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Calcium in PDB 5cna: Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure

Protein crystallography data

The structure of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure, PDB code: 5cna was solved by J.H.Naismith, C.Emmerich, J.Habash, S.J.Harrop, J.R.Helliwell, W.N.Hunter, J.Raftery, A.J.Kalb(Gilboa), J.Yariv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.700, 128.600, 67.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / n/a

Other elements in 5cna:

The structure of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure (pdb code 5cna). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure, PDB code: 5cna:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 1 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca240

b:14.9
occ:1.00
 O A:TYR12 2.3 22.2 1.0
OD2 A:ASP19 2.3 13.6 1.0
O A:HOH247 2.4 19.7 1.0
O A:HOH248 2.4 14.1 1.0
OD1 A:ASP10 2.4 8.9 1.0
OD1 A:ASN14 2.5 12.8 1.0
OD2 A:ASP10 2.8 11.2 1.0
CG A:ASP10 2.9 17.8 1.0
CG A:ASP19 3.5 9.2 1.0
C A:TYR12 3.5 18.9 1.0
CG A:ASN14 3.6 15.2 1.0
OD1 A:ASP19 3.9 12.9 1.0
N A:ASN14 4.1 25.5 1.0
CB A:ASN14 4.2 17.5 1.0
MN A:MN239 4.2 20.0 1.0
CA A:TYR12 4.3 18.9 1.0
N A:TYR12 4.4 18.0 1.0
N A:PRO13 4.4 23.1 1.0
CB A:ASP10 4.5 12.4 1.0
CA A:PRO13 4.5 24.8 1.0
O A:HOH246 4.5 14.2 1.0
CB A:TYR12 4.5 21.3 1.0
ND2 A:ASN14 4.6 16.8 1.0
C A:PRO13 4.6 26.4 1.0
CB A:ASP19 4.7 13.0 1.0
O A:ASP208 4.7 13.7 1.0
OD2 A:ASP208 4.7 12.5 1.0
CA A:ASN14 4.7 20.7 1.0
CE1 A:HIS24 4.8 20.8 1.0
CB A:ARG228 4.8 13.1 1.0
CA A:ARG228 4.9 13.3 1.0
O A:ARG228 4.9 17.8 1.0
CD1 A:TYR12 5.0 19.2 1.0

Calcium binding site 2 out of 4 in 5cna

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Calcium binding site 2 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca240

b:19.9
occ:1.00
 O B:HOH253 2.2 18.2 1.0
O B:HOH256 2.2 14.8 1.0
O B:TYR12 2.3 24.1 1.0
OD1 B:ASP10 2.3 19.3 1.0
OD2 B:ASP19 2.5 17.5 1.0
OD1 B:ASN14 2.6 21.8 1.0
OD2 B:ASP10 2.7 16.1 1.0
CG B:ASP10 2.9 24.8 1.0
C B:TYR12 3.5 18.9 1.0
CG B:ASP19 3.6 16.4 1.0
CG B:ASN14 3.7 21.7 1.0
OD1 B:ASP19 4.0 20.6 1.0
N B:ASN14 4.2 23.2 1.0
MN B:MN239 4.3 18.3 1.0
CB B:ASN14 4.3 19.6 1.0
CA B:TYR12 4.3 19.7 1.0
N B:PRO13 4.4 21.4 1.0
CB B:ASP10 4.4 19.2 1.0
N B:TYR12 4.4 22.6 1.0
CA B:PRO13 4.5 24.0 1.0
CB B:TYR12 4.5 23.7 1.0
O B:ASP208 4.5 17.7 1.0
OD2 B:ASP208 4.5 18.7 1.0
O B:HOH254 4.6 21.8 1.0
C B:PRO13 4.6 26.5 1.0
CB B:ARG228 4.8 19.4 1.0
CA B:ARG228 4.8 18.3 1.0
ND2 B:ASN14 4.8 15.5 1.0
CB B:ASP19 4.8 19.8 1.0
O B:ARG228 4.8 17.0 1.0
CE1 B:HIS24 4.9 26.9 1.0
CA B:ASN14 4.9 24.6 1.0
CD2 B:TYR12 4.9 23.8 1.0

Calcium binding site 3 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 3 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca240

b:39.9
occ:1.00
 OD2 C:ASP19 2.2 36.5 1.0
O C:HOH245 2.2 34.2 1.0
OD1 C:ASN14 2.2 48.9 1.0
O C:HOH246 2.4 56.1 1.0
O C:TYR12 2.4 46.5 1.0
OD1 C:ASP10 2.6 39.1 1.0
OD2 C:ASP10 2.9 37.0 1.0
CG C:ASP10 3.1 42.8 1.0
CG C:ASN14 3.3 51.3 1.0
CG C:ASP19 3.4 45.4 1.0
C C:TYR12 3.6 49.8 1.0
OD1 C:ASP19 3.9 50.1 1.0
CB C:ASN14 4.0 47.5 1.0
N C:ASN14 4.0 54.1 1.0
CB C:TYR12 4.2 54.9 1.0
ND2 C:ASN14 4.3 59.0 1.0
OD1 C:ASP208 4.3 44.5 1.0
CA C:TYR12 4.3 49.2 1.0
N C:TYR12 4.4 48.4 1.0
CB C:ASP19 4.5 47.5 1.0
N C:PRO13 4.6 52.5 1.0
O C:HOH244 4.6 46.7 1.0
MN C:MN239 4.6 41.4 1.0
CA C:ASN14 4.6 49.1 1.0
CB C:ASP10 4.6 34.8 1.0
O C:ASP208 4.6 34.1 1.0
CA C:PRO13 4.7 53.6 1.0
O C:ARG228 4.7 40.7 1.0
C C:PRO13 4.7 55.6 1.0
CD2 C:TYR12 4.7 55.0 1.0
CA C:ARG228 4.7 46.2 1.0

Calcium binding site 4 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 4 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca240

b:23.9
occ:1.00
 O D:HOH256 2.1 18.5 1.0
O D:HOH255 2.2 22.2 1.0
OD2 D:ASP19 2.3 34.1 1.0
O D:TYR12 2.3 29.7 1.0
OD1 D:ASP10 2.4 24.0 1.0
OD1 D:ASN14 2.5 29.6 1.0
OD2 D:ASP10 2.6 25.5 1.0
CG D:ASP10 2.8 30.7 1.0
CG D:ASP19 3.5 34.1 1.0
C D:TYR12 3.5 27.7 1.0
CG D:ASN14 3.6 27.0 1.0
OD1 D:ASP19 4.1 33.5 1.0
N D:ASN14 4.1 31.9 1.0
CB D:ASN14 4.1 24.2 1.0
MN D:MN239 4.3 26.5 1.0
CB D:ASP10 4.3 25.4 1.0
CA D:TYR12 4.4 28.4 1.0
N D:TYR12 4.4 29.1 1.0
N D:PRO13 4.5 29.5 1.0
CB D:TYR12 4.5 26.9 1.0
CA D:PRO13 4.6 28.5 1.0
O D:HOH252 4.6 22.1 1.0
ND2 D:ASN14 4.6 22.9 1.0
CB D:ASP19 4.7 33.1 1.0
OD1 D:ASP208 4.7 25.6 1.0
O D:ASP208 4.7 25.8 1.0
C D:PRO13 4.7 29.6 1.0
CA D:ASN14 4.8 27.0 1.0
CE1 D:HIS24 4.8 25.0 1.0
O D:ARG228 4.9 24.9 1.0
CA D:ARG228 4.9 25.8 1.0
CD2 D:TYR12 4.9 29.6 1.0
CB D:ARG228 4.9 27.1 1.0

Reference:

J.H.Naismith, C.Emmerich, J.Habash, S.J.Harrop, J.R.Helliwell, W.N.Hunter, J.Raftery, A.J.Kalb, J.Yariv. Refined Structure of Concanavalin A Complexed with Methyl Alpha-D-Mannopyranoside at 2.0 A Resolution and Comparison with the Saccharide-Free Structure. Acta Crystallogr.,Sect.D V. 50 847 1994.
ISSN: ISSN 0907-4449
PubMed: 15299352
DOI: 10.1107/S0907444994005287
Page generated: Wed Jul 9 04:37:50 2025

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