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Calcium in PDB 1v6n: Peanut Lectin with 9MER Peptide (Pviwssatg)

Protein crystallography data

The structure of Peanut Lectin with 9MER Peptide (Pviwssatg), PDB code: 1v6n 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) 20.00 / 3.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.150, 125.796, 84.737, 90.00, 116.19, 90.00
R / Rfree (%) 18.7 / 29.2

Other elements in 1v6n:

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

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Peanut Lectin with 9MER Peptide (Pviwssatg) (pdb code 1v6n). 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 (Pviwssatg), PDB code: 1v6n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1237

b:0.0
occ:1.00
OD1 A:ASP123 2.8 0.0 1.0
OD2 A:ASP132 2.8 3.7 1.0
OD2 A:ASP123 2.9 0.0 1.0
O A:TYR125 2.9 0.0 1.0
OD1 A:ASN127 3.0 9.1 1.0
CG A:ASP123 3.2 0.0 1.0
CG A:ASN127 3.4 9.1 1.0
CB A:ASN127 3.7 9.1 1.0
CA A:GLY104 3.8 0.0 1.0
CG A:ASP132 3.8 3.7 1.0
O A:GLY104 4.0 0.0 1.0
N A:ASN127 4.1 0.0 1.0
OD1 A:ASP132 4.1 3.7 1.0
C A:TYR125 4.1 0.0 1.0
CB A:ASP83 4.3 26.5 1.0
ND2 A:ASN127 4.4 9.1 1.0
C A:GLY104 4.4 0.0 1.0
CA A:ASN127 4.5 0.0 1.0
OD1 A:ASP83 4.6 26.5 1.0
O A:ASP83 4.6 5.6 1.0
MN A:MN1238 4.7 0.0 1.0
CB A:ASP123 4.7 0.0 1.0
CD2 A:LEU106 4.8 0.0 1.0
CG A:ASP83 4.8 26.5 1.0
C A:SER126 4.9 0.0 1.0
CB A:TYR125 5.0 38.1 1.0
N A:GLY104 5.0 0.0 1.0

Calcium binding site 2 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2237

b:0.0
occ:1.00
OD1 B:ASN127 2.7 27.6 1.0
OD1 B:ASP123 2.8 0.0 1.0
O B:TYR125 2.9 0.0 1.0
OD2 B:ASP123 3.0 0.0 1.0
OD2 B:ASP132 3.0 0.0 1.0
CG B:ASP123 3.2 0.0 1.0
CG B:ASN127 3.3 27.6 1.0
CB B:ASP83 3.9 6.8 1.0
ND2 B:ASN127 3.9 27.6 1.0
CA B:GLY104 4.0 16.0 1.0
C B:TYR125 4.0 0.0 1.0
CB B:ASN127 4.1 27.6 1.0
CG B:ASP132 4.2 0.0 1.0
CB B:TYR125 4.3 2.6 1.0
N B:TYR125 4.4 0.0 1.0
O B:ASP83 4.4 17.0 1.0
CA B:TYR125 4.5 0.0 1.0
OD1 B:ASP83 4.5 6.8 1.0
O B:GLY104 4.5 16.0 1.0
CD2 B:LEU106 4.6 0.0 1.0
CB B:ASP123 4.6 0.0 1.0
CG B:ASP83 4.6 6.8 1.0
C B:GLY104 4.7 16.0 1.0
CA B:ASP83 4.7 17.0 1.0
N B:ASN127 4.8 31.8 1.0
OD1 B:ASP132 4.9 0.0 1.0
C B:ASP83 4.9 17.0 1.0
N B:GLY104 4.9 16.0 1.0
N B:THR124 5.0 0.0 1.0

