Calcium in PDB 1v6m: Peanut Lectin with 9MER Peptide (Iwssagnva)

The structure of Peanut Lectin with 9MER Peptide (Iwssagnva), PDB code: 1v6m was solved by S.Kundhavai Natchiar, A.Arockia Jeyaprakash, T.N.C.Ramya, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	127.852, 126.139, 84.825, 90.00, 116.16, 90.00
R / Rfree (%)	21 / 26.4

The structure of Peanut Lectin with 9MER Peptide (Iwssagnva) also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Calcium atom in the Peanut Lectin with 9MER Peptide (Iwssagnva) (pdb code 1v6m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Peanut Lectin with 9MER Peptide (Iwssagnva), PDB code: 1v6m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1237 b:31.0 occ:1.00 OD1 A:ASN127 2.6 20.1 1.0 OD2 A:ASP132 2.6 46.2 1.0 OD2 A:ASP123 2.6 18.5 1.0 O A:HOH1240 2.7 20.8 1.0 O A:HOH1239 2.8 17.6 1.0 O A:TYR125 2.8 27.7 1.0 OD1 A:ASP123 2.8 16.3 1.0 CG A:ASP123 3.1 19.8 1.0 CG A:ASN127 3.5 13.8 1.0 CG A:ASP132 3.6 46.2 1.0 CB A:ASN127 3.8 10.7 1.0 N A:ASN127 3.9 18.8 1.0 C A:TYR125 3.9 27.7 1.0 OD1 A:ASP132 4.0 46.2 1.0 CA A:GLY104 4.3 20.9 1.0 CA A:ASN127 4.5 18.8 1.0 O A:GLY104 4.5 20.9 1.0 CB A:ASP123 4.6 18.1 1.0 O A:HOH1241 4.6 27.7 1.0 MN A:MN1238 4.6 42.6 1.0 ND2 A:ASN127 4.6 14.4 1.0 C A:SER126 4.6 32.5 1.0 CA A:SER126 4.7 32.4 1.0 CB A:ASP132 4.8 46.2 1.0 OD1 A:ASP83 4.8 39.4 1.0 N A:TYR125 4.8 29.2 1.0 N A:SER126 4.8 31.6 1.0 CA A:TYR125 4.8 28.2 1.0 CB A:TYR125 4.9 35.8 1.0 O A:ASP83 4.9 43.6 1.0 CD2 A:TYR125 4.9 38.6 1.0 C A:GLY104 5.0 20.9 1.0

Calcium binding site 2 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2237 b:28.6 occ:1.00 OD2 B:ASP132 2.7 36.8 1.0 O B:HOH2240 2.8 22.3 1.0 OD1 B:ASN127 2.8 30.0 1.0 OD2 B:ASP123 2.8 21.8 1.0 O B:TYR125 2.8 27.4 1.0 OD1 B:ASP123 2.9 21.8 1.0 CG B:ASP123 3.2 21.8 1.0 O B:HOH2239 3.5 37.5 1.0 CG B:ASN127 3.5 24.4 1.0 CG B:ASP132 3.6 35.6 1.0 CB B:ASN127 3.9 24.2 1.0 CA B:GLY104 4.0 22.3 1.0 C B:TYR125 4.0 27.4 1.0 OD1 B:ASP132 4.1 37.3 1.0 N B:ASN127 4.2 23.0 1.0 O B:GLY104 4.5 23.9 1.0 ND2 B:ASN127 4.5 25.0 1.0 MN B:MN2238 4.6 44.2 1.0 CA B:ASN127 4.7 21.4 1.0 CB B:ASP123 4.7 21.8 1.0 C B:GLY104 4.7 23.3 1.0 CB B:ASP132 4.8 32.7 1.0 C B:SER126 4.8 34.4 1.0 CD2 B:TYR125 4.9 48.7 1.0 CA B:TYR125 4.9 27.4 1.0 CA B:SER126 4.9 34.4 1.0 N B:SER126 4.9 33.5 1.0 CB B:TYR125 5.0 47.4 1.0 O B:ASP83 5.0 59.7 1.0 N B:TYR125 5.0 27.4 1.0

