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Calcium in PDB 1h9w: Native Dioclea Guianensis Seed Lectin

Protein crystallography data

The structure of Native Dioclea Guianensis Seed Lectin, PDB code: 1h9w was solved by A.Romero, D.A.Wah, F.G.D.Sol, B.S.Cavada, M.V.Ramos, T.B.Grangeiro, A.H.Sampaio, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.54 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 90.163, 90.163, 106.755, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.7

Other elements in 1h9w:

The structure of Native Dioclea Guianensis Seed Lectin also contains other interesting chemical elements:

Manganese (Mn) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Native Dioclea Guianensis Seed Lectin (pdb code 1h9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Native Dioclea Guianensis Seed Lectin, PDB code: 1h9w:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1h9w

Go back to Calcium Binding Sites List in 1h9w
Calcium binding site 1 out of 3 in the Native Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Dioclea Guianensis Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca239

b:20.9
occ:1.00
O A:HOH2007 2.2 22.2 1.0
OD1 A:ASP10 2.2 18.9 1.0
O A:TYR12 2.2 23.2 1.0
OD2 A:ASP19 2.3 24.3 1.0
O A:HOH2138 2.4 21.6 1.0
OD2 A:ASP10 2.4 16.9 1.0
OD1 A:ASN14 2.6 25.7 1.0
CG A:ASP10 2.7 14.1 1.0
C A:TYR12 3.5 24.1 1.0
CG A:ASP19 3.5 24.7 1.0
CG A:ASN14 3.7 27.4 1.0
N A:ASN14 4.0 25.0 1.0
OD1 A:ASP19 4.0 22.9 1.0
CB A:ASP10 4.2 19.0 1.0
MN A:MN238 4.2 11.1 1.0
CB A:ASN14 4.2 25.2 1.0
CA A:TYR12 4.3 23.4 1.0
N A:TYR12 4.4 22.7 1.0
N A:PRO13 4.4 24.1 1.0
CB A:TYR12 4.4 24.5 1.0
O A:ASP208 4.5 17.4 1.0
CA A:PRO13 4.6 24.7 1.0
CB A:ASP19 4.6 25.2 1.0
C A:PRO13 4.7 25.0 1.0
O A:HOH2146 4.7 21.7 1.0
CA A:ASN14 4.8 26.3 1.0
OD1 A:ASP208 4.8 19.9 1.0
CE1 A:HIS24 4.8 18.0 1.0
O A:ARG228 4.8 24.7 1.0
ND2 A:ASN14 4.8 25.3 1.0
CB A:ARG228 4.9 27.6 1.0
CA A:ARG228 4.9 26.0 1.0
CA A:ASP10 4.9 18.4 1.0

Calcium binding site 2 out of 3 in 1h9w

Go back to Calcium Binding Sites List in 1h9w
Calcium binding site 2 out of 3 in the Native Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Native Dioclea Guianensis Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca239

b:27.1
occ:1.00
OD1 B:ASP10 2.2 24.9 1.0
O B:HOH2004 2.2 27.9 1.0
O B:TYR12 2.3 29.1 1.0
OD1 B:ASN14 2.4 25.5 1.0
O B:HOH2108 2.4 24.4 1.0
OD2 B:ASP19 2.5 29.0 1.0
OD2 B:ASP10 2.6 22.6 1.0
CG B:ASP10 2.7 23.6 1.0
CG B:ASN14 3.5 29.9 1.0
C B:TYR12 3.5 30.0 1.0
CG B:ASP19 3.6 28.9 1.0
N B:ASN14 3.9 32.2 1.0
CB B:ASN14 4.0 29.1 1.0
CB B:ASP10 4.2 23.6 1.0
OD1 B:ASP19 4.2 27.6 1.0
MN B:MN238 4.2 16.4 1.0
CA B:TYR12 4.4 30.1 1.0
N B:TYR12 4.5 28.8 1.0
O B:ASP208 4.5 23.5 1.0
N B:PRO13 4.5 30.7 1.0
CE1 B:HIS24 4.5 33.1 1.0
CB B:TYR12 4.6 31.5 1.0
CA B:ASN14 4.6 32.8 1.0
CA B:PRO13 4.6 30.7 1.0
C B:PRO13 4.6 32.0 1.0
ND2 B:ASN14 4.6 27.0 1.0
O B:ARG228 4.7 31.0 1.0
CB B:ASP19 4.7 30.3 1.0
CB B:ARG228 4.7 30.8 1.0
CA B:ARG228 4.8 29.9 1.0
OD1 B:ASP208 4.9 25.8 1.0
CA B:ASP10 4.9 24.6 1.0
NE2 B:HIS24 5.0 31.5 1.0

Calcium binding site 3 out of 3 in 1h9w

Go back to Calcium Binding Sites List in 1h9w
Calcium binding site 3 out of 3 in the Native Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Dioclea Guianensis Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca243

b:6.5
occ:1.00
OE1 A:GLU183 2.4 33.5 1.0
OE2 A:GLU87 2.4 28.4 1.0
OE1 A:GLU87 2.4 23.2 1.0
CD A:GLU87 2.7 22.0 1.0
CD A:GLU183 3.1 31.4 1.0
OE2 A:GLU183 3.2 31.3 1.0
O A:HOH2114 3.9 10.0 1.0
CG A:GLU87 4.2 23.1 1.0
N A:LYS184 4.3 29.1 1.0
CG A:GLU183 4.6 30.4 1.0
CA A:GLU183 4.7 26.9 1.0
CB A:LYS184 4.9 33.7 1.0
CB A:GLU87 5.0 17.6 1.0

Reference:

D.A.Wah, A.Romero, F.Gallego, B.S.Cavada, M.V.Ramos, T.B.Grangeiro, A.H.Sampaio, J.J.Calvete. Crystal Structure of Native and Cd/Cd-Substituted Dioclea Guianensis Seed Lectin. A Novel Manganese-Binding Site and Structural Basis of Dimer-Tetramer Association J.Mol.Biol. V. 310 885 2001.
ISSN: ISSN 0022-2836
PubMed: 11453695
DOI: 10.1006/JMBI.2001.4814
Page generated: Thu Jul 11 10:00:00 2024

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