Calcium in PDB 1muq: X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside

The structure of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside, PDB code: 1muq was solved by J.R.Walker, B.Nagar, N.M.Young, T.Hirama, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.13 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.454, 151.234, 95.014, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.7

The structure of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Calcium atom in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside (pdb code 1muq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside, PDB code: 1muq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:31.7 occ:1.00 OD1 A:ASP120 2.2 25.8 1.0 OD1 A:ASN119 2.3 28.9 1.0 OE1 A:GLN96 2.4 33.0 1.0 OE2 A:GLU104 2.5 41.6 1.0 O A:ASP120 2.5 25.4 1.0 OD1 A:ASP98 2.5 42.7 1.0 O4 A:GAL301 2.7 54.5 1.0 O3 A:GAL301 2.8 35.9 1.0 CG A:ASP120 3.2 27.0 1.0 CD A:GLN96 3.3 38.2 1.0 CG A:ASP98 3.4 40.6 1.0 CG A:ASN119 3.4 28.8 1.0 C A:ASP120 3.6 28.2 1.0 CD A:GLU104 3.6 42.1 1.0 OD2 A:ASP98 3.7 34.9 1.0 NE2 A:GLN96 3.7 32.3 1.0 C3 A:GAL301 3.7 44.9 1.0 C4 A:GAL301 3.7 48.9 1.0 N A:ASP120 3.8 24.3 1.0 ND2 A:ASN119 3.8 26.1 1.0 OD2 A:ASP120 3.9 34.6 1.0 CA A:ASP120 4.1 26.1 1.0 OE1 A:GLU104 4.1 39.4 1.0 N A:ASP98 4.2 41.6 1.0 C2 A:GAL301 4.2 50.3 1.0 CB A:ASP120 4.2 26.3 1.0 CG A:GLN96 4.5 32.1 1.0 C A:ASN119 4.5 26.9 1.0 CB A:ASP98 4.6 29.5 1.0 CB A:TYR100 4.6 44.0 1.0 CB A:ASN119 4.6 28.9 1.0 CB A:GLU104 4.7 29.8 1.0 N A:GLN121 4.7 32.3 1.0 CG A:GLU104 4.7 32.0 1.0 N A:TYR100 4.8 40.1 1.0 CA A:ASP98 4.8 43.0 1.0 CA A:ASN119 4.8 31.4 1.0 N A:HIS99 4.8 39.6 1.0 CB A:GLN96 4.9 38.7 1.0

Calcium binding site 2 out of 5 in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:37.2 occ:1.00 OD1 B:ASP120 2.3 36.4 1.0 OD1 B:ASN119 2.4 34.0 1.0 OE2 B:GLU104 2.4 38.2 1.0 OE1 B:GLN96 2.4 52.2 1.0 OD1 B:ASP98 2.4 66.2 1.0 O3 B:TDG302 2.5 46.7 1.0 O B:ASP120 2.5 41.7 1.0 O4 B:TDG302 2.6 46.9 1.0 CG B:ASP120 3.2 39.1 1.0 CD B:GLN96 3.2 52.2 1.0 CD B:GLU104 3.4 42.6 1.0 C4 B:TDG302 3.4 48.9 1.0 C3 B:TDG302 3.4 50.5 1.0 CG B:ASN119 3.4 40.5 1.0 C B:ASP120 3.6 39.8 1.0 NE2 B:GLN96 3.6 53.4 1.0 CG B:ASP98 3.6 68.2 1.0 N B:ASP120 3.6 33.7 1.0 OE1 B:GLU104 3.8 40.1 1.0 OD2 B:ASP120 3.8 37.7 1.0 ND2 B:ASN119 3.9 37.1 1.0 C2 B:TDG302 4.0 51.4 1.0 CA B:ASP120 4.0 36.9 1.0 OD2 B:ASP98 4.2 72.0 1.0 CB B:ASP120 4.2 37.0 1.0 N B:ASP98 4.3 63.1 1.0 C B:ASN119 4.4 35.1 1.0 CG B:GLN96 4.4 55.5 1.0 CG B:GLU104 4.6 39.7 1.0 CB B:GLU104 4.6 43.8 1.0 CB B:ASN119 4.6 36.2 1.0 CA B:ASN119 4.7 36.4 1.0 N B:GLN121 4.7 35.2 1.0 N B:HIS99 4.7 57.9 1.0 O2 B:TDG302 4.8 49.8 1.0 CB B:TYR100 4.8 70.3 1.0 CB B:ASP98 4.8 61.2 1.0 C5 B:TDG302 4.8 45.1 1.0 N B:TYR100 4.8 60.4 1.0 CB B:GLN96 4.9 57.6 1.0 CA B:PRO97 5.0 60.5 1.0

