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Calcium in PDB 1vln: A Triclinic Crystal Form of the Lectin Concanavalin A

Protein crystallography data

The structure of A Triclinic Crystal Form of the Lectin Concanavalin A, PDB code: 1vln 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 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.800, 79.300, 133.300, 97.10, 90.20, 97.50
R / Rfree (%) 20.5 / 26.5

Other elements in 1vln:

The structure of A Triclinic Crystal Form of the Lectin Concanavalin A also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the A Triclinic Crystal Form of the Lectin Concanavalin A (pdb code 1vln). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the A Triclinic Crystal Form of the Lectin Concanavalin A, PDB code: 1vln:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1vln

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Calcium binding site 1 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca239

b:21.5
occ:1.00
 O A:HOH243 2.0 18.4 1.0
OD1 A:ASN14 2.1 19.9 1.0
OD2 A:ASP19 2.2 23.1 1.0
O A:TYR12 2.4 25.7 1.0
OD2 A:ASP10 2.5 23.4 1.0
OD1 A:ASP10 2.5 21.4 1.0
O A:HOH242 2.6 16.6 1.0
CG A:ASP10 2.8 22.1 1.0
CG A:ASP19 3.3 29.6 1.0
CG A:ASN14 3.4 19.3 1.0
C A:TYR12 3.5 22.3 1.0
OD1 A:ASP19 3.9 27.4 1.0
N A:ASN14 3.9 26.8 1.0
MN A:MN238 4.1 33.7 1.0
CB A:ASN14 4.2 13.3 1.0
CB A:ASP10 4.3 19.0 1.0
ND2 A:ASN14 4.3 17.6 1.0
CA A:TYR12 4.4 17.7 1.0
N A:TYR12 4.4 20.5 1.0
O A:HOH240 4.5 16.5 1.0
N A:PRO13 4.5 26.6 1.0
CB A:ASP19 4.5 26.4 1.0
CA A:PRO13 4.5 24.8 1.0
OD1 A:ASP208 4.5 18.8 1.0
CB A:TYR12 4.6 18.2 1.0
CE1 A:HIS24 4.6 20.1 1.0
O A:ASP208 4.6 21.4 1.0
C A:PRO13 4.7 28.6 1.0
CA A:ASN14 4.7 21.5 1.0
CB A:ARG228 4.8 21.0 1.0
CD2 A:TYR12 4.9 17.2 1.0
NE2 A:HIS24 4.9 21.6 1.0

Calcium binding site 2 out of 8 in 1vln

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Calcium binding site 2 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca239

b:28.0
occ:1.00
 O B:HOH242 1.9 20.5 1.0
OD2 B:ASP19 2.2 31.7 1.0
O B:TYR12 2.2 27.3 1.0
OD1 B:ASP10 2.3 29.0 1.0
O B:HOH243 2.4 24.6 1.0
OD1 B:ASN14 2.6 30.4 1.0
OD2 B:ASP10 2.6 34.8 1.0
CG B:ASP10 2.8 30.8 1.0
CG B:ASP19 3.3 31.6 1.0
C B:TYR12 3.4 28.6 1.0
CG B:ASN14 3.8 27.8 1.0
OD1 B:ASP19 3.9 41.4 1.0
MN B:MN238 4.0 39.5 1.0
N B:ASN14 4.1 30.1 1.0
CB B:ASP10 4.2 26.7 1.0
CA B:TYR12 4.3 26.0 1.0
N B:TYR12 4.3 28.5 1.0
N B:PRO13 4.4 32.9 1.0
CB B:ASN14 4.4 26.2 1.0
CE1 B:HIS24 4.4 24.3 1.0
CB B:TYR12 4.5 27.7 1.0
CA B:PRO13 4.5 32.6 1.0
CB B:ASP19 4.5 28.3 1.0
O B:HOH240 4.6 18.2 1.0
C B:PRO13 4.7 32.5 1.0
NE2 B:HIS24 4.7 29.2 1.0
ND2 B:ASN14 4.8 26.5 1.0
OD1 B:ASP208 4.8 27.2 1.0
O B:ASP208 4.9 26.4 1.0
CA B:ASN14 4.9 28.2 1.0

Calcium binding site 3 out of 8 in 1vln

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Calcium binding site 3 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca239

b:24.6
occ:1.00
 O C:HOH243 2.1 26.2 1.0
OD2 C:ASP19 2.3 27.6 1.0
O C:TYR12 2.4 34.9 1.0
OD1 C:ASP10 2.5 38.5 1.0
OD1 C:ASN14 2.5 28.1 1.0
OD2 C:ASP10 2.6 35.6 1.0
O C:HOH242 2.7 21.3 1.0
CG C:ASP10 2.8 35.0 1.0
CG C:ASP19 3.4 27.8 1.0
CG C:ASN14 3.6 27.8 1.0
C C:TYR12 3.7 33.6 1.0
OD1 C:ASP19 3.9 32.6 1.0
N C:ASN14 4.0 33.5 1.0
CB C:ASN14 4.1 25.9 1.0
O C:HOH240 4.2 27.6 1.0
MN C:MN238 4.3 41.2 1.0
CB C:ASP10 4.4 26.8 1.0
CA C:TYR12 4.5 32.6 1.0
N C:PRO13 4.6 35.8 1.0
N C:TYR12 4.6 33.8 1.0
CB C:ASP19 4.6 26.2 1.0
O C:ASP208 4.7 27.9 1.0
OD1 C:ASP208 4.7 24.3 1.0
CA C:PRO13 4.7 32.6 1.0
CA C:ASN14 4.7 30.4 1.0
CB C:ARG228 4.7 31.6 1.0
C C:PRO13 4.7 34.3 1.0
ND2 C:ASN14 4.7 30.8 1.0
CB C:TYR12 4.7 29.6 1.0
O C:ARG228 4.8 28.8 1.0
CE1 C:HIS24 4.8 24.8 1.0
CA C:ARG228 4.9 27.7 1.0

Calcium binding site 4 out of 8 in 1vln

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Calcium binding site 4 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca239

b:25.2
occ:1.00
 OD1 D:ASP10 2.3 29.0 1.0
O D:TYR12 2.4 28.6 1.0
O D:HOH243 2.4 18.1 1.0
OD2 D:ASP19 2.4 31.9 1.0
O D:HOH242 2.5 21.6 1.0
OD1 D:ASN14 2.6 22.4 1.0
OD2 D:ASP10 2.8 28.5 1.0
CG D:ASP10 2.9 27.4 1.0
C D:TYR12 3.6 24.9 1.0
CG D:ASP19 3.6 27.4 1.0
CG D:ASN14 3.7 21.9 1.0
MN D:MN238 4.1 38.5 1.0
OD1 D:ASP19 4.1 23.6 1.0
N D:ASN14 4.1 28.9 1.0
CB D:ASN14 4.2 16.1 1.0
CA D:TYR12 4.3 19.9 1.0
CB D:ASP10 4.4 20.6 1.0
N D:TYR12 4.4 20.2 1.0
CB D:TYR12 4.5 17.4 1.0
O D:HOH240 4.5 38.1 1.0
O D:ASP208 4.6 19.1 1.0
N D:PRO13 4.6 25.4 1.0
CA D:PRO13 4.7 24.4 1.0
CB D:ASP19 4.8 24.1 1.0
CB D:ARG228 4.8 20.5 1.0
CA D:ASN14 4.8 26.1 1.0
CE1 D:HIS24 4.9 24.4 1.0
ND2 D:ASN14 4.9 24.5 1.0
C D:PRO13 4.9 27.3 1.0
OD1 D:ASP208 4.9 20.9 1.0
O D:ARG228 4.9 21.4 1.0

Calcium binding site 5 out of 8 in 1vln

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Calcium binding site 5 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca239

b:26.8
occ:1.00
 O E:HOH242 2.1 18.3 1.0
OD2 E:ASP19 2.3 24.7 1.0
O E:HOH243 2.4 21.0 1.0
OD2 E:ASP10 2.4 26.3 1.0
OD1 E:ASP10 2.4 28.6 1.0
OD1 E:ASN14 2.4 33.4 1.0
O E:TYR12 2.6 32.4 1.0
CG E:ASP10 2.7 28.0 1.0
CG E:ASP19 3.5 28.8 1.0
CG E:ASN14 3.6 29.3 1.0
C E:TYR12 3.8 27.8 1.0
OD1 E:ASP19 4.0 28.3 1.0
N E:ASN14 4.0 33.3 1.0
MN E:MN238 4.1 30.8 1.0
CB E:ASN14 4.1 26.9 1.0
CB E:ASP10 4.2 23.8 1.0
O E:HOH240 4.3 23.8 1.0
CE1 E:HIS24 4.5 18.6 1.0
CA E:TYR12 4.6 23.2 1.0
N E:TYR12 4.6 25.2 1.0
CB E:ASP19 4.6 26.8 1.0
O E:ASP208 4.7 26.4 1.0
ND2 E:ASN14 4.7 30.6 1.0
N E:PRO13 4.7 30.3 1.0
CB E:TYR12 4.7 19.8 1.0
CA E:ASN14 4.7 31.4 1.0
OD2 E:ASP208 4.8 28.4 1.0
NE2 E:HIS24 4.8 22.3 1.0
CA E:PRO13 4.8 28.4 1.0
O E:ARG228 4.8 27.2 1.0
C E:PRO13 4.9 30.6 1.0
CB E:ARG228 4.9 30.7 1.0

Calcium binding site 6 out of 8 in 1vln

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Calcium binding site 6 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca239

b:26.3
occ:1.00
 O F:HOH243 1.9 22.1 1.0
OD1 F:ASN14 2.2 30.1 1.0
O F:TYR12 2.2 28.8 1.0
OD2 F:ASP19 2.3 25.8 1.0
O F:HOH242 2.5 19.1 1.0
OD2 F:ASP10 2.5 21.3 1.0
OD1 F:ASP10 2.6 25.0 1.0
CG F:ASP10 2.9 25.1 1.0
CG F:ASN14 3.2 27.4 1.0
C F:TYR12 3.4 27.2 1.0
CG F:ASP19 3.5 28.7 1.0
CB F:ASN14 3.9 26.1 1.0
N F:ASN14 3.9 31.2 1.0
OD1 F:ASP19 4.0 27.9 1.0
MN F:MN238 4.2 34.6 1.0
CA F:TYR12 4.2 24.2 1.0
O F:HOH241 4.3 27.8 1.0
ND2 F:ASN14 4.3 26.7 1.0
CB F:TYR12 4.4 25.6 1.0
N F:PRO13 4.4 25.5 1.0
CB F:ASP10 4.4 21.9 1.0
N F:TYR12 4.4 28.8 1.0
CA F:ASN14 4.5 29.5 1.0
C F:PRO13 4.6 29.3 1.0
CE1 F:HIS24 4.6 28.2 1.0
CA F:PRO13 4.7 23.4 1.0
CB F:ASP19 4.7 30.4 1.0
CD2 F:TYR12 4.8 25.4 1.0
O F:ASP208 4.8 24.2 1.0
CB F:ARG228 4.8 20.1 1.0
OD1 F:ASP208 4.8 28.7 1.0
NE2 F:HIS24 5.0 31.2 1.0

Calcium binding site 7 out of 8 in 1vln

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Calcium binding site 7 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca239

b:26.8
occ:1.00
 OD1 G:ASN14 2.3 23.6 1.0
OD2 G:ASP19 2.4 34.6 1.0
O G:TYR12 2.4 31.8 1.0
O G:HOH243 2.4 18.0 1.0
OD1 G:ASP10 2.4 25.1 1.0
OD2 G:ASP10 2.6 22.7 1.0
O G:HOH242 2.6 23.7 1.0
CG G:ASP10 2.9 22.8 1.0
CG G:ASN14 3.5 20.9 1.0
CG G:ASP19 3.6 33.3 1.0
C G:TYR12 3.6 25.5 1.0
N G:ASN14 4.0 32.6 1.0
OD1 G:ASP19 4.1 31.7 1.0
MN G:MN238 4.2 38.3 1.0
CB G:ASN14 4.2 20.3 1.0
CB G:ASP10 4.4 17.2 1.0
CA G:TYR12 4.4 24.2 1.0
O G:HOH241 4.5 29.6 1.0
N G:TYR12 4.5 25.3 1.0
N G:PRO13 4.5 27.1 1.0
O G:ASP208 4.5 21.7 1.0
CA G:PRO13 4.6 26.8 1.0
ND2 G:ASN14 4.6 19.9 1.0
CB G:TYR12 4.6 23.2 1.0
CB G:ASP19 4.7 25.1 1.0
C G:PRO13 4.7 29.6 1.0
CE1 G:HIS24 4.7 21.6 1.0
CB G:ARG228 4.8 21.5 1.0
CA G:ASN14 4.8 29.4 1.0
OD1 G:ASP208 4.9 21.7 1.0
O G:ARG228 5.0 24.9 1.0

Calcium binding site 8 out of 8 in 1vln

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Calcium binding site 8 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca239

b:29.7
occ:1.00
 O H:HOH242 2.1 21.0 1.0
O H:TYR12 2.2 28.3 1.0
OD1 H:ASP10 2.3 38.1 1.0
OD1 H:ASN14 2.4 27.0 1.0
OD2 H:ASP19 2.4 37.1 1.0
OD2 H:ASP10 2.5 37.5 1.0
O H:HOH243 2.6 24.2 1.0
CG H:ASP10 2.7 35.7 1.0
C H:TYR12 3.4 29.5 1.0
CG H:ASN14 3.4 28.4 1.0
CG H:ASP19 3.6 33.6 1.0
N H:ASN14 3.9 30.7 1.0
CB H:ASN14 4.0 23.5 1.0
OD1 H:ASP19 4.2 38.6 1.0
CB H:ASP10 4.2 30.6 1.0
MN H:MN238 4.2 40.3 1.0
CA H:TYR12 4.3 28.2 1.0
N H:TYR12 4.3 29.6 1.0
N H:PRO13 4.4 30.9 1.0
CA H:PRO13 4.5 28.7 1.0
ND2 H:ASN14 4.5 31.0 1.0
CB H:TYR12 4.6 26.2 1.0
C H:PRO13 4.6 29.5 1.0
O H:HOH241 4.6 26.9 1.0
CA H:ASN14 4.6 28.0 1.0
O H:ASP208 4.6 27.4 1.0
CB H:ASP19 4.7 31.1 1.0
CB H:ARG228 4.8 26.3 1.0
CE1 H:HIS24 4.9 21.0 1.0
OD1 H:ASP208 5.0 29.9 1.0
CD2 H:TYR12 5.0 28.6 1.0

Reference:

P.N.Kanellopoulos, P.A.Tucker, K.Pavlou, B.Agianian, S.J.Hamodrakas. A Triclinic Crystal Form of the Lectin Concanavalin A J.Struct.Biol. V. 117 16 1996.
ISSN: ISSN 1047-8477
PubMed: 8812975
DOI: 10.1006/JSBI.1996.0065
Page generated: Fri Jul 12 06:55:34 2024

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