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Manganese 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
Calcium (Ca) 2 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 2 in 1gkb

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Concanavalin A, New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:22.8
occ:1.00
OD2 A:ASP10 2.1 21.9 1.0
O A:HOH2358 2.1 20.3 1.0
OE2 A:GLU8 2.2 21.6 1.0
NE2 A:HIS24 2.3 22.5 1.0
OD1 A:ASP19 2.3 23.2 1.0
O A:HOH2357 2.3 20.6 1.0
CG A:ASP19 3.2 25.1 1.0
CG A:ASP10 3.2 21.4 1.0
CD A:GLU8 3.2 22.9 1.0
CE1 A:HIS24 3.2 23.6 1.0
CD2 A:HIS24 3.3 23.6 1.0
OD2 A:ASP19 3.6 24.6 1.0
OE1 A:GLU8 3.6 21.7 1.0
CB A:ASP10 3.6 21.5 1.0
O A:HOH2343 3.9 20.9 1.0
O A:HOH2045 4.1 29.6 1.0
OG A:SER34 4.2 21.7 1.0
CA A:CA802 4.2 20.3 1.0
OD1 A:ASP10 4.3 22.4 1.0
CB A:ASP19 4.3 24.9 1.0
ND1 A:HIS24 4.4 23.2 1.0
O A:HOH2048 4.4 38.5 1.0
CG A:HIS24 4.4 23.2 1.0
CG A:GLU8 4.6 21.5 1.0
O A:VAL32 4.6 23.1 1.0
CA A:ASP19 4.7 25.9 1.0

Manganese binding site 2 out of 2 in 1gkb

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Concanavalin A, New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:23.5
occ:1.00
O B:HOH2330 2.1 22.7 1.0
OD2 B:ASP10 2.1 23.6 1.0
OE2 B:GLU8 2.2 21.2 1.0
OD1 B:ASP19 2.2 24.8 1.0
O B:HOH2329 2.3 22.6 1.0
NE2 B:HIS24 2.3 24.1 1.0
CG B:ASP19 3.2 26.7 1.0
CG B:ASP10 3.2 24.2 1.0
CD B:GLU8 3.2 25.4 1.0
CE1 B:HIS24 3.2 24.3 1.0
CD2 B:HIS24 3.3 25.1 1.0
OE1 B:GLU8 3.5 25.0 1.0
OD2 B:ASP19 3.6 23.9 1.0
CB B:ASP10 3.7 23.4 1.0
O B:HOH2319 4.0 23.1 1.0
O B:HOH2042 4.1 37.8 1.0
OG B:SER34 4.1 23.3 1.0
O B:HOH2039 4.2 45.4 1.0
CA B:CA902 4.2 23.2 1.0
OD1 B:ASP10 4.3 23.3 1.0
CB B:ASP19 4.3 26.1 1.0
ND1 B:HIS24 4.4 23.0 1.0
CG B:HIS24 4.4 22.8 1.0
CG B:GLU8 4.6 23.1 1.0
O B:VAL32 4.6 25.9 1.0
CA B:ASP19 4.6 27.4 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 Oct 5 10:32:21 2024

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