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Calcium in PDB 5tg3: Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man

Protein crystallography data

The structure of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man, PDB code: 5tg3 was solved by M.Q.Santiago, J.L.A.Correia, V.R.Pinto-Junior, V.J.S.Osterne, R.I.Pereira, J.C.Silva-Filho, C.F.Lossio, B.A.M.Rocha, P.Delatorre, A.H.B.Neco, D.A.Araripe, 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) 33.85 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.460, 85.180, 174.580, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.9

Other elements in 5tg3:

The structure of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Bromine (Br) 4 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man (pdb code 5tg3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man, PDB code: 5tg3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5tg3

Go back to Calcium Binding Sites List in 5tg3
Calcium binding site 1 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex 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 Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:11.6
occ:1.00
 OD1 A:ASN14 2.4 17.4 1.0
OD2 A:ASP19 2.4 15.1 1.0
O A:HOH445 2.4 13.5 1.0
O A:TYR12 2.4 14.7 1.0
O A:HOH419 2.5 16.5 1.0
OD1 A:ASP10 2.5 11.1 1.0
OD2 A:ASP10 2.5 14.1 1.0
CG A:ASP10 2.9 16.6 1.0
CG A:ASP19 3.5 19.1 1.0
CG A:ASN14 3.5 17.4 1.0
C A:TYR12 3.7 14.6 1.0
OD1 A:ASP19 3.9 16.5 1.0
N A:ASN14 4.0 19.3 1.0
CB A:ASN14 4.1 16.9 1.0
MN A:MN302 4.2 14.0 1.0
CB A:ASP10 4.4 13.9 1.0
CA A:TYR12 4.5 14.3 1.0
N A:TYR12 4.5 13.1 1.0
O A:HOH442 4.6 16.0 1.0
CE1 A:HIS24 4.6 13.6 1.0
ND2 A:ASN14 4.6 14.8 1.0
N A:PRO13 4.6 15.3 1.0
CB A:TYR12 4.6 13.7 1.0
CA A:PRO13 4.7 13.7 1.0
CA A:ASN14 4.7 16.4 1.0
OD1 A:ASP208 4.7 12.6 1.0
O A:ARG228 4.7 14.8 1.0
C A:PRO13 4.7 19.8 1.0
CB A:ASP19 4.7 16.7 1.0
CB A:ARG228 4.8 13.7 1.0
CA A:ARG228 4.8 13.4 1.0
O A:ASP208 4.9 12.3 1.0
NE2 A:HIS24 4.9 12.9 1.0
CD2 A:TYR12 4.9 15.6 1.0

Calcium binding site 2 out of 4 in 5tg3

Go back to Calcium Binding Sites List in 5tg3
Calcium binding site 2 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex 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 Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:25.4
occ:1.00
 OD2 B:ASP19 2.4 20.3 1.0
O B:HOH437 2.4 21.6 1.0
O B:TYR12 2.4 19.9 1.0
OD1 B:ASP10 2.4 18.3 1.0
O B:HOH496 2.4 19.9 1.0
OD1 B:ASN14 2.4 24.9 1.0
OD2 B:ASP10 2.6 21.4 1.0
CG B:ASP10 2.8 22.3 1.0
CG B:ASP19 3.5 26.7 1.0
CG B:ASN14 3.6 24.3 1.0
C B:TYR12 3.6 21.5 1.0
OD1 B:ASP19 3.9 22.2 1.0
N B:ASN14 4.0 25.5 1.0
CB B:ASN14 4.1 24.8 1.0
MN B:MN302 4.2 83.6 1.0
CB B:ASP10 4.4 21.1 1.0
CA B:TYR12 4.4 21.4 1.0
N B:TYR12 4.5 23.0 1.0
N B:PRO13 4.5 20.9 1.0
CA B:PRO13 4.5 23.1 1.0
CB B:TYR12 4.6 21.3 1.0
C B:PRO13 4.6 26.1 1.0
CE1 B:HIS24 4.7 23.6 1.0
O B:HOH454 4.7 16.2 1.0
ND2 B:ASN14 4.7 22.8 1.0
CB B:ASP19 4.7 25.1 1.0
CA B:ASN14 4.7 25.5 1.0
OD1 B:ASP208 4.7 21.4 1.0
CB B:ARG228 4.8 21.4 1.0
CD2 B:TYR12 4.8 21.1 1.0
O B:ARG228 4.9 23.2 1.0
CA B:ARG228 4.9 22.9 1.0
O B:ASP208 4.9 18.9 1.0
NE2 B:HIS24 5.0 21.2 1.0

