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Calcium in PDB 1bjq: The Dolichos Biflorus Seed Lectin in Complex with Adenine

Protein crystallography data

The structure of The Dolichos Biflorus Seed Lectin in Complex with Adenine, PDB code: 1bjq was solved by T.W.Hamelryck, R.Loris, J.Bouckaert, M.H.Dao-Thi, L.Wyns, M.Etzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.377, 116.135, 224.620, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.6

Other elements in 1bjq:

The structure of The Dolichos Biflorus Seed Lectin in Complex with Adenine also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Dolichos Biflorus Seed Lectin in Complex with Adenine (pdb code 1bjq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Dolichos Biflorus Seed Lectin in Complex with Adenine, PDB code: 1bjq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1bjq

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Calcium binding site 1 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:12.9
occ:1.00
 OD1 A:ASN129 2.3 24.0 1.0
O A:LEU127 2.4 15.2 1.0
OD2 A:ASP133 2.4 20.3 1.0
OD1 A:ASP125 2.4 13.2 1.0
OD2 A:ASP125 2.5 10.7 1.0
CG A:ASP125 2.8 10.4 1.0
CG A:ASN129 3.5 21.8 1.0
CG A:ASP133 3.5 19.3 1.0
C A:LEU127 3.6 15.3 1.0
OD1 A:ASP133 4.0 19.7 1.0
N A:ASN129 4.2 20.6 1.0
CB A:ASP125 4.3 8.9 1.0
CB A:ASN129 4.3 21.9 1.0
NE1 A:TRP132 4.4 11.2 1.0
OD1 A:ASP85 4.4 26.2 1.0
O A:GLY103 4.4 17.7 1.0
ND2 A:ASN129 4.4 20.8 1.0
MN A:MN302 4.4 45.7 1.0
CA A:LEU127 4.5 13.4 1.0
N A:LEU127 4.5 13.3 1.0
N A:SER128 4.5 18.1 1.0
O A:ASP85 4.6 21.4 1.0
CA A:GLY103 4.6 17.6 1.0
CA A:SER128 4.6 18.8 1.0
C A:SER128 4.7 19.6 1.0
CB A:LEU127 4.7 11.5 1.0
CB A:ASP133 4.8 18.1 1.0
CA A:ASN129 4.9 21.5 1.0
CE1 A:HIS138 4.9 11.5 1.0
C A:GLY103 5.0 17.1 1.0

Calcium binding site 2 out of 8 in 1bjq

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Calcium binding site 2 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:19.9
occ:1.00
 O B:LEU127 2.2 19.4 1.0
OD1 B:ASP125 2.3 18.1 1.0
OD1 B:ASN129 2.4 26.0 1.0
OD2 B:ASP133 2.4 25.4 1.0
OD2 B:ASP125 2.5 17.0 1.0
CG B:ASP125 2.8 16.6 1.0
C B:LEU127 3.5 19.6 1.0
CG B:ASN129 3.5 24.3 1.0
CG B:ASP133 3.6 25.4 1.0
OD1 B:ASP133 4.1 25.2 1.0
N B:ASN129 4.1 23.3 1.0
CB B:ASP125 4.3 16.9 1.0
CA B:LEU127 4.3 19.4 1.0
N B:LEU127 4.4 18.1 1.0
CB B:ASN129 4.4 24.2 1.0
OD1 B:ASP85 4.4 26.9 1.0
N B:SER128 4.4 20.4 1.0
MN B:MN302 4.4 46.2 1.0
ND2 B:ASN129 4.5 23.2 1.0
O B:ASP85 4.5 22.6 1.0
NE1 B:TRP132 4.5 12.9 1.0
CA B:SER128 4.5 21.8 1.0
O B:GLY103 4.5 18.7 1.0
CB B:LEU127 4.6 19.7 1.0
C B:SER128 4.6 22.2 1.0
CA B:GLY103 4.7 18.1 1.0
CB B:ASP133 4.8 24.1 1.0
CE1 B:HIS138 4.8 10.3 1.0
CA B:ASN129 4.9 24.2 1.0
CA B:ASP125 5.0 14.4 1.0

Calcium binding site 3 out of 8 in 1bjq

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Calcium binding site 3 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:19.2
occ:1.00
 O C:LEU127 2.2 25.8 1.0
OD1 C:ASP125 2.3 13.7 1.0
OD1 C:ASN129 2.4 27.4 1.0
OD2 C:ASP133 2.4 19.2 1.0
OD2 C:ASP125 2.6 11.8 1.0
CG C:ASP125 2.8 13.2 1.0
C C:LEU127 3.4 23.5 1.0
CG C:ASN129 3.5 25.4 1.0
CG C:ASP133 3.6 21.6 1.0
OD1 C:ASP133 4.1 22.9 1.0
N C:ASN129 4.1 26.6 1.0
CB C:ASP125 4.3 14.0 1.0
CA C:LEU127 4.3 22.0 1.0
N C:LEU127 4.3 22.0 1.0
OD1 C:ASP85 4.4 23.0 1.0
CB C:ASN129 4.4 26.4 1.0
N C:SER128 4.4 23.5 1.0
O C:ASP85 4.5 21.3 1.0
ND2 C:ASN129 4.5 25.0 1.0
CA C:SER128 4.5 24.2 1.0
MN C:MN302 4.5 41.5 1.0
NE1 C:TRP132 4.5 15.8 1.0
O C:GLY103 4.5 20.9 1.0
CB C:LEU127 4.6 22.1 1.0
C C:SER128 4.6 25.3 1.0
CA C:GLY103 4.7 20.6 1.0
CB C:ASP133 4.8 23.2 1.0
CE1 C:HIS138 4.8 22.0 1.0
CA C:ASN129 4.9 26.9 1.0
CA C:ASP125 5.0 15.7 1.0

Calcium binding site 4 out of 8 in 1bjq

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Calcium binding site 4 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:11.1
occ:1.00
 O D:LEU127 2.3 21.3 1.0
OD1 D:ASN129 2.3 24.9 1.0
OD1 D:ASP125 2.4 12.1 1.0
OD2 D:ASP133 2.5 17.4 1.0
OD2 D:ASP125 2.7 9.1 1.0
CG D:ASP125 2.9 10.2 1.0
C D:LEU127 3.5 19.3 1.0
CG D:ASN129 3.5 21.5 1.0
CG D:ASP133 3.6 19.5 1.0
N D:ASN129 4.1 21.4 1.0
OD1 D:ASP133 4.1 20.0 1.0
OD1 D:ASP85 4.3 18.7 1.0
CB D:ASN129 4.3 20.4 1.0
CA D:LEU127 4.3 18.9 1.0
CB D:ASP125 4.3 12.2 1.0
N D:LEU127 4.4 18.1 1.0
ND2 D:ASN129 4.4 22.0 1.0
N D:SER128 4.4 20.2 1.0
O D:GLY103 4.4 15.3 1.0
O D:ASP85 4.5 16.0 1.0
NE1 D:TRP132 4.5 5.2 1.0
MN D:MN302 4.5 46.1 1.0
CA D:SER128 4.5 20.0 1.0
CB D:LEU127 4.5 18.4 1.0
CA D:GLY103 4.6 12.9 1.0
C D:SER128 4.6 20.9 1.0
CB D:ASP133 4.8 19.5 1.0
CA D:ASN129 4.9 21.1 1.0
CE1 D:HIS138 5.0 15.0 1.0

Calcium binding site 5 out of 8 in 1bjq

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Calcium binding site 5 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:28.3
occ:1.00
 O E:LEU127 2.3 27.7 1.0
OD1 E:ASN129 2.3 33.4 1.0
OD2 E:ASP133 2.4 29.4 1.0
OD1 E:ASP125 2.4 19.4 1.0
OD2 E:ASP125 2.6 19.1 1.0
CG E:ASP125 2.8 19.1 1.0
CG E:ASN129 3.5 32.9 1.0
C E:LEU127 3.5 27.1 1.0
CG E:ASP133 3.5 28.6 1.0
OD1 E:ASP133 4.0 28.0 1.0
N E:ASN129 4.1 29.4 1.0
CB E:ASN129 4.3 31.7 1.0
CB E:ASP125 4.3 18.2 1.0
OD1 E:ASP85 4.4 27.1 1.0
NE1 E:TRP132 4.4 22.5 1.0
CA E:LEU127 4.4 26.1 1.0
ND2 E:ASN129 4.4 31.9 1.0
MN E:MN302 4.4 52.6 1.0
N E:SER128 4.5 28.4 1.0
O E:GLY103 4.5 21.9 1.0
N E:LEU127 4.5 24.9 1.0
CA E:SER128 4.5 28.2 1.0
O E:ASP85 4.6 25.8 1.0
C E:SER128 4.6 29.1 1.0
CB E:LEU127 4.6 26.1 1.0
CA E:GLY103 4.7 20.7 1.0
CB E:ASP133 4.7 29.9 1.0
CA E:ASN129 4.8 30.1 1.0
CE1 E:HIS138 4.9 25.1 1.0

