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Calcium 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:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:18.9
occ:1.00
 O A:TYR12 2.3 21.3 1.0
OD1 A:ASN14 2.3 26.1 1.0
OD1 A:ASP10 2.5 19.0 1.0
O A:HOH245 2.5 4.5 1.0
OD2 A:ASP19 2.5 24.0 1.0
OD2 A:ASP10 2.7 9.4 1.0
CG A:ASP10 3.0 15.8 1.0
CG A:ASN14 3.5 21.2 1.0
C A:TYR12 3.5 20.2 1.0
CG A:ASP19 3.7 25.0 1.0
N A:ASN14 4.1 25.0 1.0
CB A:ASN14 4.2 25.7 1.0
OD1 A:ASP19 4.3 27.9 1.0
MN A:MN238 4.3 28.7 1.0
CA A:TYR12 4.3 18.2 1.0
N A:TYR12 4.4 20.1 1.0
CB A:ASP10 4.5 13.1 1.0
ND2 A:ASN14 4.5 21.1 1.0
N A:PRO13 4.5 20.9 1.0
O A:HOH246 4.5 32.6 1.0
CB A:TYR12 4.5 19.7 1.0
CA A:PRO13 4.5 23.4 1.0
OD2 A:ASP208 4.5 23.2 1.0
O A:ASP208 4.6 18.9 1.0
CB A:ARG228 4.6 18.5 1.0
C A:PRO13 4.7 24.7 1.0
CA A:ARG228 4.8 19.3 1.0
CE1 A:HIS24 4.8 14.9 1.0
CA A:ASN14 4.8 24.2 1.0
CD2 A:TYR12 4.9 13.3 1.0
CB A:ASP19 4.9 26.8 1.0
O A:ARG228 5.0 22.0 1.0

Calcium binding site 2 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:27.0
occ:1.00
 O B:HOH245 2.4 27.5 1.0
OD1 B:ASN14 2.4 36.6 1.0
OD2 B:ASP19 2.4 27.8 1.0
O B:TYR12 2.4 25.9 1.0
OD2 B:ASP10 2.5 20.5 1.0
OD1 B:ASP10 2.5 20.0 1.0
O B:HOH248 2.6 28.6 1.0
CG B:ASP10 2.9 24.7 1.0
CG B:ASN14 3.5 33.8 1.0
CG B:ASP19 3.6 32.7 1.0
C B:TYR12 3.6 24.7 1.0
MN B:MN238 4.0 24.1 1.0
N B:ASN14 4.0 31.2 1.0
OD1 B:ASP19 4.1 36.5 1.0
CB B:ASN14 4.1 32.5 1.0
CB B:ASP10 4.4 21.2 1.0
CA B:TYR12 4.5 24.2 1.0
CB B:ARG228 4.5 34.8 1.0
N B:TYR12 4.5 26.6 1.0
CA B:PRO13 4.5 27.1 1.0
N B:PRO13 4.6 25.9 1.0
O B:HOH246 4.6 24.7 1.0
C B:PRO13 4.6 28.7 1.0
ND2 B:ASN14 4.6 35.8 1.0
OD1 B:ASP208 4.7 28.8 1.0
O B:ASP208 4.7 20.6 1.0
CA B:ASN14 4.7 33.1 1.0
CE1 B:HIS24 4.7 28.6 1.0
CA B:ARG228 4.7 30.1 1.0
CB B:TYR12 4.7 25.0 1.0
CB B:ASP19 4.8 33.9 1.0
O B:ARG228 4.8 25.9 1.0

Calcium binding site 3 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:22.3
occ:1.00
 O C:HOH245 2.2 9.2 1.0
O C:TYR12 2.3 24.3 1.0
OD1 C:ASN14 2.4 32.2 1.0
O C:HOH257 2.4 24.8 1.0
OD1 C:ASP10 2.4 15.3 1.0
OD2 C:ASP19 2.5 21.1 1.0
OD2 C:ASP10 2.6 9.4 1.0
CG C:ASP10 2.9 16.7 1.0
C C:TYR12 3.5 22.8 1.0
CG C:ASN14 3.6 28.1 1.0
CG C:ASP19 3.7 30.1 1.0
N C:ASN14 4.1 32.1 1.0
OD1 C:ASP19 4.2 28.8 1.0
CB C:ASN14 4.3 27.3 1.0
MN C:MN238 4.3 24.4 1.0
OD2 C:ASP208 4.4 34.0 1.0
O C:HOH246 4.4 21.1 1.0
CB C:ASP10 4.4 15.8 1.0
CA C:TYR12 4.4 23.0 1.0
CA C:PRO13 4.5 29.7 1.0
N C:PRO13 4.5 25.5 1.0
N C:TYR12 4.5 25.7 1.0
O C:ASP208 4.5 18.4 1.0
ND2 C:ASN14 4.6 28.8 1.0
C C:PRO13 4.6 31.5 1.0
CB C:TYR12 4.6 22.8 1.0
CA C:ARG228 4.7 19.8 1.0
CB C:ARG228 4.7 21.3 1.0
O C:ARG228 4.8 23.9 1.0
CB C:ASP19 4.8 31.0 1.0
CA C:ASN14 4.9 27.7 1.0
CE1 C:HIS24 4.9 23.1 1.0

