Calcium in PDB 5t7p: Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man

Protein crystallography data

The structure of Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man, PDB code: 5t7p was solved by V.R.Pinto-Junior, M.Q.Santiago, V.J.S.Osterne, J.C.Silva-Filho, B.A.M.Rocha, P.Delatorre, K.S.Nascimento, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.28 / 2.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.770, 62.970, 66.740, 90.00, 94.27, 90.00
R / Rfree (%) 17 / 22.1

Other elements in 5t7p:

The structure of Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Manganese (Mn) 2 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man (pdb code 5t7p). 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 Pisum Arvense Lectin (Pal) Complexed with X-Man, PDB code: 5t7p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5t7p

Go back to Calcium Binding Sites List in 5t7p
Calcium binding site 1 out of 2 in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man


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 Pisum Arvense Lectin (Pal) Complexed with X-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:16.3
occ:1.00
O A:PHE123 2.3 15.9 1.0
OD2 A:ASP129 2.3 15.3 1.0
O A:HOH449 2.4 13.9 1.0
OD1 A:ASN125 2.4 16.2 1.0
OD1 A:ASP121 2.4 15.2 1.0
O A:HOH507 2.4 15.2 1.0
OD2 A:ASP121 2.5 14.1 1.0
CG A:ASP121 2.8 13.5 1.0
CG A:ASP129 3.4 18.4 1.0
C A:PHE123 3.5 17.0 1.0
CG A:ASN125 3.5 16.7 1.0
OD1 A:ASP129 3.8 17.8 1.0
N A:ASN125 3.9 18.2 1.0
CB A:ASN125 4.1 15.4 1.0
MN A:MN301 4.1 19.3 1.0
NE1 A:TRP128 4.2 16.4 1.0
CB A:ASP121 4.3 13.3 1.0
CA A:PHE123 4.3 18.6 1.0
N A:PHE123 4.3 16.0 1.0
O A:GLY99 4.4 17.0 1.0
N A:TYR124 4.5 15.2 1.0
O A:HOH408 4.5 11.0 1.0
CB A:PHE123 4.5 14.4 1.0
C A:TYR124 4.6 17.8 1.0
CA A:TYR124 4.6 20.3 1.0
ND2 A:ASN125 4.6 13.6 1.0
CA A:ASN125 4.6 18.3 1.0
CA A:GLY99 4.7 18.6 1.0
CB A:ASP129 4.7 13.6 1.0
CE1 A:HIS136 4.7 15.3 1.0
O A:ASP81 4.8 14.3 1.0
CD2 A:PHE123 4.9 17.4 1.0

Calcium binding site 2 out of 2 in 5t7p

Go back to Calcium Binding Sites List in 5t7p
Calcium binding site 2 out of 2 in the Crystal Structure of Pisum Arvense Lectin (Pal) Complexed with X-Man


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 Pisum Arvense Lectin (Pal) Complexed with X-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:19.1
occ:1.00
O B:PHE123 2.2 21.5 1.0
OD2 B:ASP129 2.3 19.3 1.0
OD1 B:ASN125 2.4 20.4 1.0
O B:HOH430 2.4 20.2 1.0
OD2 B:ASP121 2.5 13.4 1.0
OD1 B:ASP121 2.5 14.8 1.0
O B:HOH461 2.6 20.3 1.0
CG B:ASP121 2.8 16.2 1.0
CG B:ASP129 3.3 20.6 1.0
C B:PHE123 3.4 21.0 1.0
CG B:ASN125 3.5 23.2 1.0
OD1 B:ASP129 3.7 17.4 1.0
N B:ASN125 3.9 24.6 1.0
CB B:ASN125 4.1 19.4 1.0
MN B:MN301 4.1 22.3 1.0
CA B:PHE123 4.3 19.3 1.0
N B:PHE123 4.3 20.9 1.0
NE1 B:TRP128 4.3 20.9 1.0
CB B:ASP121 4.3 17.0 1.0
O B:HOH414 4.4 17.5 1.0
N B:TYR124 4.4 18.5 1.0
O B:GLY99 4.4 21.1 1.0
CB B:PHE123 4.4 19.0 1.0
C B:TYR124 4.5 22.4 1.0
CA B:TYR124 4.5 19.8 1.0
ND2 B:ASN125 4.6 18.0 1.0
CA B:ASN125 4.6 23.0 1.0
O B:ASP81 4.6 21.4 1.0
CB B:ASP129 4.7 18.4 1.0
CA B:GLY99 4.7 19.5 1.0
CD2 B:PHE123 4.7 20.5 1.0
CE1 B:HIS136 4.8 18.2 1.0
OD1 B:ASP81 5.0 20.8 1.0

Reference:

V.R.Pinto-Junior, M.Q.Santiago, C.B.Nobre, V.J.S.Osterne, R.B.Leal, J.B.Cajazeiras, C.F.Lossio, B.A.M.Rocha, M.G.Q.Martins, C.A.S.Nobre, M.T.L.Silva, K.S.Nascimento, B.S.Cavada. Crystal Structure of Pisum Arvense Seed Lectin (Pal) and Characterization of Its Interaction with Carbohydrates By Molecular Docking and Dynamics. Arch. Biochem. Biophys. V. 630 27 2017.
ISSN: ESSN 1096-0384
PubMed: 28754321
DOI: 10.1016/J.ABB.2017.07.013
Page generated: Sat Dec 12 05:43:46 2020

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