Calcium binding site 6 out of 8 in 1bjq

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Calcium binding site 6 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:36.9
occ:1.00
 OD2 F:ASP133 2.2 35.0 1.0
OD1 F:ASN129 2.3 43.5 1.0
OD2 F:ASP125 2.4 30.0 1.0
O F:LEU127 2.5 35.7 1.0
OD1 F:ASP125 2.5 33.0 1.0
CG F:ASP125 2.8 32.4 1.0
CG F:ASP133 3.3 35.7 1.0
CG F:ASN129 3.5 40.0 1.0
C F:LEU127 3.7 35.2 1.0
OD1 F:ASP133 3.8 35.7 1.0
N F:ASN129 4.1 37.5 1.0
NE1 F:TRP132 4.2 33.1 1.0
CB F:ASN129 4.2 38.9 1.0
CB F:ASP125 4.3 31.1 1.0
O F:GLY103 4.4 34.4 1.0
MN F:MN302 4.4 64.0 1.0
ND2 F:ASN129 4.5 40.3 1.0
CB F:ASP133 4.5 35.7 1.0
CA F:SER128 4.6 35.8 1.0
N F:SER128 4.6 35.6 1.0
OD1 F:ASP85 4.6 33.1 1.0
CA F:LEU127 4.6 33.2 1.0
C F:SER128 4.7 36.6 1.0
N F:LEU127 4.7 33.8 1.0
CA F:GLY103 4.7 34.4 1.0
CE1 F:HIS138 4.8 33.0 1.0
O F:ASP85 4.8 30.5 1.0
CA F:ASN129 4.8 38.2 1.0
CB F:LEU127 4.9 33.2 1.0
CE2 F:TRP132 5.0 32.5 1.0

Calcium binding site 7 out of 8 in 1bjq

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Calcium binding site 7 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:59.0
occ:1.00
 OD1 G:ASN129 2.2 50.7 1.0
O G:LEU127 2.4 37.5 1.0
OD2 G:ASP133 2.4 46.0 1.0
OD1 G:ASP125 2.6 27.6 1.0
OD2 G:ASP125 2.7 26.5 1.0
CG G:ASP125 3.0 28.2 1.0
CG G:ASN129 3.4 49.0 1.0
CG G:ASP133 3.5 45.3 1.0
C G:LEU127 3.6 38.3 1.0
OD1 G:ASP133 4.0 45.9 1.0
N G:ASN129 4.1 44.4 1.0
CB G:ASN129 4.2 47.6 1.0
NE1 G:TRP132 4.3 40.5 1.0
ND2 G:ASN129 4.3 48.9 1.0
O G:GLY103 4.3 43.0 1.0
OD1 G:ASP85 4.4 40.8 1.0
CB G:ASP125 4.4 29.1 1.0
MN G:MN302 4.5 67.6 1.0
CA G:LEU127 4.5 36.7 1.0
CA G:GLY103 4.5 42.9 1.0
N G:SER128 4.5 40.5 1.0
N G:LEU127 4.6 35.4 1.0
CA G:SER128 4.6 43.1 1.0
O G:ASP85 4.6 41.6 1.0
C G:SER128 4.6 43.9 1.0
CB G:LEU127 4.7 37.6 1.0
CB G:ASP133 4.8 44.5 1.0
CA G:ASN129 4.8 46.1 1.0
C G:GLY103 4.9 42.0 1.0
CE1 G:HIS138 5.0 41.1 1.0

Calcium binding site 8 out of 8 in 1bjq

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Calcium binding site 8 out of 8 in the The Dolichos Biflorus Seed Lectin in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Dolichos Biflorus Seed Lectin in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:29.9
occ:1.00
 OD1 H:ASN129 2.2 26.6 1.0
O H:LEU127 2.3 24.7 1.0
OD2 H:ASP133 2.4 27.0 1.0
OD1 H:ASP125 2.5 13.2 1.0
OD2 H:ASP125 2.6 12.1 1.0
CG H:ASP125 2.9 12.7 1.0
CG H:ASN129 3.4 26.4 1.0
CG H:ASP133 3.5 28.1 1.0
C H:LEU127 3.5 21.4 1.0
OD1 H:ASP133 4.0 27.3 1.0
N H:ASN129 4.1 26.9 1.0
CB H:ASN129 4.3 27.2 1.0
OD1 H:ASP85 4.4 26.9 1.0
CB H:ASP125 4.4 12.8 1.0
NE1 H:TRP132 4.4 22.5 1.0
ND2 H:ASN129 4.4 25.1 1.0
MN H:MN302 4.4 45.7 1.0
CA H:LEU127 4.4 18.9 1.0
O H:GLY103 4.4 24.2 1.0
N H:LEU127 4.5 17.5 1.0
N H:SER128 4.5 23.9 1.0
CA H:SER128 4.5 25.6 1.0
O H:ASP85 4.6 20.9 1.0
CA H:GLY103 4.6 20.8 1.0
C H:SER128 4.6 26.3 1.0
CB H:LEU127 4.6 18.4 1.0
CB H:ASP133 4.8 28.9 1.0
CA H:ASN129 4.8 27.3 1.0
CE1 H:HIS138 4.9 15.0 1.0

Reference:

T.W.Hamelryck, R.Loris, J.Bouckaert, M.H.Dao-Thi, G.Strecker, A.Imberty, E.Fernandez, L.Wyns, M.E.Etzler. Carbohydrate Binding, Quaternary Structure and A Novel Hydrophobic Binding Site in Two Legume Lectin Oligomers From Dolichos Biflorus. J.Mol.Biol. V. 286 1161 1999.
ISSN: ISSN 0022-2836
PubMed: 10047489
DOI: 10.1006/JMBI.1998.2534
Page generated: Thu Jul 11 06:29:06 2024

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