Calcium binding site 4 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:33.0
occ:1.00
 O D:TYR12 2.4 28.6 1.0
OD1 D:ASN14 2.5 33.4 1.0
OD1 D:ASP10 2.5 19.2 1.0
OD2 D:ASP19 2.5 24.2 1.0
OD2 D:ASP10 2.6 13.4 1.0
CG D:ASP10 2.8 19.1 1.0
CG D:ASN14 3.6 30.9 1.0
CG D:ASP19 3.6 29.7 1.0
C D:TYR12 3.7 27.0 1.0
OD1 D:ASP19 4.1 32.1 1.0
MN D:MN238 4.2 32.9 1.0
N D:ASN14 4.2 31.8 1.0
CB D:ASN14 4.3 31.6 1.0
CB D:ASP10 4.3 18.5 1.0
OD2 D:ASP208 4.5 33.8 1.0
O D:ASP208 4.5 24.8 1.0
CA D:TYR12 4.5 27.3 1.0
N D:TYR12 4.6 31.0 1.0
N D:PRO13 4.6 25.2 1.0
CA D:PRO13 4.6 26.6 1.0
ND2 D:ASN14 4.7 31.7 1.0
CB D:ARG228 4.7 30.4 1.0
CA D:ARG228 4.7 27.9 1.0
C D:PRO13 4.7 31.1 1.0
CB D:TYR12 4.8 28.2 1.0
CE1 D:HIS24 4.8 23.3 1.0
O D:ARG228 4.8 28.9 1.0
CB D:ASP19 4.9 32.6 1.0
CA D:ASN14 4.9 35.1 1.0

Calcium binding site 5 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:13.3
occ:1.00
 O E:HOH245 2.2 14.5 1.0
OD2 E:ASP19 2.3 22.4 1.0
O E:TYR12 2.3 24.9 1.0
OD1 E:ASN14 2.5 27.3 1.0
OD2 E:ASP10 2.5 8.4 1.0
O E:HOH262 2.6 20.7 1.0
OD1 E:ASP10 2.6 12.5 1.0
CG E:ASP10 2.9 16.2 1.0
CG E:ASP19 3.5 25.4 1.0
C E:TYR12 3.6 22.5 1.0
CG E:ASN14 3.6 22.2 1.0
N E:ASN14 4.0 26.8 1.0
OD1 E:ASP19 4.1 27.3 1.0
MN E:MN238 4.1 24.2 1.0
CB E:ASN14 4.1 23.7 1.0
CB E:ASP10 4.4 15.7 1.0
CA E:PRO13 4.4 24.9 1.0
CA E:TYR12 4.5 21.1 1.0
N E:PRO13 4.5 25.1 1.0
O E:HOH246 4.5 34.0 1.0
C E:PRO13 4.5 26.8 1.0
CB E:ARG228 4.6 7.4 1.0
N E:TYR12 4.6 22.7 1.0
ND2 E:ASN14 4.7 22.6 1.0
CB E:ASP19 4.7 25.5 1.0
CB E:TYR12 4.7 21.4 1.0
CA E:ARG228 4.7 9.0 1.0
CE1 E:HIS24 4.7 22.6 1.0
CA E:ASN14 4.7 25.0 1.0
OD2 E:ASP208 4.7 21.4 1.0
O E:ASP208 4.8 17.5 1.0
CD2 E:TYR12 4.9 20.5 1.0

