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Calcium in PDB 1joj: Concanavalin A-Hexapeptide Complex

Protein crystallography data

The structure of Concanavalin A-Hexapeptide Complex, PDB code: 1joj was solved by D.Jain, K.Kaur, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 102.685, 118.384, 253.593, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.1

Other elements in 1joj:

The structure of Concanavalin A-Hexapeptide Complex also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Concanavalin A-Hexapeptide Complex (pdb code 1joj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Concanavalin A-Hexapeptide Complex, PDB code: 1joj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1joj

Go back to Calcium Binding Sites List in 1joj
Calcium binding site 1 out of 4 in the Concanavalin A-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A-Hexapeptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:22.2
occ:1.00
O A:TYR12 2.5 14.6 1.0
O A:HOH328 2.5 17.4 1.0
OD2 A:ASP19 2.6 21.1 1.0
OD1 A:ASP10 2.8 16.6 1.0
OD2 A:ASP10 2.9 16.6 1.0
CG A:ASN14 3.2 26.2 1.0
CG A:ASP10 3.2 16.6 1.0
ND2 A:ASN14 3.4 26.2 1.0
OD1 A:ASN14 3.4 26.2 1.0
CG A:ASP19 3.5 21.1 1.0
C A:TYR12 3.7 14.6 1.0
N A:ASN14 3.8 22.9 1.0
CB A:ASN14 3.8 26.2 1.0
OD1 A:ASP19 3.9 21.1 1.0
CA A:ASN14 4.4 22.9 1.0
CA A:TYR12 4.5 14.6 1.0
CA A:PRO13 4.6 15.8 1.0
C A:PRO13 4.6 15.8 1.0
CB A:ASP19 4.6 21.1 1.0
CB A:TYR12 4.6 46.5 1.0
N A:PRO13 4.6 15.8 1.0
CB A:ARG228 4.6 27.1 1.0
N A:TYR12 4.6 14.6 1.0
OD2 A:ASP208 4.7 18.6 1.0
MN A:MN301 4.7 22.2 1.0
CA A:ARG228 4.7 18.4 1.0
CB A:ASP10 4.8 16.6 1.0
O A:ARG228 4.9 18.4 1.0
O A:ASP208 4.9 15.2 1.0

Calcium binding site 2 out of 4 in 1joj

Go back to Calcium Binding Sites List in 1joj
Calcium binding site 2 out of 4 in the Concanavalin A-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A-Hexapeptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:22.2
occ:1.00
OD1 B:ASP10 2.4 18.5 1.0
OD1 B:ASN14 2.5 30.1 1.0
OD2 B:ASP19 2.5 28.4 1.0
O B:TYR12 2.5 21.8 1.0
OD2 B:ASP10 2.6 18.5 1.0
CG B:ASP10 2.8 18.5 1.0
CG B:ASN14 3.6 30.1 1.0
CG B:ASP19 3.6 28.4 1.0
C B:TYR12 3.7 21.8 1.0
OD1 B:ASP19 4.1 28.4 1.0
N B:ASN14 4.2 26.0 1.0
CB B:ASN14 4.2 30.1 1.0
CB B:ASP10 4.3 18.5 1.0
O B:ASP208 4.3 32.5 1.0
N B:TYR12 4.5 21.8 1.0
CA B:TYR12 4.5 21.8 1.0
MN B:MN303 4.6 22.2 1.0
OD2 B:ASP208 4.6 32.0 1.0
CA B:ARG228 4.7 24.9 1.0
ND2 B:ASN14 4.7 30.1 1.0
CB B:TYR12 4.7 29.6 1.0
N B:PRO13 4.7 22.1 1.0
O B:ARG228 4.7 24.9 1.0
CA B:ASN14 4.9 26.0 1.0
CB B:ARG228 4.9 51.9 1.0
CB B:ASP19 4.9 28.4 1.0
CA B:PRO13 4.9 22.1 1.0
C B:PRO13 5.0 22.1 1.0

