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Calcium in PDB 2d7f: Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid

Protein crystallography data

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid, PDB code: 2d7f was solved by P.Delatorre, B.A.M.Rocha, E.P.Souza, B.T.Freitas, F.B.B.M.Moreno, A.H.Sampaio, W.F.Azevedo Jr., B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 2.31
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 100.915, 115.754, 241.626, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.7

Other elements in 2d7f:

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid (pdb code 2d7f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid, PDB code: 2d7f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2d7f

Go back to Calcium Binding Sites List in 2d7f
Calcium binding site 1 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca240

b:18.3
occ:1.00
O A:TYR12 2.3 17.1 1.0
OD2 A:ASP19 2.3 12.4 1.0
OD2 A:ASP10 2.5 11.5 1.0
OD1 A:ASN14 2.5 15.3 1.0
OD1 A:ASP10 2.6 13.2 1.0
CG A:ASP10 2.9 15.6 1.0
CG A:ASP19 3.5 16.2 1.0
C A:TYR12 3.5 16.7 1.0
CG A:ASN14 3.6 16.6 1.0
OD1 A:ASP19 3.9 11.3 1.0
CB A:ASN14 4.0 16.4 1.0
N A:ASN14 4.0 16.8 1.0
MN A:MN239 4.2 17.6 1.0
CA A:TYR12 4.3 16.5 1.0
CB A:ASP10 4.3 15.9 1.0
N A:TYR12 4.4 16.9 1.0
CB A:TYR12 4.4 16.9 1.0
O A:ASP208 4.4 15.6 1.0
CB A:ARG228 4.4 14.3 1.0
N A:PRO13 4.5 16.4 1.0
CA A:ARG228 4.5 14.3 1.0
CE1 A:HIS24 4.5 12.8 1.0
O A:ARG228 4.6 14.7 1.0
CA A:ASN14 4.6 16.7 1.0
CA A:PRO13 4.6 17.7 1.0
OD2 A:ASP208 4.7 11.8 1.0
CB A:ASP19 4.7 16.0 1.0
NE2 A:HIS24 4.7 13.8 1.0
C A:PRO13 4.7 16.7 1.0
ND2 A:ASN14 4.7 13.3 1.0
CD1 A:TYR12 4.9 16.7 1.0

Calcium binding site 2 out of 4 in 2d7f

Go back to Calcium Binding Sites List in 2d7f
Calcium binding site 2 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca240

b:19.2
occ:1.00
O F:TYR12 2.3 19.5 1.0
OD1 F:ASN14 2.3 14.6 1.0
OD2 F:ASP19 2.4 15.1 1.0
OD2 F:ASP10 2.5 10.2 1.0
OD1 F:ASP10 2.5 10.0 1.0
CG F:ASP10 2.9 12.5 1.0
C F:TYR12 3.4 17.9 1.0
CG F:ASN14 3.5 13.8 1.0
CG F:ASP19 3.6 16.3 1.0
N F:ASN14 4.0 16.4 1.0
OD1 F:ASP19 4.0 15.2 1.0
CB F:ASN14 4.2 15.2 1.0
MN F:MN239 4.2 20.8 1.0
CA F:TYR12 4.2 17.7 1.0
CB F:TYR12 4.3 17.6 1.0
N F:TYR12 4.3 18.3 1.0
CB F:ASP10 4.4 14.5 1.0
N F:PRO13 4.4 17.6 1.0
O F:ASP208 4.5 13.9 1.0
CA F:PRO13 4.5 18.0 1.0
ND2 F:ASN14 4.5 11.2 1.0
CB F:ARG228 4.5 16.5 1.0
OD2 F:ASP208 4.5 10.1 1.0
C F:PRO13 4.6 16.0 1.0
CA F:ARG228 4.6 14.8 1.0
CE1 F:HIS24 4.7 16.9 1.0
CB F:ASP19 4.7 16.5 1.0
CA F:ASN14 4.8 15.2 1.0
CD1 F:TYR12 4.8 17.3 1.0
O F:ARG228 4.8 15.7 1.0
NE2 F:HIS24 4.9 18.9 1.0

Calcium binding site 3 out of 4 in 2d7f

Go back to Calcium Binding Sites List in 2d7f
Calcium binding site 3 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca240

b:19.9
occ:1.00
OD2 L:ASP19 2.3 20.5 1.0
O L:TYR12 2.3 25.2 1.0
OD1 L:ASN14 2.4 20.9 1.0
OD1 L:ASP10 2.4 10.3 1.0
OD2 L:ASP10 2.6 11.9 1.0
CG L:ASP10 2.9 17.8 1.0
CG L:ASP19 3.4 23.2 1.0
C L:TYR12 3.5 23.3 1.0
CG L:ASN14 3.6 21.3 1.0
OD1 L:ASP19 3.9 20.1 1.0
N L:ASN14 3.9 25.2 1.0
MN L:MN239 4.1 22.1 1.0
CB L:ASN14 4.2 24.0 1.0
N L:TYR12 4.3 19.4 1.0
CA L:TYR12 4.3 20.9 1.0
CB L:ASP10 4.4 16.5 1.0
N L:PRO13 4.5 23.6 1.0
CB L:TYR12 4.5 22.4 1.0
CA L:PRO13 4.5 24.5 1.0
O L:ASP208 4.5 19.6 1.0
CA L:ARG228 4.6 24.0 1.0
C L:PRO13 4.6 24.5 1.0
ND2 L:ASN14 4.6 12.1 1.0
CB L:ARG228 4.6 24.0 1.0
CE1 L:HIS24 4.6 14.2 1.0
CA L:ASN14 4.7 24.7 1.0
CB L:ASP19 4.7 21.6 1.0
OD2 L:ASP208 4.7 13.5 1.0
O L:ARG228 4.7 22.5 1.0
NE2 L:HIS24 4.8 13.5 1.0
CD1 L:TYR12 4.9 23.1 1.0

Calcium binding site 4 out of 4 in 2d7f

Go back to Calcium Binding Sites List in 2d7f
Calcium binding site 4 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca240

b:20.7
occ:1.00
OD1 S:ASN14 2.3 16.2 1.0
OD2 S:ASP19 2.3 21.6 1.0
O S:TYR12 2.3 19.2 1.0
OD1 S:ASP10 2.5 14.1 1.0
OD2 S:ASP10 2.6 12.8 1.0
CG S:ASP10 2.9 18.4 1.0
CG S:ASP19 3.4 21.6 1.0
CG S:ASN14 3.5 17.8 1.0
C S:TYR12 3.5 18.5 1.0
OD1 S:ASP19 3.8 17.1 1.0
N S:ASN14 4.0 17.9 1.0
CB S:ASN14 4.1 16.1 1.0
MN S:MN239 4.2 21.9 1.0
CA S:TYR12 4.2 19.1 1.0
N S:TYR12 4.3 18.5 1.0
CB S:TYR12 4.3 19.1 1.0
CB S:ASP10 4.4 16.3 1.0
CA S:ARG228 4.5 23.3 1.0
N S:PRO13 4.5 18.9 1.0
ND2 S:ASN14 4.5 15.3 1.0
O S:ASP208 4.5 20.4 1.0
CE1 S:HIS24 4.6 15.6 1.0
CB S:ARG228 4.6 24.3 1.0
CA S:PRO13 4.6 18.8 1.0
OD2 S:ASP208 4.6 19.9 1.0
C S:PRO13 4.6 18.3 1.0
CB S:ASP19 4.7 22.9 1.0
CA S:ASN14 4.7 17.0 1.0
O S:ARG228 4.8 21.6 1.0
NE2 S:HIS24 4.9 17.5 1.0
CD1 S:TYR12 4.9 19.8 1.0

Reference:

P.Delatorre, B.A.M.Rocha, E.P.Souza, T.M.Oliveira, G.A.Bezerra, F.B.M.B.Moreno, B.T.Freitas, T.Santi-Gadelha, A.H.Sampaio, W.F.Azevedo Jr., B.S.Cavada. Structure of A Lectin From Canavalia Gladiata Seeds: New Structural Insights For Old Molecules Bmc Struct.Biol. V. 7 52 2007.
ISSN: ESSN 1472-6807
PubMed: 17683532
DOI: 10.1186/1472-6807-7-52
Page generated: Sat Dec 12 03:34:51 2020

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