Calcium binding site 6 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:52.5
occ:1.00
 O F:TYR12 2.0 30.6 0.0
OD2 F:ASP19 2.2 46.2 1.0
OD1 F:ASN14 2.4 59.9 1.0
OD1 F:ASP10 2.5 31.4 1.0
OD2 F:ASP10 2.7 23.2 1.0
CG F:ASP10 2.9 29.9 1.0
C F:TYR12 3.2 29.4 0.0
CG F:ASP19 3.4 47.9 1.0
CG F:ASN14 3.5 55.0 1.0
N F:ASN14 3.8 46.4 1.0
OD1 F:ASP19 4.0 48.0 1.0
CA F:PRO13 4.0 42.7 1.0
N F:PRO13 4.1 41.0 1.0
CB F:ASN14 4.1 51.0 1.0
C F:PRO13 4.2 44.9 1.0
CA F:TYR12 4.2 37.2 1.0
MN F:MN238 4.3 50.1 1.0
N F:TYR12 4.4 41.1 1.0
CB F:ASP10 4.4 28.1 1.0
CB F:ASP19 4.5 48.5 1.0
CE1 F:HIS24 4.5 40.4 1.0
CB F:TYR12 4.6 30.6 1.0
CA F:ASN14 4.6 49.9 1.0
ND2 F:ASN14 4.6 54.8 1.0
O F:HOH245 4.8 29.4 1.0
O F:ASP208 4.8 35.0 1.0
CD2 F:TYR12 4.9 24.4 0.0

Calcium binding site 7 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca239

b:31.6
occ:1.00
 O G:TYR12 2.4 26.5 1.0
OD1 G:ASN14 2.4 32.5 1.0
O G:HOH249 2.5 26.8 1.0
OD1 G:ASP10 2.5 23.1 1.0
OD2 G:ASP19 2.5 30.7 1.0
OD2 G:ASP10 2.7 19.1 1.0
O G:HOH245 2.8 29.3 1.0
CG G:ASP10 2.9 19.3 1.0
CG G:ASN14 3.6 25.6 1.0
C G:TYR12 3.6 26.2 1.0
CG G:ASP19 3.7 31.4 1.0
N G:ASN14 4.1 32.2 1.0
OD1 G:ASP19 4.2 31.7 1.0
CB G:ASN14 4.3 26.2 1.0
MN G:MN238 4.4 32.7 1.0
CB G:ASP10 4.4 20.8 1.0
CA G:PRO13 4.5 28.6 1.0
CA G:TYR12 4.5 24.8 1.0
N G:PRO13 4.5 28.2 1.0
N G:TYR12 4.6 27.9 1.0
OD2 G:ASP208 4.6 32.6 1.0
ND2 G:ASN14 4.6 30.7 1.0
O G:ASP208 4.6 21.1 1.0
C G:PRO13 4.7 31.1 1.0
CB G:TYR12 4.7 28.3 1.0
O G:HOH246 4.7 17.4 1.0
CA G:ARG228 4.7 29.1 1.0
CB G:ARG228 4.7 27.6 1.0
CE1 G:HIS24 4.8 25.9 1.0
CB G:ASP19 4.8 28.3 1.0
O G:ARG228 4.9 32.5 1.0
CA G:ASN14 4.9 30.1 1.0
CD2 G:TYR12 4.9 32.6 1.0

Calcium binding site 8 out of 8 in 1tei

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Calcium 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 Calcium with other atoms in the Ca 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:Ca246

b:47.6
occ:1.00
 O H:TYR12 1.9 28.1 0.0
OD2 H:ASP19 2.1 35.8 1.0
OD1 H:ASP10 2.4 25.1 1.0
OD2 H:ASP10 2.5 25.9 1.0
OD1 H:ASN14 2.6 50.5 1.0
O H:HOH247 2.7 18.7 1.0
CG H:ASP10 2.8 27.7 1.0
C H:TYR12 3.2 29.7 0.0
CG H:ASP19 3.3 41.5 1.0
CG H:ASN14 3.7 45.2 1.0
N H:ASN14 3.8 43.8 1.0
OD1 H:ASP19 3.9 47.0 1.0
N H:PRO13 4.0 36.4 1.0
CA H:PRO13 4.0 39.5 1.0
CA H:TYR12 4.2 31.4 0.0
CB H:ASP10 4.2 28.1 1.0
MN H:MN245 4.3 42.6 1.0
C H:PRO13 4.3 43.0 1.0
N H:TYR12 4.3 30.2 0.0
CB H:ASN14 4.3 42.4 1.0
CE1 H:HIS24 4.4 36.2 1.0
CB H:ASP19 4.4 41.8 1.0
O H:HOH248 4.5 15.9 1.0
CB H:TYR12 4.6 23.8 0.0
CA H:ASN14 4.7 43.9 1.0
ND2 H:ASN14 4.8 48.7 1.0
O H:ASP208 4.8 29.8 1.0
OD2 H:ASP208 4.8 32.0 1.0
NE2 H:HIS24 4.9 33.0 1.0
CB H:ARG228 5.0 43.0 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: Thu Jul 11 23:01:44 2024

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