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Calcium in PDB 1gkb: Concanavalin A, New Crystal Form

Protein crystallography data

The structure of Concanavalin A, New Crystal Form, PDB code: 1gkb was solved by K.Kantardjieff, B.Rupp, P.Hoechtl, B.Segelke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.63 / 1.56
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.700, 101.380, 111.970, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.6

Other elements in 1gkb:

The structure of Concanavalin A, New Crystal Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Manganese (Mn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Concanavalin A, New Crystal Form (pdb code 1gkb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Concanavalin A, New Crystal Form, PDB code: 1gkb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1gkb

Go back to Calcium Binding Sites List in 1gkb
Calcium binding site 1 out of 2 in the Concanavalin A, New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A, New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:20.3
occ:1.00
O A:HOH2318 2.3 23.0 1.0
OD1 A:ASN14 2.3 24.7 1.0
OD2 A:ASP19 2.4 24.6 1.0
O A:TYR12 2.4 24.1 1.0
OD1 A:ASP10 2.4 22.4 1.0
O A:HOH2343 2.5 20.9 1.0
OD2 A:ASP10 2.5 21.9 1.0
CG A:ASP10 2.9 21.4 1.0
CG A:ASN14 3.5 24.9 1.0
CG A:ASP19 3.5 25.1 1.0
C A:TYR12 3.6 24.4 1.0
N A:ASN14 3.9 26.1 1.0
OD1 A:ASP19 3.9 23.2 1.0
CB A:ASN14 4.1 24.9 1.0
MN A:MN801 4.2 22.8 1.0
CB A:ASP10 4.4 21.5 1.0
CA A:TYR12 4.4 24.2 1.0
N A:TYR12 4.5 23.1 1.0
N A:PRO13 4.5 25.9 1.0
CB A:TYR12 4.5 24.1 1.0
CA A:PRO13 4.6 26.2 1.0
CB A:ARG228 4.6 21.8 1.0
ND2 A:ASN14 4.6 24.8 1.0
C A:PRO13 4.6 27.4 1.0
O A:HOH2357 4.6 20.6 1.0
CE1 A:HIS24 4.6 23.6 1.0
CA A:ASN14 4.7 25.7 1.0
O A:ASP208 4.7 22.5 1.0
OD1 A:ASP208 4.7 21.6 1.0
O A:ARG228 4.8 24.3 1.0
CB A:ASP19 4.8 24.9 1.0
CD2 A:TYR12 4.8 25.7 1.0
CA A:ARG228 4.9 22.4 1.0
NE2 A:HIS24 4.9 22.5 1.0

Calcium binding site 2 out of 2 in 1gkb

Go back to Calcium Binding Sites List in 1gkb
Calcium binding site 2 out of 2 in the Concanavalin A, New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A, New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:23.2
occ:1.00
O B:HOH2299 2.3 24.6 1.0
OD1 B:ASN14 2.4 27.1 1.0
O B:TYR12 2.4 24.8 1.0
OD2 B:ASP19 2.4 23.9 1.0
O B:HOH2319 2.4 23.1 1.0
OD1 B:ASP10 2.4 23.3 1.0
OD2 B:ASP10 2.6 23.6 1.0
CG B:ASP10 2.8 24.2 1.0
CG B:ASP19 3.5 26.7 1.0
CG B:ASN14 3.5 29.6 1.0
C B:TYR12 3.5 25.1 1.0
N B:ASN14 3.9 27.5 1.0
OD1 B:ASP19 4.0 24.8 1.0
CB B:ASN14 4.1 28.4 1.0
MN B:MN901 4.2 23.5 1.0
CA B:TYR12 4.3 24.9 1.0
CB B:ASP10 4.4 23.4 1.0
N B:TYR12 4.4 23.9 1.0
CB B:TYR12 4.5 24.8 1.0
N B:PRO13 4.6 25.7 1.0
O B:HOH2329 4.6 22.6 1.0
CE1 B:HIS24 4.6 24.3 1.0
O B:ASP208 4.6 21.8 1.0
OD1 B:ASP208 4.6 24.2 1.0
ND2 B:ASN14 4.6 30.3 1.0
CA B:PRO13 4.7 26.6 1.0
CA B:ASN14 4.7 28.0 1.0
CB B:ARG228 4.7 28.8 1.0
C B:PRO13 4.7 28.5 1.0
CB B:ASP19 4.8 26.1 1.0
O B:ARG228 4.8 26.7 1.0
CA B:ARG228 4.9 27.3 1.0
NE2 B:HIS24 4.9 24.1 1.0

Reference:

K.Kantardjieff, P.Hochtl, B.Segelke, F.Tao, B.Rupp. Concanavalin A in A Dimeric Crystal Form: Revisiting Structural Accuracy and Molecular Flexibility Acta Crystallogr.,Sect.D V. 58 735 2002.
ISSN: ISSN 0907-4449
PubMed: 11976483
DOI: 10.1107/S0907444901019588
Page generated: Sat Dec 12 02:57:57 2020

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