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Manganese in PDB 1tei: Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man

Protein crystallography data

The structure of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man, PDB code: 1tei was solved by J.H.Naismith, D.N.Moothoo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.500, 122.800, 124.600, 90.00, 134.20, 90.00
R / Rfree (%) 17.9 / 21.9

Other elements in 1tei:

The structure of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man (pdb code 1tei). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man, PDB code: 1tei:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1tei

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Manganese binding site 1 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:28.7
occ:1.00
 OD2 A:ASP10 2.0 9.4 1.0
O A:HOH247 2.1 21.8 1.0
O A:HOH246 2.2 32.6 1.0
OD1 A:ASP19 2.2 27.9 1.0
OE2 A:GLU8 2.4 21.4 1.0
NE2 A:HIS24 2.4 16.5 1.0
CG A:ASP19 3.1 25.0 1.0
CG A:ASP10 3.1 15.8 1.0
CE1 A:HIS24 3.3 14.9 1.0
CD A:GLU8 3.3 20.0 1.0
CD2 A:HIS24 3.3 17.6 1.0
OD2 A:ASP19 3.3 24.0 1.0
OE1 A:GLU8 3.5 16.6 1.0
CB A:ASP10 3.5 13.1 1.0
O A:HOH245 4.0 4.5 1.0
OG A:SER34 4.1 19.1 1.0
OD1 A:ASP10 4.2 19.0 1.0
CA A:CA239 4.3 18.9 1.0
CB A:ASP19 4.4 26.8 1.0
ND1 A:HIS24 4.4 16.8 1.0
CG A:HIS24 4.5 17.9 1.0
CG A:GLU8 4.7 13.8 1.0
O A:VAL32 4.7 16.4 1.0
CA A:ASP19 4.8 25.4 1.0

Manganese binding site 2 out of 8 in 1tei

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Manganese binding site 2 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:24.1
occ:1.00
 OD2 B:ASP10 1.9 20.5 1.0
O B:HOH247 2.3 15.1 1.0
O B:HOH246 2.3 24.7 1.0
OD1 B:ASP19 2.3 36.5 1.0
OE2 B:GLU8 2.4 36.3 1.0
NE2 B:HIS24 2.4 29.2 1.0
CG B:ASP10 3.0 24.7 1.0
CG B:ASP19 3.1 32.7 1.0
CE1 B:HIS24 3.2 28.6 1.0
OD2 B:ASP19 3.3 27.8 1.0
CD B:GLU8 3.3 28.9 1.0
CB B:ASP10 3.4 21.2 1.0
CD2 B:HIS24 3.4 28.9 1.0
OE1 B:GLU8 3.6 26.9 1.0
O B:HOH245 3.9 27.5 1.0
CA B:CA239 4.0 27.0 1.0
OD1 B:ASP10 4.1 20.0 1.0
OG B:SER34 4.2 22.0 1.0
ND1 B:HIS24 4.4 31.5 1.0
CB B:ASP19 4.4 33.9 1.0
CG B:HIS24 4.5 28.2 1.0
O B:VAL32 4.7 24.6 1.0
CG B:GLU8 4.7 24.3 1.0
CA B:ASP19 4.9 35.3 1.0
CA B:ASP10 4.9 22.7 1.0

Manganese binding site 3 out of 8 in 1tei

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Manganese binding site 3 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:24.4
occ:1.00
 O C:HOH247 2.0 19.8 1.0
O C:HOH246 2.0 21.1 1.0
OD2 C:ASP10 2.1 9.4 1.0
OE2 C:GLU8 2.3 24.1 1.0
NE2 C:HIS24 2.4 20.2 1.0
OD1 C:ASP19 2.4 28.8 1.0
CG C:ASP10 3.1 16.7 1.0
CG C:ASP19 3.2 30.1 1.0
CE1 C:HIS24 3.3 23.1 1.0
CD C:GLU8 3.3 21.4 1.0
CD2 C:HIS24 3.4 24.5 1.0
OD2 C:ASP19 3.4 21.1 1.0
CB C:ASP10 3.5 15.8 1.0
OE1 C:GLU8 3.7 21.8 1.0
O C:HOH245 4.0 9.2 1.0
OG C:SER34 4.1 22.4 1.0
OD1 C:ASP10 4.2 15.3 1.0
CA C:CA239 4.3 22.3 1.0
ND1 C:HIS24 4.4 23.3 1.0
CB C:ASP19 4.5 31.0 1.0
CG C:HIS24 4.5 26.6 1.0
O C:VAL32 4.7 25.9 1.0
CG C:GLU8 4.7 18.9 1.0
CA C:ASP19 4.8 33.9 1.0
CA C:ASP10 5.0 20.3 1.0

Manganese binding site 4 out of 8 in 1tei

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Manganese binding site 4 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:32.9
occ:1.00
 O D:HOH245 2.0 28.6 1.0
OD2 D:ASP10 2.1 13.4 1.0
OD1 D:ASP19 2.3 32.1 1.0
OE2 D:GLU8 2.4 25.2 1.0
NE2 D:HIS24 2.4 18.5 1.0
CG D:ASP19 3.1 29.7 1.0
CG D:ASP10 3.2 19.1 1.0
CE1 D:HIS24 3.3 23.3 1.0
CD D:GLU8 3.4 26.2 1.0
OD2 D:ASP19 3.4 24.2 1.0
CD2 D:HIS24 3.4 24.1 1.0
CB D:ASP10 3.6 18.5 1.0
OE1 D:GLU8 3.6 26.8 1.0
OG D:SER34 4.1 16.5 1.0
CA D:CA239 4.2 33.0 1.0
OD1 D:ASP10 4.3 19.2 1.0
CB D:ASP19 4.4 32.6 1.0
ND1 D:HIS24 4.4 28.3 1.0
CG D:HIS24 4.5 30.4 1.0
O D:VAL32 4.6 23.3 1.0
CG D:GLU8 4.7 25.2 1.0
CA D:ASP19 4.7 33.2 1.0
CD D:PRO20 5.0 41.0 1.0

Manganese binding site 5 out of 8 in 1tei

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Manganese binding site 5 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn238

b:24.2
occ:1.00
 O E:HOH247 2.0 12.3 1.0
O E:HOH246 2.1 34.0 1.0
OD1 E:ASP19 2.2 27.3 1.0
OD2 E:ASP10 2.2 8.4 1.0
OE2 E:GLU8 2.3 22.9 1.0
NE2 E:HIS24 2.5 20.1 1.0
CG E:ASP19 3.1 25.4 1.0
CD E:GLU8 3.3 21.3 1.0
CG E:ASP10 3.3 16.2 1.0
O E:HOH245 3.3 14.5 1.0
OD2 E:ASP19 3.4 22.4 1.0
CE1 E:HIS24 3.4 22.6 1.0
OE1 E:GLU8 3.5 16.7 1.0
CD2 E:HIS24 3.5 21.7 1.0
CB E:ASP10 3.7 15.7 1.0
OG E:SER34 4.0 10.3 1.0
CA E:CA239 4.1 13.3 1.0
OD1 E:ASP10 4.4 12.5 1.0
CB E:ASP19 4.4 25.5 1.0
O E:VAL32 4.5 24.6 1.0
ND1 E:HIS24 4.6 24.4 1.0
CG E:HIS24 4.7 22.1 1.0
CG E:GLU8 4.7 17.3 1.0
CA E:ASP19 4.8 28.6 1.0

Manganese binding site 6 out of 8 in 1tei

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Manganese binding site 6 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn238

b:50.1
occ:1.00
 O F:HOH246 1.9 16.0 1.0
OD2 F:ASP10 2.2 23.2 1.0
O F:HOH245 2.2 29.4 1.0
OE2 F:GLU8 2.3 40.2 1.0
OD1 F:ASP19 2.4 48.0 1.0
NE2 F:HIS24 2.4 36.4 1.0
CG F:ASP19 3.2 47.9 1.0
CG F:ASP10 3.2 29.9 1.0
CD F:GLU8 3.3 34.8 1.0
CE1 F:HIS24 3.3 40.4 1.0
CD2 F:HIS24 3.4 38.3 1.0
OD2 F:ASP19 3.5 46.2 1.0
OE1 F:GLU8 3.5 33.1 1.0
CB F:ASP10 3.7 28.1 1.0
OG F:SER34 3.9 24.3 1.0
CA F:CA239 4.3 52.5 1.0
OD1 F:ASP10 4.4 31.4 1.0
ND1 F:HIS24 4.4 42.8 1.0
O F:VAL32 4.5 34.4 1.0
CB F:ASP19 4.5 48.5 1.0
CG F:HIS24 4.5 39.9 1.0
CG F:GLU8 4.6 32.5 1.0
CA F:ASP19 4.8 48.2 1.0
CD F:PRO20 5.0 51.8 1.0

Manganese binding site 7 out of 8 in 1tei

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Manganese binding site 7 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn238

b:32.7
occ:1.00
 O G:HOH247 2.1 13.9 1.0
OD2 G:ASP10 2.1 19.1 1.0
OE2 G:GLU8 2.2 32.8 1.0
NE2 G:HIS24 2.3 26.6 1.0
O G:HOH246 2.4 17.4 1.0
OD1 G:ASP19 2.4 31.7 1.0
CG G:ASP10 3.1 19.3 1.0
CD G:GLU8 3.2 29.1 1.0
CD2 G:HIS24 3.2 30.5 1.0
CG G:ASP19 3.3 31.4 1.0
CE1 G:HIS24 3.3 25.9 1.0
OE1 G:GLU8 3.5 28.6 1.0
CB G:ASP10 3.5 20.8 1.0
OD2 G:ASP19 3.6 30.7 1.0
OG G:SER34 4.0 26.6 1.0
O G:HOH245 4.1 29.3 1.0
OD1 G:ASP10 4.3 23.1 1.0
CG G:HIS24 4.4 32.3 1.0
ND1 G:HIS24 4.4 31.2 1.0
CA G:CA239 4.4 31.6 1.0
CG G:GLU8 4.6 25.4 1.0
CB G:ASP19 4.6 28.3 1.0
O G:VAL32 4.6 21.9 1.0
CA G:ASP19 4.9 33.5 1.0

Manganese binding site 8 out of 8 in 1tei

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Manganese binding site 8 out of 8 in the Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Concanavalin A Complexed to Beta-D-Glcnac (1,2)Alpha-D- Man-(1,6)[Beta-D-Glcnac(1,2)Alpha-D-Man (1,6)]Alpha-D-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn245

b:42.6
occ:1.00
 OD2 H:ASP10 2.2 25.9 1.0
OD1 H:ASP19 2.2 47.0 1.0
OE2 H:GLU8 2.3 35.5 1.0
NE2 H:HIS24 2.4 33.0 1.0
O H:HOH248 2.6 15.9 1.0
CG H:ASP19 3.2 41.5 1.0
CD H:GLU8 3.2 33.3 1.0
CE1 H:HIS24 3.3 36.2 1.0
CG H:ASP10 3.3 27.7 1.0
CD2 H:HIS24 3.4 36.2 1.0
OE1 H:GLU8 3.4 33.5 1.0
OD2 H:ASP19 3.5 35.8 1.0
CB H:ASP10 3.7 28.1 1.0
OG H:SER34 3.9 42.4 1.0
O H:HOH247 4.1 18.7 1.0
CA H:CA246 4.3 47.6 1.0
OD1 H:ASP10 4.4 25.1 1.0
ND1 H:HIS24 4.4 38.4 1.0
CB H:ASP19 4.5 41.8 1.0
CG H:HIS24 4.5 36.4 1.0
O H:VAL32 4.5 36.4 1.0
CG H:GLU8 4.6 31.9 1.0
CA H:ASP19 4.8 41.9 1.0
CD H:PRO20 5.0 45.5 1.0

Reference:

D.N.Moothoo, J.H.Naismith. Concanavalin A Distorts the Beta-Glcnac-(1-->2)-Man Linkage of Beta-Glcnac-(1-->2)-Alpha-Man-(1-->3)-[Beta-Glcnac-(1-- >2)-Alpha-Man- (1-->6)]-Man Upon Binding. Glycobiology V. 8 173 1998.
ISSN: ISSN 0959-6658
PubMed: 9451027
DOI: 10.1093/GLYCOB/8.2.173
Page generated: Sat Oct 5 12:34:18 2024

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