Atomistry » Calcium » PDB 4xut-4y9b » 4xxa
Atomistry »
  Calcium »
    PDB 4xut-4y9b »
      4xxa »

Calcium in PDB 4xxa: Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin

Protein crystallography data

The structure of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin, PDB code: 4xxa was solved by B.L.Sousa, J.C.Silva-Filho, P.Kumar, A.Lyskowski, G.A.Bezerra, P.Delatorre, B.A.M.Rocha, R.M.S.Cunha, C.S.Nagano, K.Gruber, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.21 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.083, 96.083, 85.099, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.5

Other elements in 4xxa:

The structure of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin (pdb code 4xxa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin, PDB code: 4xxa:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4xxa

Go back to Calcium Binding Sites List in 4xxa
Calcium binding site 1 out of 2 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:35.2
occ:1.00
OD2 A:ASP126 2.2 31.9 1.0
O A:HOH433 2.3 30.0 1.0
OD2 A:ASP133 2.3 41.3 1.0
O A:PHE128 2.4 40.0 1.0
ND2 A:ASN130 2.5 34.7 1.0
OD1 A:ASP126 2.5 33.4 1.0
O A:HOH429 2.5 30.0 1.0
CG A:ASP126 2.7 31.4 1.0
CG A:ASP133 3.5 41.6 1.0
C A:PHE128 3.6 39.5 1.0
CG A:ASN130 3.7 44.1 1.0
OD1 A:ASP133 4.0 37.3 1.0
N A:ASN130 4.0 44.6 1.0
MN A:MN302 4.1 35.2 1.0
CB A:ASP126 4.2 30.5 1.0
CB A:ASN130 4.2 42.7 1.0
O A:HOH465 4.3 30.0 1.0
N A:PHE128 4.4 35.2 1.0
CA A:PHE128 4.4 38.9 1.0
NE1 A:TRP132 4.4 42.4 1.0
O A:ASP88 4.5 34.1 1.0
O A:GLY106 4.5 35.3 1.0
CB A:PHE128 4.6 39.3 1.0
N A:SER129 4.6 42.3 1.0
OD1 A:ASP88 4.6 35.5 1.0
OD1 A:ASN130 4.6 44.0 1.0
CE1 A:HIS138 4.6 40.6 1.0
CB A:ASP133 4.7 44.8 1.0
CA A:SER129 4.7 42.2 1.0
CA A:ASN130 4.8 45.7 1.0
CA A:GLY106 4.8 37.3 1.0
C A:SER129 4.8 44.9 1.0
CD2 A:PHE128 4.9 41.3 1.0
NE2 A:HIS138 5.0 39.4 1.0

Calcium binding site 2 out of 2 in 4xxa

Go back to Calcium Binding Sites List in 4xxa
Calcium binding site 2 out of 2 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:35.2
occ:1.00
OD2 B:ASP126 2.1 31.1 1.0
O B:PHE128 2.3 36.9 1.0
OD2 B:ASP133 2.4 32.2 1.0
O B:HOH427 2.4 30.0 1.0
OD1 B:ASP126 2.5 26.3 1.0
ND2 B:ASN130 2.5 26.0 1.0
O B:HOH442 2.6 30.0 1.0
CG B:ASP126 2.6 26.7 1.0
CG B:ASP133 3.5 34.0 1.0
C B:PHE128 3.5 33.3 1.0
CG B:ASN130 3.7 35.4 1.0
N B:ASN130 4.0 36.4 1.0
OD1 B:ASP133 4.0 29.0 1.0
MN B:MN302 4.1 35.2 1.0
CB B:ASP126 4.1 28.3 1.0
CB B:ASN130 4.2 32.2 1.0
O B:HOH472 4.2 27.4 1.0
CA B:PHE128 4.4 34.5 1.0
N B:PHE128 4.4 33.4 1.0
NE1 B:TRP132 4.4 40.3 1.0
O B:GLY106 4.5 31.6 1.0
N B:SER129 4.5 37.5 1.0
O B:ASP88 4.5 31.3 1.0
CA B:GLY106 4.7 29.6 1.0
CA B:SER129 4.7 34.4 1.0
CB B:ASP133 4.7 33.3 1.0
CB B:PHE128 4.7 35.6 1.0
OD1 B:ASN130 4.7 33.7 1.0
OD1 B:ASP88 4.7 35.8 1.0
CA B:ASN130 4.7 35.4 1.0
C B:SER129 4.8 36.3 1.0
CE1 B:HIS138 4.8 30.6 1.0
CD2 B:PHE128 4.9 38.0 1.0

Reference:

B.L.Sousa, J.C.Silva-Filho, P.Kumar, A.Lyskowski, G.A.Bezerra, P.Delatorre, B.A.M.Rocha, R.M.S.Cunha, C.S.Nagano, K.Gruber, B.S.Cavada. Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Int.J.Biochem.Cell Biol. 2016.
ISSN: ISSN 1357-2725
Page generated: Sun Jul 14 14:44:55 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy