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Magnesium 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:

Manganese (Mn) 2 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 1gkb

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Concanavalin A, New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:36.0
occ:1.00
O A:ASN131 2.2 34.1 1.0
O B:HOH2202 2.3 33.4 1.0
O A:LEU107 2.3 21.1 1.0
O A:HOH2268 2.4 34.9 1.0
O A:HOH2232 2.5 46.8 1.0
O B:HOH2093 2.6 31.9 1.0
C A:ASN131 3.3 29.6 1.0
C A:LEU107 3.5 21.3 1.0
O A:HOH2264 3.9 49.0 1.0
CA A:ASN131 4.0 27.6 1.0
CA A:LEU107 4.1 22.6 1.0
CB A:LEU107 4.1 24.1 1.0
N A:GLN132 4.3 30.7 1.0
OE2 B:GLU122 4.4 46.5 1.0
CA A:GLN132 4.4 31.9 1.0
CB A:ASN131 4.5 27.6 1.0
O A:HOH2310 4.5 47.7 1.0
OD1 A:ASN153 4.5 28.6 1.0
N A:SER108 4.5 20.3 1.0
OE1 B:GLU122 4.7 47.4 1.0
O A:HOH2269 4.8 44.4 1.0
O B:HOH2198 4.8 37.1 1.0
CD B:GLU122 4.8 44.7 1.0
CB A:GLN132 4.8 34.4 1.0
CB A:SER108 4.8 22.5 1.0
OD1 A:ASN131 4.8 30.1 1.0
CA A:SER108 4.8 20.8 1.0
O A:GLY152 4.9 23.5 1.0
CG A:LEU107 4.9 27.9 1.0

Magnesium binding site 2 out of 2 in 1gkb

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Concanavalin A, New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:38.1
occ:1.00
O B:HOH2249 2.2 38.0 1.0
O B:ASN131 2.3 34.2 1.0
O B:LEU107 2.3 23.0 1.0
O A:HOH2221 2.4 37.4 1.0
O B:HOH2118 2.6 38.7 1.0
O A:HOH2223 2.6 38.4 1.0
C B:ASN131 3.4 32.6 1.0
C B:LEU107 3.4 23.8 1.0
O B:HOH2245 3.8 43.3 1.0
CA B:LEU107 4.0 23.8 1.0
CB B:LEU107 4.1 24.6 1.0
CA B:ASN131 4.2 30.9 1.0
OE2 A:GLU122 4.2 45.0 1.0
OD1 B:ASN153 4.3 31.7 1.0
N B:GLN132 4.4 32.9 1.0
CA B:GLN132 4.5 34.3 1.0
O B:HOH2292 4.5 43.1 1.0
N B:SER108 4.5 22.8 1.0
CB B:ASN131 4.7 31.3 1.0
OE1 A:GLU122 4.7 45.5 1.0
O B:HOH2248 4.7 62.6 1.0
CD A:GLU122 4.8 43.9 1.0
O B:GLY152 4.8 30.7 1.0
CB B:SER108 4.8 21.6 0.5
O A:HOH2218 4.8 47.9 1.0
CA B:SER108 4.9 22.1 1.0
CB B:SER108 4.9 22.2 0.5
CB B:GLN132 4.9 37.0 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: Mon Dec 14 05:57:54 2020

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