Atomistry » Manganese » PDB 5svc-5uqn » 5t7p
Atomistry »
  Manganese »
    PDB 5svc-5uqn »
      5t7p »

Manganese 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
Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 2 in 5t7p

Go back to Manganese Binding Sites List in 5t7p
Manganese 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 Manganese with other atoms in the Mn 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:Mn301

b:19.3
occ:1.00
OD2 A:ASP121 2.1 14.1 1.0
NE2 A:HIS136 2.2 12.3 1.0
OD1 A:ASP129 2.2 17.8 1.0
OE1 A:GLU119 2.2 11.9 1.0
O A:HOH429 2.3 16.9 1.0
O A:HOH408 2.3 11.0 1.0
CE1 A:HIS136 3.1 15.3 1.0
CD A:GLU119 3.1 12.8 1.0
CG A:ASP129 3.1 18.4 1.0
CG A:ASP121 3.2 13.5 1.0
CD2 A:HIS136 3.2 16.0 1.0
OE2 A:GLU119 3.4 10.0 1.0
CB A:ASP121 3.6 13.3 1.0
OD2 A:ASP129 3.6 15.3 1.0
O A:HOH449 3.7 13.9 1.0
CA A:CA302 4.1 16.3 1.0
ND1 A:HIS136 4.2 19.1 1.0
OD1 A:ASP121 4.2 15.2 1.0
OG A:SER146 4.3 17.1 1.0
CG A:HIS136 4.3 16.0 1.0
CB A:ASP129 4.4 13.6 1.0
O A:ILE144 4.4 15.0 1.0
CD1 A:TRP128 4.5 15.9 1.0
CG A:GLU119 4.5 14.4 1.0
CD A:PRO130 4.5 15.2 1.0
NE1 A:TRP128 4.5 16.4 1.0
O A:HOH435 4.6 15.1 1.0
CA A:ASP129 4.7 16.2 1.0

Manganese binding site 2 out of 2 in 5t7p

Go back to Manganese Binding Sites List in 5t7p
Manganese 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 Manganese with other atoms in the Mn 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:Mn301

b:22.3
occ:1.00
O B:HOH467 2.1 15.0 1.0
OD2 B:ASP121 2.1 13.4 1.0
NE2 B:HIS136 2.2 20.0 1.0
OE1 B:GLU119 2.2 17.7 1.0
OD1 B:ASP129 2.3 17.4 1.0
O B:HOH414 2.4 17.5 1.0
CE1 B:HIS136 3.0 18.2 1.0
CG B:ASP121 3.2 16.2 1.0
CD B:GLU119 3.2 19.1 1.0
CD2 B:HIS136 3.2 18.7 1.0
CG B:ASP129 3.3 20.6 1.0
OE2 B:GLU119 3.5 15.1 1.0
CB B:ASP121 3.5 17.0 1.0
O B:HOH430 3.8 20.2 1.0
OD2 B:ASP129 3.8 19.3 1.0
CA B:CA302 4.1 19.1 1.0
ND1 B:HIS136 4.2 18.8 1.0
OG B:SER146 4.2 19.9 1.0
OD1 B:ASP121 4.3 14.8 1.0
CG B:HIS136 4.3 20.1 1.0
CB B:ASP129 4.4 18.4 1.0
O B:ILE144 4.5 20.0 1.0
CD B:PRO130 4.5 21.5 1.0
CG B:GLU119 4.6 18.0 1.0
NE1 B:TRP128 4.6 20.9 1.0
CD1 B:TRP128 4.6 21.5 1.0
O B:HOH452 4.6 19.4 1.0
CA B:ASP129 4.7 19.6 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: Tue Dec 15 04:46:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy