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Manganese in PDB 2ef6: Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome

Protein crystallography data

The structure of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome, PDB code: 2ef6 was solved by F.B.M.B.Moreno, G.A.Bezerra, T.M.Oliveira, E.P.De Souza, B.A.M.Da Rocha, R.G.Benevides, P.Delatorre, B.S.Cavada, W.F.De Azevedo Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.92 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 69.391, 69.391, 161.298, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 24.5

Other elements in 2ef6:

The structure of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome (pdb code 2ef6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome, PDB code: 2ef6:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2ef6

Go back to Manganese Binding Sites List in 2ef6
Manganese binding site 1 out of 4 in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn239

b:17.9
occ:1.00
O A:HOH1118 2.1 17.5 1.0
OD2 A:ASP10 2.1 11.8 1.0
OE2 A:GLU8 2.1 12.5 1.0
NE2 A:HIS24 2.2 12.8 1.0
O A:HOH1063 2.4 16.1 1.0
OD1 A:ASP19 2.5 16.2 1.0
CE1 A:HIS24 3.0 13.3 1.0
CG A:ASP10 3.1 17.5 1.0
CD A:GLU8 3.2 14.6 1.0
CG A:ASP19 3.2 22.1 1.0
CD2 A:HIS24 3.2 16.9 1.0
CB A:ASP10 3.5 16.8 1.0
OD2 A:ASP19 3.5 23.2 1.0
OE1 A:GLU8 3.5 14.8 1.0
O A:HOH1037 3.7 13.8 1.0
CA A:CA238 4.0 18.2 1.0
O A:HOH1038 4.0 30.4 1.0
OG A:SER34 4.1 16.6 1.0
ND1 A:HIS24 4.2 12.4 1.0
O A:HOH1089 4.2 29.6 1.0
OD1 A:ASP10 4.2 16.2 1.0
O A:VAL32 4.3 14.3 1.0
CG A:HIS24 4.3 14.7 1.0
CG A:GLU8 4.5 12.9 1.0
CB A:ASP19 4.5 20.3 1.0
CA A:ASP19 4.8 20.4 1.0
CA A:ASP10 5.0 16.0 1.0

Manganese binding site 2 out of 4 in 2ef6

Go back to Manganese Binding Sites List in 2ef6
Manganese binding site 2 out of 4 in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn239

b:17.5
occ:1.00
O B:HOH1033 2.0 13.6 1.0
OD2 B:ASP10 2.1 11.4 1.0
NE2 B:HIS24 2.2 14.9 1.0
OE2 B:GLU8 2.2 10.0 1.0
O B:HOH1138 2.2 18.9 1.0
OD1 B:ASP19 2.3 18.4 1.0
CE1 B:HIS24 3.0 14.8 1.0
CG B:ASP19 3.1 21.1 1.0
CG B:ASP10 3.2 16.8 1.0
CD B:GLU8 3.2 13.3 1.0
CD2 B:HIS24 3.3 20.0 1.0
OD2 B:ASP19 3.5 23.1 1.0
OE1 B:GLU8 3.5 17.2 1.0
CB B:ASP10 3.5 15.7 1.0
O B:HOH1063 3.7 15.1 1.0
CA B:CA238 4.1 17.7 1.0
OG B:SER34 4.2 14.7 1.0
ND1 B:HIS24 4.2 15.0 1.0
OD1 B:ASP10 4.3 16.8 1.0
CG B:HIS24 4.4 16.0 1.0
O B:HOH1064 4.4 31.8 1.0
O B:VAL32 4.4 13.3 1.0
CB B:ASP19 4.4 21.4 1.0
CG B:GLU8 4.5 11.1 1.0
CA B:ASP19 4.7 20.9 1.0

Manganese binding site 3 out of 4 in 2ef6

Go back to Manganese Binding Sites List in 2ef6
Manganese binding site 3 out of 4 in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn239

b:22.7
occ:1.00
OD2 C:ASP10 2.2 19.7 1.0
OE2 C:GLU8 2.2 19.2 1.0
O C:HOH1078 2.3 21.6 1.0
O C:HOH1079 2.3 16.7 1.0
NE2 C:HIS24 2.3 15.7 1.0
OD1 C:ASP19 2.4 21.2 1.0
CG C:ASP19 3.1 25.1 1.0
CG C:ASP10 3.1 21.0 1.0
CD2 C:HIS24 3.2 18.3 1.0
CD C:GLU8 3.3 18.7 1.0
CE1 C:HIS24 3.3 16.5 1.0
OD2 C:ASP19 3.4 25.2 1.0
CB C:ASP10 3.5 19.2 1.0
OE1 C:GLU8 3.7 22.4 1.0
O C:HOH1032 3.9 12.1 1.0
CA C:CA238 4.1 20.0 1.0
CB C:ASP19 4.2 24.1 1.0
OG C:SER34 4.2 18.4 1.0
OD1 C:ASP10 4.2 19.5 1.0
O C:HOH1053 4.2 34.2 1.0
CG C:HIS24 4.4 17.0 1.0
ND1 C:HIS24 4.4 17.8 1.0
O C:VAL32 4.4 23.9 1.0
CA C:ASP19 4.5 25.1 1.0
CG C:GLU8 4.6 17.6 1.0
CD C:PRO20 5.0 24.9 1.0

Manganese binding site 4 out of 4 in 2ef6

Go back to Manganese Binding Sites List in 2ef6
Manganese binding site 4 out of 4 in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn239

b:23.9
occ:1.00
OD2 D:ASP10 2.0 20.4 1.0
O D:HOH1068 2.1 17.6 1.0
OE2 D:GLU8 2.2 18.8 1.0
NE2 D:HIS24 2.2 14.2 1.0
OD1 D:ASP19 2.4 23.7 1.0
CG D:ASP10 3.1 21.0 1.0
CG D:ASP19 3.1 26.7 1.0
CD2 D:HIS24 3.2 18.9 1.0
CE1 D:HIS24 3.2 15.6 1.0
CD D:GLU8 3.2 17.4 1.0
OD2 D:ASP19 3.5 24.9 1.0
CB D:ASP10 3.5 20.9 1.0
OE1 D:GLU8 3.6 22.1 1.0
O D:HOH1043 3.9 19.1 1.0
OD1 D:ASP10 4.1 18.4 1.0
CA D:CA238 4.1 21.6 1.0
OG D:SER34 4.2 18.4 1.0
CB D:ASP19 4.3 24.7 1.0
ND1 D:HIS24 4.3 17.3 1.0
CG D:HIS24 4.3 18.3 1.0
O D:VAL32 4.5 21.8 1.0
CG D:GLU8 4.5 16.0 1.0
CA D:ASP19 4.6 25.9 1.0

Reference:

G.A.Bezerra, T.M.Oliveira, F.B.M.B.Moreno, E.P.De Souza, B.A.M.Da Rocha, R.G.Benevides, P.Delatorre, W.F.De Azevedo Jr., B.S.Cavada. Structural Analysis of Canavalia Maritima and Canavalia Gladiata Lectins Complexed with Different Dimannosides: New Insights Into the Understanding of the Structure-Biological Activity Relationship in Legume Lectins J.Struct.Biol. V. 160 168 2007.
ISSN: ISSN 1047-8477
PubMed: 17881248
DOI: 10.1016/J.JSB.2007.07.012
Page generated: Sat Oct 5 13:58:42 2024

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