119 4.6 20.0 1.0 CA G:ASP129 4.7 25.2 1.0 CD G:PRO130 4.8 29.4 1.0

Y.Bourne, A.Ayouba, P.Rouge, C.Cambillau. Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall. A Crystallographic Study. J.Biol.Chem. V. 269 9429 1994.
ISSN: ISSN 0021-9258
PubMed: 8144527