Calcium binding site 3 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3237 b:25.9 occ:1.00 O C:TYR125 2.6 32.8 1.0 OD1 C:ASN127 2.7 54.0 1.0 OD2 C:ASP132 2.7 41.5 1.0 OD2 C:ASP123 2.7 24.3 1.0 O C:HOH3239 2.8 19.8 1.0 OD1 C:ASP123 3.0 18.8 1.0 CG C:ASP123 3.3 20.1 1.0 CG C:ASN127 3.3 49.4 1.0 CG C:ASP132 3.4 41.5 1.0 CB C:ASN127 3.6 48.3 1.0 OD1 C:ASP132 3.7 41.5 1.0 N C:ASN127 3.7 35.3 1.0 C C:TYR125 3.8 32.8 1.0 CA C:GLY104 4.0 40.2 1.0 CA C:ASN127 4.3 35.0 1.0 C C:SER126 4.3 43.4 1.0 CA C:SER126 4.4 42.3 1.0 ND2 C:ASN127 4.4 49.9 1.0 MN C:MN3238 4.5 62.1 1.0 O C:GLY104 4.5 40.1 1.0 CB C:ASP132 4.6 41.5 1.0 N C:SER126 4.6 39.9 1.0 CB C:ASP123 4.8 19.1 1.0 C C:GLY104 4.8 41.5 1.0 CA C:TYR125 4.8 32.8 1.0 N C:TYR125 4.9 32.8 1.0 CB C:TYR125 5.0 53.4 1.0 CB C:ASP83 5.0 41.8 1.0

Calcium binding site 4 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4237 b:37.1 occ:1.00 OD1 D:ASN127 2.8 61.3 1.0 OD1 D:ASP123 2.8 67.2 1.0 O D:TYR125 2.8 36.7 1.0 OD2 D:ASP123 2.9 60.5 1.0 OD2 D:ASP132 3.0 34.6 1.0 CG D:ASP123 3.1 59.8 1.0 CG D:ASN127 3.8 57.1 1.0 CA D:GLY104 3.9 53.6 1.0 C D:TYR125 4.0 38.5 1.0 CG D:ASP132 4.0 30.1 1.0 OD1 D:ASP83 4.2 60.8 1.0 CB D:ASP83 4.2 53.0 1.0 O D:GLY104 4.2 52.0 1.0 OD1 D:ASP132 4.4 31.8 1.0 N D:ASN127 4.5 50.4 1.0 CB D:ASN127 4.5 54.9 1.0 CB D:ASP123 4.6 58.2 1.0 MN D:MN4238 4.6 55.4 1.0 C D:GLY104 4.6 51.4 1.0 CG D:ASP83 4.6 57.5 1.0 ND2 D:ASN127 4.6 53.2 1.0 CB D:TYR125 4.7 92.4 1.0 CA D:TYR125 4.7 39.4 1.0 N D:TYR125 4.8 39.0 1.0 CD2 D:TYR125 4.9 96.7 1.0 N D:SER126 4.9 35.4 1.0 N D:GLY104 4.9 56.0 1.0 CA D:SER126 5.0 36.9 1.0

Calcium binding site 5 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca5237 b:39.4 occ:1.00 OD1 E:ASN127 2.7 32.1 1.0 O E:TYR125 2.8 18.2 1.0 OD2 E:ASP132 2.8 23.8 1.0 OD2 E:ASP123 2.8 20.5 1.0 O E:HOH5239 2.8 17.6 1.0 OD1 E:ASP123 2.8 20.7 1.0 CG E:ASP123 3.1 22.1 1.0 CG E:ASN127 3.6 29.0 1.0 CG E:ASP132 3.8 23.8 1.0 CA E:GLY104 3.9 17.3 1.0 C E:TYR125 3.9 19.1 1.0 CB E:ASN127 4.1 26.8 1.0 N E:ASN127 4.2 23.9 1.0 O E:GLY104 4.3 17.3 1.0 OD1 E:ASP132 4.3 23.8 1.0 CB E:ASP83 4.5 54.6 1.0 MN E:MN5238 4.6 48.2 1.0 CB E:ASP123 4.6 18.3 1.0 C E:GLY104 4.6 17.3 1.0 ND2 E:ASN127 4.6 30.3 1.0 CB E:TYR125 4.6 41.5 1.0 CA E:TYR125 4.7 20.8 1.0 OD1 E:ASP83 4.7 61.4 1.0 N E:TYR125 4.7 23.0 1.0 CA E:ASN127 4.8 22.3 1.0 CD2 E:TYR125 4.8 46.3 1.0 N E:SER126 4.9 17.6 1.0 N E:GLY104 5.0 17.3 1.0 C E:SER126 5.0 23.7 1.0

Calcium binding site 6 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca6237 b:23.6 occ:1.00 O F:TYR125 2.7 17.8 1.0 OD1 F:ASN127 2.7 37.2 1.0 OD2 F:ASP123 2.7 21.2 1.0 OD1 F:ASP123 2.7 21.2 1.0 OD2 F:ASP132 2.9 26.3 1.0 CG F:ASP123 3.1 21.2 1.0 CG F:ASN127 3.5 37.2 1.0 C F:TYR125 3.8 17.3 1.0 CG F:ASP132 3.8 25.0 1.0 CA F:GLY104 3.9 21.3 1.0 CB F:ASN127 3.9 37.2 1.0 N F:ASN127 4.2 21.0 1.0 OD1 F:ASP132 4.2 25.6 1.0 O F:GLY104 4.3 24.4 1.0 CB F:ASP83 4.5 17.1 1.0 ND2 F:ASN127 4.5 37.2 1.0 CB F:TYR125 4.5 45.0 1.0 CA F:TYR125 4.5 15.6 1.0 CB F:ASP123 4.6 21.2 1.0 MN F:MN6238 4.6 44.2 1.0 C F:GLY104 4.6 23.5 1.0 O F:ASP83 4.7 37.9 1.0 N F:TYR125 4.7 14.5 1.0 CA F:ASN127 4.7 18.9 1.0 N F:SER126 4.8 21.9 1.0 C F:SER126 4.8 25.5 1.0 OD1 F:ASP83 4.8 17.1 1.0 CA F:SER126 4.9 24.0 1.0 CD2 F:TYR125 4.9 45.0 1.0 CD2 F:LEU106 5.0 11.4 1.0 N F:GLY104 5.0 22.0 1.0 CB F:ASP132 5.0 24.1 1.0

