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Calcium in PDB 1vam: Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside

Protein crystallography data

The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside, PDB code: 1vam was solved by P.N.Kanellopoulos, P.A.Tucker, S.J.Hamodrakas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 135.190, 155.380, 71.250, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 26

Other elements in 1vam:

The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside (pdb code 1vam). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside, PDB code: 1vam:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1vam

Go back to Calcium Binding Sites List in 1vam
Calcium binding site 1 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-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 Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca239

b:34.3
occ:1.00
O A:TYR12 2.2 30.4 1.0
O A:HOH242 2.2 35.0 1.0
OD2 A:ASP19 2.3 45.1 1.0
OD1 A:ASN14 2.3 49.4 1.0
OD1 A:ASP10 2.4 24.8 1.0
O A:HOH249 2.4 26.0 1.0
OD2 A:ASP10 2.5 24.1 1.0
CG A:ASP10 2.8 25.2 1.0
CG A:ASN14 3.2 44.3 1.0
C A:TYR12 3.4 33.5 1.0
CG A:ASP19 3.5 43.6 1.0
N A:ASN14 3.8 38.5 1.0
CB A:ASN14 3.9 42.2 1.0
OD1 A:ASP19 4.0 45.4 1.0
ND2 A:ASN14 4.1 44.8 1.0
N A:PRO13 4.3 35.6 1.0
OD2 A:ASP208 4.3 46.3 1.0
CA A:TYR12 4.3 31.3 1.0
CB A:ASP10 4.3 21.6 1.0
N A:TYR12 4.3 31.4 1.0
MN A:MN238 4.4 33.1 1.0
CA A:PRO13 4.4 34.6 1.0
CA A:ASN14 4.5 40.8 1.0
C A:PRO13 4.5 36.4 1.0
CB A:ASP19 4.6 42.2 1.0
O A:HOH247 4.6 31.4 1.0
CE1 A:HIS24 4.6 29.6 1.0
O A:ASP208 4.7 32.9 1.0
CB A:TYR12 4.7 30.7 1.0
NE2 A:HIS24 4.9 28.8 1.0
CD1 A:TYR12 4.9 34.4 1.0

Calcium binding site 2 out of 4 in 1vam

Go back to Calcium Binding Sites List in 1vam
Calcium binding site 2 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-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 Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca239

b:30.1
occ:1.00
O B:HOH247 2.1 21.7 1.0
O B:HOH248 2.1 30.3 1.0
OD2 B:ASP19 2.2 31.0 1.0
OD1 B:ASN14 2.3 32.2 1.0
OD2 B:ASP10 2.4 18.6 1.0
O B:TYR12 2.5 24.3 1.0
OD1 B:ASP10 2.5 21.4 1.0
CG B:ASP10 2.8 20.3 1.0
CG B:ASP19 3.2 34.1 1.0
CG B:ASN14 3.5 26.6 1.0
OD1 B:ASP19 3.6 36.9 1.0
C B:TYR12 3.7 28.1 1.0
O B:HOH246 4.0 44.2 1.0
MN B:MN238 4.1 34.6 1.0
N B:ASN14 4.1 39.2 1.0
CB B:ASN14 4.2 31.1 1.0
CB B:ASP10 4.3 20.0 1.0
CA B:TYR12 4.5 27.7 1.0
ND2 B:ASN14 4.5 25.5 1.0
N B:TYR12 4.5 29.5 1.0
CB B:ASP19 4.5 31.1 1.0
O B:ASP208 4.6 27.4 1.0
N B:PRO13 4.7 28.7 1.0
CA B:PRO13 4.7 32.4 1.0
CB B:TYR12 4.7 26.9 1.0
OD2 B:ASP208 4.7 29.8 1.0
O B:ARG228 4.8 35.0 1.0
C B:PRO13 4.8 38.3 1.0
CA B:ASN14 4.8 35.1 1.0
CE1 B:HIS24 4.9 26.3 1.0
CA B:ARG228 4.9 27.6 1.0
CD1 B:TYR12 4.9 34.0 1.0
CB B:ARG228 4.9 27.4 1.0

Calcium binding site 3 out of 4 in 1vam

Go back to Calcium Binding Sites List in 1vam
Calcium binding site 3 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-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 Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca239

b:24.3
occ:1.00
O C:TYR12 2.1 24.6 1.0
O C:HOH247 2.2 23.1 1.0
OD1 C:ASN14 2.5 39.9 1.0
O C:HOH248 2.5 23.3 1.0
OD2 C:ASP10 2.5 36.8 1.0
OD1 C:ASP10 2.6 36.1 1.0
OD2 C:ASP19 2.7 28.7 1.0
CG C:ASP10 2.9 37.1 1.0
C C:TYR12 3.4 26.1 1.0
CG C:ASN14 3.6 33.0 1.0
N C:ASN14 3.8 29.5 1.0
CG C:ASP19 3.9 27.9 1.0
MN C:MN238 4.2 27.9 1.0
CB C:ASN14 4.2 29.5 1.0
N C:PRO13 4.3 26.9 1.0
CA C:TYR12 4.3 26.1 1.0
CA C:PRO13 4.3 29.4 1.0
OD1 C:ASP19 4.3 31.7 1.0
CB C:ASP10 4.4 30.1 1.0
N C:TYR12 4.4 30.2 1.0
O C:HOH246 4.4 25.8 1.0
C C:PRO13 4.5 30.7 1.0
CB C:TYR12 4.5 26.4 1.0
CA C:ASN14 4.6 28.3 1.0
ND2 C:ASN14 4.7 34.4 1.0
CE1 C:HIS24 4.7 21.2 1.0
CD2 C:TYR12 4.9 30.2 1.0
O C:ARG228 4.9 25.9 1.0
CA C:ARG228 4.9 22.6 1.0
O C:ASP208 5.0 27.1 1.0
OD2 C:ASP208 5.0 31.5 1.0
CB C:ARG228 5.0 20.8 1.0

Calcium binding site 4 out of 4 in 1vam

Go back to Calcium Binding Sites List in 1vam
Calcium binding site 4 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-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 Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca239

b:36.4
occ:1.00
O D:TYR12 2.1 43.6 1.0
OD2 D:ASP19 2.1 35.1 1.0
OD1 D:ASP10 2.3 31.9 1.0
O D:HOH245 2.5 31.9 1.0
OD2 D:ASP10 2.5 32.9 1.0
OD1 D:ASN14 2.5 48.0 1.0
O D:HOH246 2.6 34.9 1.0
CG D:ASP10 2.7 31.1 1.0
CG D:ASP19 3.3 42.3 1.0
C D:TYR12 3.3 43.3 1.0
CG D:ASN14 3.7 46.9 1.0
OD1 D:ASP19 3.8 41.6 1.0
N D:ASN14 4.0 47.4 1.0
CA D:TYR12 4.1 41.2 1.0
N D:TYR12 4.2 40.0 1.0
CB D:ASP10 4.2 31.5 1.0
MN D:MN238 4.2 42.6 1.0
CB D:TYR12 4.3 43.0 1.0
N D:PRO13 4.3 44.1 1.0
CB D:ASN14 4.3 45.0 1.0
CB D:ASP19 4.4 41.9 1.0
O D:HOH247 4.5 34.2 1.0
O D:ASP208 4.5 42.0 1.0
CA D:PRO13 4.5 43.7 1.0
ND2 D:ASN14 4.7 49.3 1.0
C D:PRO13 4.7 44.7 1.0
CE1 D:HIS24 4.8 32.8 1.0
OD1 D:ASP208 4.8 50.7 1.0
CD1 D:TYR12 4.8 40.0 1.0
CA D:ASN14 4.9 48.0 1.0
O D:ARG228 5.0 36.2 1.0

Reference:

P.N.Kanellopoulos, K.Pavlou, A.Perrakis, B.Agianian, C.E.Vorgias, C.Mavrommatis, M.Soufi, P.A.Tucker, S.J.Hamodrakas. The Crystal Structure of the Complexes of Concanavalin A with 4'-Nitrophenyl-Alpha-D-Mannopyranoside and 4'-Nitrophenyl-Alpha-D-Glucopyranoside. J.Struct.Biol. V. 116 345 1996.
ISSN: ISSN 1047-8477
PubMed: 8812993
DOI: 10.1006/JSBI.1996.0052
Page generated: Sat Dec 12 03:24:47 2020

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