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Calcium in PDB 1g7y: The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus

Protein crystallography data

The structure of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus, PDB code: 1g7y was solved by L.Buts, T.W.Hamelryck, R.Loris, M.-H.Dao-Thi, L.Wyns, M.E.Etzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.941, 130.272, 137.124, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24.7

Other elements in 1g7y:

The structure of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus (pdb code 1g7y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus, PDB code: 1g7y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1g7y

Go back to Calcium Binding Sites List in 1g7y
Calcium binding site 1 out of 6 in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca254

b:43.2
occ:1.00
 OD2 A:ASP133 2.2 39.5 1.0
O A:PHE127 2.3 40.1 1.0
O A:HOH1256 2.3 23.9 1.0
O A:HOH1255 2.3 37.7 1.0
OD1 A:ASP125 2.4 38.9 1.0
OD1 A:ASN129 2.4 29.7 1.0
OD2 A:ASP125 2.6 38.0 1.0
CG A:ASP125 2.8 39.1 1.0
CG A:ASP133 3.3 45.5 1.0
CG A:ASN129 3.4 35.0 1.0
C A:PHE127 3.5 41.3 1.0
OD1 A:ASP133 3.8 43.5 1.0
N A:ASN129 3.9 41.0 1.0
MN A:MN257 4.1 29.4 1.0
CB A:ASN129 4.2 24.4 1.0
O A:HOH1258 4.3 35.6 1.0
CB A:ASP125 4.3 38.7 1.0
ND2 A:ASN129 4.4 43.9 1.0
NE1 A:TRP132 4.4 48.6 1.0
CA A:SER128 4.4 42.4 1.0
N A:SER128 4.4 43.9 1.0
CA A:PHE127 4.5 35.7 1.0
CB A:ASP133 4.5 42.4 1.0
CD1 A:PHE127 4.5 48.2 1.0
C A:SER128 4.6 42.7 1.0
N A:PHE127 4.6 36.2 1.0
O A:GLY103 4.6 36.5 1.0
CA A:ASN129 4.7 28.0 1.0
CE1 A:HIS138 4.7 29.7 1.0
CB A:PHE127 4.7 44.3 1.0
O A:ASP85 4.8 38.7 1.0
OD1 A:ASP85 4.9 40.8 1.0
CA A:GLY103 5.0 33.3 1.0

Calcium binding site 2 out of 6 in 1g7y

Go back to Calcium Binding Sites List in 1g7y
Calcium binding site 2 out of 6 in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca254

b:31.3
occ:1.00
 OD1 B:ASP125 2.3 35.8 1.0
O B:PHE127 2.3 37.6 1.0
O B:HOH2255 2.3 23.5 1.0
OD2 B:ASP133 2.3 40.7 1.0
OD1 B:ASN129 2.4 24.2 1.0
O B:HOH2256 2.4 19.3 1.0
OD2 B:ASP125 2.6 38.2 1.0
CG B:ASP125 2.8 35.2 1.0
CG B:ASP133 3.5 41.4 1.0
CG B:ASN129 3.5 26.9 1.0
C B:PHE127 3.5 38.8 1.0
N B:ASN129 3.9 35.3 1.0
OD1 B:ASP133 3.9 39.4 1.0
CB B:ASN129 4.1 28.9 1.0
MN B:MN257 4.2 29.4 1.0
CB B:ASP125 4.2 36.6 1.0
O B:HOH2258 4.4 34.0 1.0
CA B:PHE127 4.4 37.7 1.0
N B:SER128 4.4 38.8 1.0
CA B:SER128 4.5 42.7 1.0
N B:PHE127 4.5 35.6 1.0
NE1 B:TRP132 4.5 38.4 1.0
CD1 B:PHE127 4.5 46.4 1.0
ND2 B:ASN129 4.6 23.8 1.0
O B:GLY103 4.6 32.0 1.0
C B:SER128 4.6 39.7 1.0
O B:ASP85 4.6 31.5 1.0
CB B:ASP133 4.6 45.4 1.0
CA B:ASN129 4.7 27.7 1.0
CB B:PHE127 4.7 42.9 1.0
CE1 B:HIS138 4.8 25.3 1.0
OD1 B:ASP85 4.8 38.2 1.0
CA B:GLY103 4.9 31.2 1.0

Calcium binding site 3 out of 6 in 1g7y

Go back to Calcium Binding Sites List in 1g7y
Calcium binding site 3 out of 6 in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca254

b:36.6
occ:1.00
 O C:HOH3255 2.2 33.6 1.0
O C:PHE127 2.3 33.9 1.0
O C:HOH3256 2.3 30.0 1.0
OD2 C:ASP133 2.3 41.8 1.0
OD1 C:ASP125 2.3 35.8 1.0
OD1 C:ASN129 2.5 41.1 1.0
OD2 C:ASP125 2.7 34.2 1.0
CG C:ASP125 2.8 37.3 1.0
CG C:ASP133 3.5 45.4 1.0
C C:PHE127 3.5 38.9 1.0
CG C:ASN129 3.6 31.2 1.0
N C:ASN129 3.9 43.9 1.0
OD1 C:ASP133 4.0 43.1 1.0
CB C:ASN129 4.2 32.3 1.0
MN C:MN257 4.2 29.6 1.0
CB C:ASP125 4.3 39.0 1.0
CA C:PHE127 4.4 35.1 1.0
N C:SER128 4.4 40.8 1.0
CD1 C:PHE127 4.5 46.8 1.0
CA C:SER128 4.5 45.5 1.0
N C:PHE127 4.5 33.2 1.0
O C:GLY103 4.6 37.0 1.0
NE1 C:TRP132 4.6 47.1 1.0
O C:HOH3258 4.6 36.4 1.0
C C:SER128 4.6 43.0 1.0
ND2 C:ASN129 4.6 38.1 1.0
CB C:PHE127 4.6 43.8 1.0
CA C:ASN129 4.6 36.0 1.0
CB C:ASP133 4.7 44.2 1.0
O C:ASP85 4.7 35.2 1.0
OD1 C:ASP85 4.8 37.4 1.0
CE1 C:HIS138 4.9 26.9 1.0
CA C:GLY103 4.9 34.5 1.0

Calcium binding site 4 out of 6 in 1g7y

Go back to Calcium Binding Sites List in 1g7y
Calcium binding site 4 out of 6 in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca254

b:41.9
occ:1.00
 OD1 D:ASP125 2.2 42.7 1.0
O D:PHE127 2.3 32.8 1.0
O D:HOH4255 2.3 57.3 1.0
OD2 D:ASP133 2.5 44.0 1.0
O D:HOH4256 2.5 41.4 1.0
OD1 D:ASN129 2.5 45.0 1.0
OD2 D:ASP125 2.6 43.3 1.0
CG D:ASP125 2.7 42.8 1.0
C D:PHE127 3.5 40.2 1.0
CG D:ASP133 3.6 46.3 1.0
CG D:ASN129 3.6 60.2 1.0
N D:ASN129 4.0 46.2 1.0
OD1 D:ASP133 4.1 46.0 1.0
CB D:ASP125 4.2 42.1 1.0
MN D:MN257 4.2 35.4 1.0
CB D:ASN129 4.3 48.5 1.0
O D:HOH4258 4.4 25.1 1.0
CA D:PHE127 4.4 38.8 1.0
N D:PHE127 4.4 36.8 1.0
NE1 D:TRP132 4.5 64.5 1.0
O D:ASP85 4.5 41.0 1.0
N D:SER128 4.5 40.9 1.0
CD1 D:PHE127 4.5 47.9 1.0
O D:GLY103 4.5 37.7 1.0
CA D:SER128 4.6 44.3 1.0
CB D:PHE127 4.6 45.7 1.0
ND2 D:ASN129 4.7 59.7 1.0
OD1 D:ASP85 4.7 40.4 1.0
C D:SER128 4.7 42.4 1.0
CB D:ASP133 4.8 44.6 1.0
CA D:ASN129 4.8 54.2 1.0
CE1 D:HIS138 4.8 24.3 1.0
CA D:GLY103 4.9 35.2 1.0
CA D:ASP125 4.9 38.3 1.0

Calcium binding site 5 out of 6 in 1g7y

Go back to Calcium Binding Sites List in 1g7y
Calcium binding site 5 out of 6 in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca254

b:30.2
occ:1.00
 OD2 E:ASP133 2.1 36.0 1.0
O E:PHE127 2.3 39.0 1.0
O E:HOH5255 2.3 27.8 1.0
OD1 E:ASP125 2.3 36.8 1.0
OD1 E:ASN129 2.3 32.7 1.0
O E:HOH5256 2.4 26.1 1.0
OD2 E:ASP125 2.5 30.1 1.0
CG E:ASP125 2.7 31.6 1.0
CG E:ASP133 3.2 43.5 1.0
CG E:ASN129 3.5 30.0 1.0
C E:PHE127 3.5 38.7 1.0
OD1 E:ASP133 3.8 46.0 1.0
N E:ASN129 3.8 36.5 1.0
MN E:MN257 4.0 23.2 1.0
CB E:ASN129 4.1 33.5 1.0
CB E:ASP125 4.2 36.1 1.0
O E:HOH5258 4.3 15.9 1.0
NE1 E:TRP132 4.3 40.5 1.0
CA E:SER128 4.4 45.1 1.0
N E:SER128 4.4 40.1 1.0
CB E:ASP133 4.4 43.6 1.0
CA E:PHE127 4.4 36.0 1.0
C E:SER128 4.5 39.6 1.0
N E:PHE127 4.5 33.5 1.0
CA E:ASN129 4.6 32.4 1.0
ND2 E:ASN129 4.6 26.6 1.0
CD1 E:PHE127 4.6 46.4 1.0
CE1 E:HIS138 4.6 25.2 1.0
O E:GLY103 4.7 29.9 1.0
CB E:PHE127 4.7 43.6 1.0
O E:ASP85 4.8 31.7 1.0
NE2 E:HIS138 4.9 30.6 1.0

Calcium binding site 6 out of 6 in 1g7y

Go back to Calcium Binding Sites List in 1g7y
Calcium binding site 6 out of 6 in the The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of the 58KD Vegetative Lectin From the Tropical Legume Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca254

b:54.4
occ:1.00
 OD2 F:ASP133 2.3 44.6 1.0
O F:PHE127 2.3 36.1 1.0
O F:HOH6255 2.4 50.5 1.0
O F:HOH6256 2.4 62.5 1.0
OD1 F:ASP125 2.5 42.4 1.0
OD2 F:ASP125 2.7 34.6 1.0
CG F:ASP125 3.0 39.9 1.0
ND2 F:ASN129 3.2 56.8 1.0
CG F:ASN129 3.3 61.1 1.0
CG F:ASP133 3.4 47.2 1.0
C F:PHE127 3.5 38.8 1.0
OD1 F:ASN129 3.6 62.2 1.0
N F:ASN129 3.8 46.8 1.0
OD1 F:ASP133 4.0 48.8 1.0
CB F:ASN129 4.0 50.7 1.0
MN F:MN257 4.2 39.0 1.0
O F:HOH6258 4.4 23.7 1.0
CD1 F:PHE127 4.4 48.6 1.0
NE1 F:TRP132 4.4 57.3 1.0
CB F:ASP125 4.4 37.4 1.0
N F:SER128 4.4 41.7 1.0
CA F:SER128 4.5 47.6 1.0
CA F:PHE127 4.5 39.7 1.0
CA F:ASN129 4.5 54.1 1.0
C F:SER128 4.5 45.3 1.0
O F:GLY103 4.5 40.5 1.0
CB F:ASP133 4.6 44.9 1.0
N F:PHE127 4.6 40.6 1.0
CB F:PHE127 4.7 45.6 1.0
OD1 F:ASP85 4.8 45.3 1.0
O F:ASP85 4.8 41.0 1.0
CA F:GLY103 4.8 34.2 1.0
CE1 F:HIS138 4.9 31.4 1.0

Reference:

L.Buts, M.H.Dao-Thi, R.Loris, L.Wyns, M.Etzler, T.Hamelryck. Weak Protein-Protein Interactions in Lectins: the Crystal Structure of A Vegetative Lectin From the Legume Dolichos Biflorus. J.Mol.Biol. V. 309 193 2001.
ISSN: ISSN 0022-2836
PubMed: 11491289
DOI: 10.1006/JMBI.2001.4639
Page generated: Thu Jul 11 08:33:01 2024

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