Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Interaction of A Legume Lectin with Two Components of the Bacterial Cell Wall, PDB code: 1lod:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca228 b:28.1 occ:1.00 O A:HOH268 2.1 12.5 1.0 O A:PHE123 2.2 16.4 1.0 OD1 A:ASN125 2.3 14.5 1.0 OD1 A:ASP121 2.4 18.5 1.0 O A:HOH269 2.4 14.6 1.0 OD2 A:ASP129 2.6 16.5 1.0 OD2 A:ASP121 2.6 21.9 1.0 CG A:ASP121 2.9 17.0 1.0 CG A:ASN125 3.4 12.8 1.0 C A:PHE123 3.4 12.0 1.0 CG A:ASP129 3.6 12.8 1.0 OD1 A:ASP129 3.9 18.1 1.0 N A:ASN125 4.0 14.7 1.0 CB A:ASN125 4.1 12.8 1.0 CA A:PHE123 4.3 12.0 1.0 O A:GLY99 4.4 11.0 1.0 N A:PHE123 4.4 10.8 1.0 N A:TYR124 4.4 11.9 1.0 MN A:MN229 4.5 41.5 1.0 O A:HOH275 4.5 23.3 1.0 CB A:ASP121 4.5 14.5 1.0 NE1 A:TRP128 4.5 13.3 1.0 ND2 A:ASN125 4.5 11.9 1.0 CB A:PHE123 4.5 11.9 1.0 C A:TYR124 4.6 15.4 1.0 O A:ASP81 4.6 12.5 1.0 CA A:GLY99 4.6 9.9 1.0 CA A:TYR124 4.6 14.6 1.0 OD1 A:ASP81 4.7 12.1 1.0 CA A:ASN125 4.7 14.5 1.0 CD2 A:PHE123 4.7 11.8 1.0 CB A:ASP129 4.9 14.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca458 b:44.8 occ:1.00 O C:HOH490 2.0 45.2 1.0 OD1 C:ASN125 2.0 32.5 1.0 O C:HOH491 2.0 37.6 1.0 O C:PHE123 2.1 35.9 1.0 OD2 C:ASP129 2.7 33.7 1.0 OD1 C:ASP121 2.7 30.5 1.0 OD2 C:ASP121 2.8 30.3 1.0 CG C:ASP121 3.2 28.6 1.0 CG C:ASN125 3.2 32.1 1.0 C C:PHE123 3.3 34.0 1.0 CG C:ASP129 3.8 32.6 1.0 N C:ASN125 4.0 34.4 1.0 CB C:ASN125 4.1 31.6 1.0 OD1 C:ASP129 4.2 34.1 1.0 ND2 C:ASN125 4.2 31.4 1.0 CA C:PHE123 4.2 32.8 1.0 N C:TYR124 4.3 34.8 1.0 CB C:PHE123 4.3 31.9 1.0 O C:GLY99 4.3 24.5 1.0 OD1 C:ASP81 4.3 27.8 1.0 N C:PHE123 4.4 32.7 1.0 CA C:GLY99 4.4 23.6 1.0 CD1 C:PHE123 4.4 32.7 1.0 C C:TYR124 4.4 33.6 1.0 CA C:TYR124 4.5 35.2 1.0 O C:ASP81 4.6 28.4 1.0 NE1 C:TRP128 4.6 31.4 1.0 CA C:ASN125 4.6 32.9 1.0 CB C:ASP121 4.7 27.0 1.0 O C:HOH492 4.8 28.5 1.0 CG C:PHE123 4.9 33.1 1.0 O4 C:MUR460 4.9 34.7 1.0 C C:GLY99 4.9 24.0 1.0 MN C:MN459 5.0 37.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca688 b:29.9 occ:1.00 O E:HOH713 2.0 21.8 1.0 OD1 E:ASN125 2.1 22.1 1.0 O E:HOH714 2.1 41.6 1.0 O E:PHE123 2.1 26.5 1.0 OD1 E:ASP121 2.4 19.9 1.0 OD2 E:ASP129 2.5 25.5 1.0 OD2 E:ASP121 3.0 16.2 1.0 CG E:ASP121 3.1 17.5 1.0 CG E:ASN125 3.3 22.4 1.0 C E:PHE123 3.3 25.8 1.0 CG E:ASP129 3.6 26.6 1.0 OD1 E:ASP129 4.0 27.2 1.0 CB E:ASN125 4.2 24.9 1.0 CA E:PHE123 4.2 23.7 1.0 OD1 E:ASP81 4.2 25.0 1.0 N E:PHE123 4.2 25.3 1.0 N E:ASN125 4.3 26.8 1.0 ND2 E:ASN125 4.3 21.8 1.0 CB E:PHE123 4.3 24.3 1.0 N E:TYR124 4.4 25.9 1.0 O E:ASP81 4.4 21.1 1.0 NE1 E:TRP128 4.4 19.2 1.0 O E:GLY99 4.5 18.9 1.0 CD1 E:PHE123 4.5 25.4 1.0 CB E:ASP121 4.6 17.9 1.0 CA E:GLY99 4.6 19.5 1.0 C E:TYR124 4.6 27.5 1.0 CA E:TYR124 4.7 27.6 1.0 O E:HOH715 4.7 43.7 1.0 MN E:MN689 4.7 16.5 1.0 CA E:ASN125 4.8 25.7 1.0 CB E:ASP129 4.9 26.1 1.0 CG E:PHE123 5.0 25.7 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca918 b:22.9 occ:1.00 O G:HOH950 2.0 26.6 1.0 O G:HOH951 2.1 19.5 1.0 OD1 G:ASN125 2.1 23.9 1.0 O G:PHE123 2.1 25.5 1.0 OD2 G:ASP129 2.5 22.2 1.0 OD1 G:ASP121 2.6 21.1 1.0 OD2 G:ASP121 2.8 23.6 1.0 CG G:ASP121 3.0 19.5 1.0 CG G:ASN125 3.3 22.0 1.0 C G:PHE123 3.4 22.6 1.0 CG G:ASP129 3.5 24.1 1.0 OD1 G:ASP129 3.8 26.8 1.0 N G:ASN125 4.0 22.2 1.0 CB G:ASN125 4.1 22.1 1.0 NE1 G:TRP128 4.2 20.5 1.0 CA G:PHE123 4.3 20.4 1.0 ND2 G:ASN125 4.3 20.2 1.0 N G:PHE123 4.3 20.6 1.0 O G:GLY99 4.4 16.8 1.0 N G:TYR124 4.4 23.9 1.0 CB G:PHE123 4.4 18.4 1.0 MN G:MN919 4.4 11.1 1.0 OD1 G:ASP81 4.4 22.0 1.0 CB G:ASP121 4.6 18.2 1.0 CA G:TYR124 4.6 24.2 1.0 O G:HOH952 4.6 22.1 1.0 O G:ASP81 4.6 19.4 1.0 CD1 G:PHE123 4.6 16.9 1.0 CA G:ASN125 4.7 22.6 1.0 C G:TYR124 4.7 24.4 1.0 CA G:GLY99 4.7 17.7 1.0 CB G:ASP129 4.9 24.2 1.0 CE2 G:TRP128 5.0 19.5 1.0 CZ2 G:TRP128 5.0 19.2 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