Calcium binding site 7 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca7237 b:27.4 occ:1.00 O G:HOH7240 2.7 26.5 1.0 OD1 G:ASN127 2.8 57.7 1.0 OD2 G:ASP132 2.8 26.2 1.0 O G:TYR125 2.8 16.6 1.0 OD2 G:ASP123 2.8 17.1 1.0 OD1 G:ASP123 2.9 15.9 1.0 O G:HOH7239 3.1 32.3 1.0 CG G:ASP123 3.2 15.9 1.0 CG G:ASN127 3.4 56.0 1.0 CG G:ASP132 3.6 26.2 1.0 CB G:ASN127 3.7 55.5 1.0 CA G:GLY104 3.8 26.0 1.0 OD1 G:ASP132 3.9 26.2 1.0 N G:ASN127 3.9 45.9 1.0 C G:TYR125 4.0 16.6 1.0 O G:GLY104 4.4 26.0 1.0 ND2 G:ASN127 4.5 56.7 1.0 CA G:ASN127 4.5 44.3 1.0 C G:GLY104 4.6 25.3 1.0 MN G:MN7238 4.6 39.5 1.0 C G:SER126 4.7 37.5 1.0 CB G:ASP132 4.7 26.2 1.0 CB G:ASP123 4.7 15.9 1.0 CA G:SER126 4.8 35.5 1.0 CD2 G:TYR125 4.8 35.2 1.0 N G:SER126 4.9 31.2 1.0 CD1 G:TYR130 4.9 36.5 1.0 N G:GLY104 4.9 30.1 1.0 CA G:TYR125 4.9 16.6 1.0 CB G:TYR125 5.0 31.3 1.0

Calcium binding site 8 out of 8 in the Peanut Lectin with 9MER Peptide (Iwssagnva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Peanut Lectin with 9MER Peptide (Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca8237 b:26.6 occ:1.00 O H:TYR125 2.8 30.4 1.0 OD2 H:ASP132 2.8 28.2 1.0 OD2 H:ASP123 2.8 38.8 1.0 OD1 H:ASP123 2.9 49.5 1.0 OD1 H:ASN127 2.9 42.0 1.0 CG H:ASP123 3.2 40.5 1.0 CG H:ASN127 3.4 41.2 1.0 CG H:ASP83 3.6 0.7 1.0 OD1 H:ASP83 3.6 0.7 1.0 CA H:GLY104 3.6 52.0 1.0 CG H:ASP132 3.8 28.2 1.0 C H:TYR125 3.9 34.0 1.0 CB H:ASP83 3.9 0.2 1.0 OD2 H:ASP83 3.9 0.2 1.0 CB H:ASN127 4.0 40.7 1.0 O H:HOH8239 4.0 17.6 1.0 ND2 H:ASN127 4.2 44.5 1.0 N H:ASN127 4.2 27.0 1.0 OD1 H:ASP132 4.2 28.2 1.0 O H:GLY104 4.4 52.1 1.0 CB H:TYR125 4.5 42.8 1.0 C H:GLY104 4.5 51.1 1.0 N H:GLY104 4.6 55.2 1.0 O H:ASP83 4.6 0.4 1.0 CA H:TYR125 4.6 32.8 1.0 CB H:ASP123 4.7 38.8 1.0 CA H:ASN127 4.8 25.9 1.0 N H:TYR125 4.8 32.8 1.0 N H:SER126 4.8 31.5 1.0 CD2 H:TYR125 4.8 47.8 1.0 C H:SER126 4.9 34.9 1.0 MN H:MN8238 4.9 44.8 1.0 CA H:SER126 5.0 35.0 1.0

S.Kundhavai Natchiar, A.Arockia Jeyaprakash, T.N.Ramya, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan. Structural Plasticity of Peanut Lectin: An X-Ray Analysis Involving Variation in pH, Ligand Binding and Crystal Structure. Acta Crystallogr.,Sect.D V. 60 211 2004.
ISSN: ISSN 0907-4449
PubMed: 14747696
DOI: 10.1107/S090744490302849X