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Calcium in PDB 1ona: Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside

Protein crystallography data

The structure of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside, PDB code: 1ona was solved by J.Bouckaert, D.Maes, F.Poortmans, L.Wyns, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.830, 64.840, 125.920, 90.00, 93.87, 90.00
R / Rfree (%) 22.1 / 28.2

Other elements in 1ona:

The structure of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside (pdb code 1ona). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside, PDB code: 1ona:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ona

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Calcium binding site 1 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca239

b:10.3
occ:1.00
OD1 A:ASN14 2.1 24.2 1.0
O A:TYR12 2.1 15.7 1.0
OD1 A:ASP10 2.4 19.7 1.0
O A:HOH247 2.5 6.8 1.0
OD2 A:ASP19 2.6 15.8 1.0
OD2 A:ASP10 2.7 19.0 1.0
CG A:ASP10 2.9 18.1 1.0
CG A:ASN14 3.3 20.2 1.0
C A:TYR12 3.4 15.7 1.0
CG A:ASP19 3.8 12.7 1.0
N A:ASN14 3.8 9.6 1.0
CB A:ASN14 4.1 11.9 1.0
N A:PRO13 4.3 14.6 1.0
ND2 A:ASN14 4.3 17.6 1.0
CA A:PRO13 4.3 12.4 1.0
C A:PRO13 4.3 10.0 1.0
MN A:MN238 4.3 20.3 1.0
CA A:TYR12 4.4 11.9 1.0
CB A:ASP10 4.4 8.2 1.0
OD1 A:ASP19 4.5 12.6 1.0
CB A:TYR12 4.5 7.8 1.0
OD2 A:ASP208 4.5 8.6 1.0
N A:TYR12 4.6 12.0 1.0
CA A:ASN14 4.6 10.0 1.0
O A:ASP208 4.7 3.6 1.0
CB A:ARG228 4.7 9.6 1.0
CD2 A:TYR12 4.7 15.3 1.0
CB A:ASP19 4.8 15.5 1.0
CE1 A:HIS24 4.8 7.0 1.0
CA A:ARG228 4.9 5.4 1.0

Calcium binding site 2 out of 4 in 1ona

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Calcium binding site 2 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca239

b:12.7
occ:1.00
O C:TYR12 2.1 8.5 1.0
OD1 C:ASP10 2.2 4.5 1.0
OD1 C:ASN14 2.2 20.2 1.0
O C:HOH248 2.3 7.6 1.0
OD2 C:ASP10 2.5 11.6 1.0
OD2 C:ASP19 2.5 11.8 1.0
CG C:ASP10 2.7 9.8 1.0
O C:HOH246 2.7 6.5 1.0
C C:TYR12 3.4 7.6 1.0
CG C:ASN14 3.4 12.6 1.0
CG C:ASP19 3.8 15.3 1.0
N C:ASN14 4.0 12.3 1.0
CB C:ASP10 4.2 9.4 1.0
CB C:ASN14 4.2 5.6 1.0
MN B:MN238 4.2 14.4 1.0
N C:PRO13 4.3 6.2 1.0
CA C:PRO13 4.3 6.6 1.0
CA C:TYR12 4.3 9.8 1.0
ND2 C:ASN14 4.4 7.7 1.0
OD1 C:ASP19 4.4 16.4 1.0
C C:PRO13 4.4 9.6 1.0
N C:TYR12 4.5 15.4 1.0
CB C:TYR12 4.6 12.2 1.0
O C:ASP208 4.6 2.0 1.0
OD2 C:ASP208 4.7 12.1 1.0
CA C:ASN14 4.7 9.4 1.0
CE1 C:HIS24 4.7 7.0 1.0
O C:HOH257 4.8 10.6 1.0
CB C:ASP19 4.8 20.5 1.0
CB C:ARG228 4.8 6.3 1.0
CD2 C:TYR12 4.9 16.0 1.0
CA C:ASP10 4.9 8.2 1.0
CA C:ARG228 5.0 6.3 1.0