Calcium binding site 3 out of 4 in 5tg3

Go back to Calcium Binding Sites List in 5tg3
Calcium binding site 3 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:18.9
occ:1.00
 OD1 C:ASN14 2.2 20.6 1.0
O C:HOH483 2.4 22.3 1.0
O C:TYR12 2.4 25.3 1.0
OD2 C:ASP19 2.4 24.2 1.0
O C:HOH421 2.5 24.0 1.0
OD1 C:ASP10 2.5 19.3 1.0
OD2 C:ASP10 2.7 21.0 1.0
CG C:ASP10 3.0 19.3 1.0
CG C:ASN14 3.4 28.6 1.0
CG C:ASP19 3.6 26.3 1.0
C C:TYR12 3.6 23.6 1.0
N C:ASN14 3.9 20.9 1.0
CB C:ASN14 4.1 22.8 1.0
OD1 C:ASP19 4.1 17.8 1.0
MN C:MN302 4.3 18.2 1.0
ND2 C:ASN14 4.4 25.8 1.0
CA C:TYR12 4.5 25.5 1.0
CB C:ASP10 4.5 17.6 1.0
N C:TYR12 4.5 22.4 1.0
CB C:TYR12 4.6 26.5 1.0
N C:PRO13 4.6 24.1 1.0
CB C:ARG228 4.6 28.8 1.0
CA C:ASN14 4.6 23.4 1.0
CA C:PRO13 4.6 24.2 1.0
C C:PRO13 4.6 28.1 1.0
O C:HOH418 4.7 24.8 1.0
OD1 C:ASP208 4.7 24.5 1.0
CD2 C:TYR12 4.7 24.1 1.0
O C:ARG228 4.7 27.4 1.0
CA C:ARG228 4.7 28.4 1.0
CE1 C:HIS24 4.8 21.9 1.0
CB C:ASP19 4.8 19.7 1.0
O C:ASP208 4.9 22.4 1.0
NE2 C:HIS24 5.0 23.7 1.0

Calcium binding site 4 out of 4 in 5tg3

Go back to Calcium Binding Sites List in 5tg3
Calcium binding site 4 out of 4 in the Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Dioclea Reflexa Seed Lectin (Drfl) in Complex with X-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:24.1
occ:1.00
 OD1 D:ASN14 2.3 25.9 1.0
OD1 D:ASP10 2.3 21.5 1.0
O D:TYR12 2.4 23.5 1.0
OD2 D:ASP19 2.4 28.0 1.0
O D:HOH430 2.4 21.8 1.0
O D:HOH424 2.5 26.1 1.0
OD2 D:ASP10 2.6 20.3 1.0
CG D:ASP10 2.8 19.4 1.0
CG D:ASN14 3.4 31.6 1.0
CG D:ASP19 3.6 25.3 1.0
C D:TYR12 3.6 24.6 1.0
N D:ASN14 4.0 29.1 1.0
CB D:ASN14 4.0 27.9 1.0
OD1 D:ASP19 4.1 25.1 1.0
MN D:MN302 4.3 21.2 1.0
CB D:ASP10 4.3 19.0 1.0
CA D:TYR12 4.4 24.9 1.0
N D:TYR12 4.4 22.5 1.0
CA D:PRO13 4.5 23.0 1.0
N D:PRO13 4.5 25.3 1.0
ND2 D:ASN14 4.5 26.3 1.0
C D:PRO13 4.6 31.0 1.0
CB D:TYR12 4.6 26.0 1.0
CA D:ASN14 4.7 30.1 1.0
CE1 D:HIS24 4.7 22.6 1.0
OD1 D:ASP208 4.7 30.6 1.0
O D:ARG228 4.7 23.2 1.0
O D:ASP208 4.7 26.6 1.0
O D:HOH409 4.8 19.7 1.0
CB D:ASP19 4.8 22.3 1.0
CD2 D:TYR12 4.8 24.1 1.0
CA D:ARG228 4.8 30.2 1.0
CB D:ARG228 4.9 32.8 1.0

Reference:

V.R.Pinto-Junior, V.J.Osterne, M.Q.Santiago, J.L.Correia, F.N.Pereira-Junior, R.B.Leal, M.G.Pereira, L.S.Chicas, C.S.Nagano, B.A.Rocha, J.C.Silva-Filho, W.P.Ferreira, C.R.Rocha, K.S.Nascimento, A.M.Assreuy, B.S.Cavada. Structural Studies of A Vasorelaxant Lectin From Dioclea Reflexa Hook Seeds: Crystal Structure, Molecular Docking and Dynamics. Int. J. Biol. Macromol. V. 98 12 2017.
ISSN: ISSN 1879-0003
PubMed: 28130130
DOI: 10.1016/J.IJBIOMAC.2017.01.092
Page generated: Wed Jul 9 10:17:41 2025

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