Calcium binding site 3 out of 4 in 1joj

Go back to Calcium Binding Sites List in 1joj
Calcium binding site 3 out of 4 in the Concanavalin A-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin A-Hexapeptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca306

b:22.2
occ:1.00
OD2 C:ASP19 2.2 31.8 1.0
O C:HOH342 2.4 12.2 1.0
O C:TYR12 2.4 12.5 1.0
OD1 C:ASN14 2.5 14.2 1.0
OD1 C:ASP10 2.5 17.7 1.0
OD2 C:ASP10 2.6 17.7 1.0
CG C:ASP10 2.8 17.7 1.0
CG C:ASP19 3.4 31.8 1.0
CG C:ASN14 3.6 14.2 1.0
C C:TYR12 3.7 12.5 1.0
OD1 C:ASP19 3.9 31.8 1.0
N C:ASN14 4.0 12.2 1.0
CB C:ASN14 4.1 14.2 1.0
CB C:ASP10 4.3 17.7 1.0
MN C:MN305 4.4 22.2 1.0
CA C:TYR12 4.5 12.5 1.0
N C:TYR12 4.6 12.5 1.0
CB C:ASP19 4.6 31.8 1.0
O C:ASP208 4.6 15.4 1.0
N C:PRO13 4.6 12.5 1.0
ND2 C:ASN14 4.7 14.2 1.0
CA C:ASN14 4.7 12.2 1.0
CA C:PRO13 4.7 12.5 1.0
CE1 C:HIS24 4.8 20.3 1.0
CB C:TYR12 4.8 25.3 1.0
C C:PRO13 4.8 12.5 1.0
CA C:ARG228 4.9 16.1 1.0
O C:ARG228 4.9 16.1 1.0
OD2 C:ASP208 4.9 18.8 1.0
NE2 C:HIS24 4.9 20.3 1.0
CB C:ARG228 5.0 25.5 1.0

Calcium binding site 4 out of 4 in 1joj

Go back to Calcium Binding Sites List in 1joj
Calcium binding site 4 out of 4 in the Concanavalin A-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin A-Hexapeptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca308

b:22.2
occ:1.00
O D:TYR12 2.4 25.1 1.0
OD2 D:ASP19 2.6 31.7 1.0
O D:HOH321 2.7 12.2 1.0
OD1 D:ASP10 2.9 16.8 1.0
OD2 D:ASP10 3.0 16.8 1.0
CG D:ASN14 3.2 21.6 1.0
OD1 D:ASN14 3.2 21.6 1.0
CG D:ASP10 3.3 16.8 1.0
ND2 D:ASN14 3.4 21.6 1.0
CG D:ASP19 3.4 31.7 1.0
C D:TYR12 3.6 25.1 1.0
N D:ASN14 3.7 25.9 1.0
CB D:ASN14 3.7 21.6 1.0
OD1 D:ASP19 3.9 31.7 1.0
CA D:ASN14 4.3 25.9 1.0
C D:PRO13 4.5 20.1 1.0
CA D:PRO13 4.5 20.1 1.0
CA D:TYR12 4.5 25.1 1.0
CB D:ASP19 4.5 31.7 1.0
N D:PRO13 4.6 20.1 1.0
CB D:TYR12 4.6 43.4 1.0
CB D:ARG228 4.6 49.7 1.0
N D:TYR12 4.6 25.1 1.0
OD2 D:ASP208 4.7 22.8 1.0
MN D:MN307 4.7 22.2 1.0
CA D:ARG228 4.7 23.7 1.0
CB D:ASP10 4.8 16.8 1.0
O D:ARG228 4.9 23.7 1.0
O D:ASP208 5.0 16.1 1.0

Reference:

D.Jain, K.J.Kaur, D.M.Salunke. Enhanced Binding of A Rationally Designed Peptide Ligand of Concanavalin A Arises From Improved Geometrical Complementarity. Biochemistry V. 40 12059 2001.
ISSN: ISSN 0006-2960
PubMed: 11580281
DOI: 10.1021/BI011254F
Page generated: Thu Jul 11 10:50:37 2024

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