Calcium binding site 3 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3237

b:0.0
occ:1.00
OD1 C:ASN127 2.7 8.2 1.0
OD1 C:ASP123 2.7 0.0 1.0
OD2 C:ASP132 2.8 0.0 1.0
O C:TYR125 2.9 0.0 1.0
OD2 C:ASP123 2.9 0.0 1.0
CG C:ASP123 3.2 0.0 1.0
CG C:ASN127 3.3 8.2 1.0
CB C:ASN127 3.7 8.2 1.0
MN C:MN3238 3.8 0.0 1.0
CA C:GLY104 4.0 8.5 1.0
CG C:ASP132 4.0 0.0 1.0
C C:TYR125 4.1 0.0 1.0
N C:ASN127 4.1 1.6 1.0
ND2 C:ASN127 4.2 8.2 1.0
CB C:ASP83 4.5 0.0 1.0
OD1 C:ASP132 4.6 0.0 1.0
CA C:ASN127 4.6 1.6 1.0
CB C:ASP123 4.7 0.0 1.0
O C:ASP83 4.7 0.0 1.0
C C:GLY104 4.7 8.5 1.0
O C:GLY104 4.8 8.5 1.0
N C:TYR125 4.8 0.0 1.0
CE1 C:HIS137 4.8 3.9 1.0
CD2 C:LEU106 4.8 0.0 1.0
CA C:TYR125 4.9 0.0 1.0
OD1 C:ASP83 4.9 0.0 1.0
CB C:TYR125 5.0 37.2 1.0

Calcium binding site 4 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4237

b:0.0
occ:1.00
O D:TYR125 2.8 6.3 1.0
OD1 D:ASP123 2.9 0.0 1.0
OD1 D:ASN127 3.0 4.0 1.0
OD2 D:ASP123 3.0 0.0 1.0
OD2 D:ASP132 3.2 25.2 1.0
CG D:ASP123 3.3 0.0 1.0
CG D:ASN127 3.6 4.0 1.0
CA D:GLY104 3.9 46.4 1.0
CB D:ASN127 3.9 4.0 1.0
C D:TYR125 4.0 6.3 1.0
CB D:ASP83 4.0 0.0 1.0
CG D:ASP132 4.1 25.2 1.0
N D:ASN127 4.2 20.5 1.0
OD1 D:ASP83 4.3 0.0 1.0
OD1 D:ASP132 4.5 25.2 1.0
CG D:ASP83 4.6 0.0 1.0
O D:ASP83 4.6 47.5 1.0
CB D:TYR125 4.6 88.7 1.0
ND2 D:ASN127 4.7 4.0 1.0
O D:GLY104 4.7 46.4 1.0
CA D:TYR125 4.7 6.3 1.0
CA D:ASN127 4.7 20.5 1.0
N D:TYR125 4.7 6.3 1.0
C D:GLY104 4.8 46.4 1.0
CB D:ASP123 4.8 0.0 1.0
CA D:ASP83 4.8 47.5 1.0
N D:GLY104 4.8 46.4 1.0
N D:SER126 4.9 0.1 1.0
C D:SER126 5.0 0.1 1.0

Calcium binding site 5 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5237

b:0.0
occ:1.00
OD1 E:ASP123 2.7 3.9 1.0
OD2 E:ASP123 2.8 3.9 1.0
OD1 E:ASN127 2.8 23.8 1.0
CG E:ASP123 3.1 3.9 1.0
OD2 E:ASP132 3.1 6.6 1.0
O E:TYR125 3.1 0.0 1.0
CG E:ASN127 3.2 23.8 1.0
CB E:ASN127 3.6 23.8 1.0
O E:GLY104 3.7 0.0 1.0
CG E:ASP132 4.0 6.6 1.0
N E:ASN127 4.0 0.5 1.0
CA E:GLY104 4.1 0.0 1.0
ND2 E:ASN127 4.1 23.8 1.0
OD1 E:ASP132 4.2 6.6 1.0
MN E:MN5238 4.3 0.0 1.0
C E:TYR125 4.3 0.0 1.0
C E:GLY104 4.4 0.0 1.0
CA E:ASN127 4.5 0.5 1.0
CB E:ASP83 4.5 21.1 1.0
CB E:ASP123 4.5 3.9 1.0
CD2 E:LEU106 4.8 0.0 1.0
OD1 E:ASP83 4.8 21.1 1.0
O E:ASP83 5.0 0.0 1.0
CB E:TYR125 5.0 33.5 1.0