Calcium binding site 3 out of 4 in 1ona

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Calcium binding site 3 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca239

b:18.0
occ:1.00
O D:TYR12 2.1 19.8 1.0
OD1 D:ASP10 2.3 10.2 1.0
OD1 D:ASN14 2.3 31.0 1.0
O D:HOH268 2.5 18.7 1.0
OD2 D:ASP10 2.5 4.5 1.0
OD2 D:ASP19 2.5 29.2 1.0
O D:HOH247 2.5 8.2 1.0
CG D:ASP10 2.7 8.2 1.0
C D:TYR12 3.3 14.3 1.0
CG D:ASN14 3.5 23.2 1.0
CG D:ASP19 3.8 24.9 1.0
N D:ASN14 3.9 19.0 1.0
CA D:PRO13 4.2 18.1 1.0
N D:PRO13 4.2 18.1 1.0
CB D:ASP10 4.2 11.9 1.0
CB D:ASN14 4.2 21.5 1.0
C D:PRO13 4.3 19.1 1.0
CA D:TYR12 4.3 10.7 1.0
MN C:MN238 4.4 21.4 1.0
ND2 D:ASN14 4.5 16.2 1.0
CE1 D:HIS24 4.5 11.8 1.0
OD1 D:ASP19 4.5 24.1 1.0
N D:TYR12 4.5 13.8 1.0
O D:ASP208 4.6 4.3 1.0
CB D:TYR12 4.6 11.8 1.0
CA D:ASN14 4.7 20.9 1.0
CB D:ASP19 4.7 23.6 1.0
OD2 D:ASP208 4.7 14.8 1.0
O D:HOH257 4.8 12.6 1.0
CD2 D:TYR12 4.9 18.8 1.0
CB D:ARG228 4.9 12.2 1.0
NE2 D:HIS24 5.0 13.4 1.0
CA D:ASP10 5.0 6.0 1.0

Calcium binding site 4 out of 4 in 1ona

Go back to Calcium Binding Sites List in 1ona
Calcium binding site 4 out of 4 in the Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Co-Crystals of Concanavalin A with Methyl-3,6-Di-O-(Alpha-D- Mannopyranosyl)-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca239

b:14.3
occ:1.00
OD1 B:ASP10 2.2 6.6 1.0
O B:HOH261 2.3 17.7 1.0
OD1 B:ASN14 2.3 21.9 1.0
O B:TYR12 2.3 14.7 1.0
OD2 B:ASP10 2.5 6.7 1.0
OD2 B:ASP19 2.6 25.9 1.0
CG B:ASP10 2.7 6.5 1.0
CG B:ASN14 3.5 19.6 1.0
C B:TYR12 3.6 14.3 1.0
CG B:ASP19 3.8 22.6 1.0
N B:ASN14 4.1 17.3 1.0
CB B:ASP10 4.1 9.9 1.0
CB B:ASN14 4.3 14.7 1.0
MN D:MN238 4.3 15.9 1.0
ND2 B:ASN14 4.4 17.9 1.0
N B:PRO13 4.5 14.8 1.0
OD1 B:ASP19 4.5 22.4 1.0
CA B:TYR12 4.5 12.2 1.0
CA B:PRO13 4.5 14.7 1.0
O B:HOH248 4.6 10.4 1.0
O B:ASP208 4.6 8.2 1.0
N B:TYR12 4.6 16.6 1.0
C B:PRO13 4.6 15.6 1.0
OD2 B:ASP208 4.7 17.2 1.0
CB B:TYR12 4.7 14.0 1.0
CB B:ARG228 4.7 6.1 1.0
CE1 B:HIS24 4.8 9.9 1.0
CA B:ARG228 4.8 6.5 1.0
CA B:ASN14 4.8 16.3 1.0
CB B:ASP19 4.9 20.3 1.0
CA B:ASP10 4.9 13.0 1.0
O B:ARG228 4.9 5.6 1.0
CD2 B:TYR12 5.0 14.1 1.0

Reference:

R.Loris, D.Maes, F.Poortmans, L.Wyns, J.Bouckaert. A Structure of the Complex Between Concanavalin A and Methyl-3,6-Di-O-(Alpha-D-Mannopyranosyl) -Alpha-D-Mannopyranoside Reveals Two Binding Modes. J.Biol.Chem. V. 271 30614 1996.
ISSN: ISSN 0021-9258
PubMed: 8940035
DOI: 10.1074/JBC.271.48.30614
Page generated: Sat Dec 12 03:12:48 2020

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