Calcium binding site 6 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca6237

b:0.0
occ:1.00
OD1 F:ASN127 2.7 17.2 1.0
OD2 F:ASP123 2.8 15.9 1.0
OD1 F:ASP123 2.8 15.9 1.0
O F:TYR125 3.0 0.0 1.0
OD2 F:ASP132 3.1 0.0 1.0
CG F:ASN127 3.1 17.2 1.0
CG F:ASP123 3.1 15.9 1.0
CA F:GLY104 3.5 0.0 1.0
CB F:ASN127 3.7 17.2 1.0
ND2 F:ASN127 3.8 17.2 1.0
CB F:ASP83 4.0 0.8 1.0
O F:GLY104 4.0 0.0 1.0
C F:TYR125 4.1 0.0 1.0
CG F:ASP132 4.3 0.0 1.0
C F:GLY104 4.3 0.0 1.0
N F:ASN127 4.4 9.8 1.0
OD1 F:ASP83 4.4 0.8 1.0
N F:GLY104 4.5 0.0 1.0
CG F:ASP83 4.6 0.8 1.0
CB F:ASP123 4.6 15.9 1.0
O F:ASP83 4.7 4.9 1.0
MN F:MN6238 4.7 0.0 1.0
CA F:ASN127 4.7 9.8 1.0
CB F:TYR125 4.8 0.0 1.0
CD2 F:TYR125 4.8 0.0 1.0
OD1 F:ASP132 4.8 0.0 1.0
CA F:TYR125 4.9 0.0 1.0
CA F:ASP83 4.9 4.9 1.0
C F:SER126 5.0 0.0 1.0

Calcium binding site 7 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca7237

b:0.0
occ:1.00
OD1 G:ASP123 2.7 0.0 1.0
O G:TYR125 2.8 0.0 1.0
OD1 G:ASN127 2.8 0.0 1.0
OD2 G:ASP123 3.0 0.0 1.0
OD2 G:ASP132 3.1 0.0 1.0
CG G:ASP123 3.2 0.0 1.0
CG G:ASN127 3.3 0.0 1.0
C G:TYR125 3.8 0.0 1.0
CB G:ASP83 3.9 0.0 1.0
ND2 G:ASN127 3.9 0.0 1.0
CB G:ASN127 4.0 0.0 1.0
CB G:TYR125 4.1 21.4 1.0
CA G:GLY104 4.1 0.0 1.0
N G:ASN127 4.3 41.7 1.0
CA G:TYR125 4.3 0.0 1.0
O G:GLY104 4.4 0.0 1.0
N G:TYR125 4.4 0.0 1.0
CG G:ASP132 4.4 0.0 1.0
OD1 G:ASP83 4.4 0.0 1.0
CG G:ASP83 4.4 0.0 1.0
O G:ASP83 4.6 0.0 1.0
CB G:ASP123 4.7 0.0 1.0
CA G:ASP83 4.7 0.0 1.0
MN G:MN7238 4.7 0.0 1.0
C G:GLY104 4.7 0.0 1.0
CA G:ASN127 4.8 41.7 1.0
N G:SER126 4.9 17.5 1.0
CD2 G:TYR125 5.0 21.4 1.0
CD2 G:LEU106 5.0 0.0 1.0
CG G:TYR125 5.0 21.4 1.0
C G:ASP83 5.0 0.0 1.0

Calcium binding site 8 out of 8 in 1v6n

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


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 (Pviwssatg) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca8237

b:0.0
occ:1.00
OD1 H:ASN127 2.9 0.0 1.0
OD2 H:ASP123 3.0 0.2 1.0
OD1 H:ASP123 3.1 0.2 1.0
O H:TYR125 3.1 0.0 1.0
OD2 H:ASP132 3.2 5.9 1.0
CG H:ASP123 3.2 0.2 1.0
CG H:ASN127 3.4 0.0 1.0
CA H:GLY104 3.7 0.0 1.0
CB H:ASN127 4.0 0.0 1.0
ND2 H:ASN127 4.0 0.0 1.0
CG H:ASP132 4.1 5.9 1.0
O H:GLY104 4.1 0.0 1.0
MN H:MN8238 4.2 0.0 1.0
OD1 H:ASP132 4.3 5.9 1.0
C H:TYR125 4.3 0.0 1.0
CB H:ASP123 4.4 0.2 1.0
N H:ASN127 4.4 39.1 1.0
C H:GLY104 4.4 0.0 1.0
CB H:ASP83 4.5 0.0 1.0
N H:GLY104 4.7 0.0 1.0
CA H:ASN127 4.9 39.1 1.0
OD1 H:ASP83 4.9 0.0 1.0
CG H:ASP83 5.0 0.0 1.0

Reference:

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
Page generated: Sat Dec 12 03:24:36 2020

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