Calcium binding site 3 out of 5 in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:53.5 occ:1.00 OD1 C:ASN119 2.4 50.3 1.0 O3 C:GAL304 2.4 53.5 1.0 OD1 C:ASP98 2.5 52.3 1.0 OE2 C:GLU104 2.5 60.2 1.0 O C:ASP120 2.5 52.3 1.0 O4 C:GAL304 2.5 57.5 1.0 OE1 C:GLN96 2.5 41.0 1.0 OD1 C:ASP120 2.5 65.8 1.0 CG C:ASP120 3.0 61.1 1.0 OD2 C:ASP120 3.3 68.7 1.0 CG C:ASN119 3.3 38.7 1.0 CG C:ASP98 3.3 57.1 1.0 C4 C:GAL304 3.3 59.2 1.0 CD C:GLN96 3.4 51.9 1.0 C3 C:GAL304 3.4 57.1 1.0 CD C:GLU104 3.5 59.0 1.0 C C:ASP120 3.5 52.5 1.0 OD2 C:ASP98 3.6 50.4 1.0 ND2 C:ASN119 3.6 36.7 1.0 N C:ASP120 3.7 48.2 1.0 NE2 C:GLN96 3.8 53.3 1.0 OE1 C:GLU104 4.0 64.9 1.0 CA C:ASP120 4.0 50.3 1.0 CB C:ASP120 4.1 58.0 1.0 C2 C:GAL304 4.1 57.1 1.0 N C:ASP98 4.3 59.0 1.0 CG C:GLN96 4.5 56.0 1.0 C C:ASN119 4.6 42.0 1.0 CB C:ASP98 4.6 56.5 1.0 CB C:GLU104 4.6 60.3 1.0 CG C:GLU104 4.6 57.6 1.0 CB C:TYR100 4.6 82.8 1.0 CB C:ASN119 4.6 45.5 1.0 N C:GLN121 4.7 49.2 1.0 C5 C:GAL304 4.7 59.1 1.0 N C:HIS99 4.7 75.1 1.0 N C:TYR100 4.8 82.9 1.0 CA C:ASN119 4.9 43.3 1.0 CA C:ASP98 5.0 63.5 1.0 O2 C:GAL304 5.0 51.5 1.0

Calcium binding site 4 out of 5 in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:90.8 occ:1.00 O D:ASP120 2.7 75.4 1.0 OD1 D:ASN119 2.7 76.8 1.0 OE2 D:GLU104 2.8 0.1 1.0 OE1 D:GLN96 3.1 90.8 1.0 OD1 D:ASP120 3.2 84.0 1.0 CG D:ASP120 3.6 89.1 1.0 CG D:ASN119 3.6 76.1 1.0 OD1 D:ASP98 3.6 0.1 1.0 OD2 D:ASP120 3.7 92.8 1.0 ND2 D:ASN119 3.8 78.3 1.0 CD D:GLU104 3.8 0.1 1.0 C D:ASP120 3.9 80.1 1.0 CD D:GLN96 4.0 95.4 1.0 OE1 D:GLU104 4.2 99.7 1.0 OD2 D:ASP98 4.3 0.1 1.0 CG D:ASP98 4.4 0.1 1.0 NE2 D:GLN96 4.4 97.0 1.0 CB D:TYR100 4.5 0.1 1.0 N D:ASP120 4.5 84.3 1.0 CA D:ASP120 4.6 84.1 1.0 OE1 D:GLN121 4.6 89.5 1.0 CB D:ASP120 4.7 86.2 1.0 N D:GLN121 4.8 78.1 1.0 CA D:GLN121 5.0 76.9 1.0

Calcium binding site 5 out of 5 in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca205 b:32.7 occ:1.00 OD1 E:ASN119 2.2 31.6 1.0 OE2 E:GLU104 2.3 38.0 1.0 OE1 E:GLN96 2.3 28.3 1.0 OD1 E:ASP120 2.4 36.6 1.0 O E:ASP120 2.4 28.3 1.0 OD1 E:ASP98 2.6 43.8 1.0 O4 E:GAL305 2.6 35.7 1.0 O3 E:GAL305 2.7 37.3 1.0 CG E:ASP120 3.2 31.7 1.0 CG E:ASN119 3.3 28.1 1.0 CD E:GLN96 3.3 33.4 1.0 CD E:GLU104 3.4 33.1 1.0 C E:ASP120 3.5 26.9 1.0 CG E:ASP98 3.5 47.7 1.0 N E:ASP120 3.5 25.6 1.0 C4 E:GAL305 3.5 46.6 1.0 C3 E:GAL305 3.6 47.9 1.0 ND2 E:ASN119 3.7 30.5 1.0 NE2 E:GLN96 3.7 29.8 1.0 OE1 E:GLU104 3.8 36.3 1.0 OD2 E:ASP98 3.8 48.5 1.0 OD2 E:ASP120 3.9 34.2 1.0 CA E:ASP120 3.9 23.9 1.0 CB E:ASP120 4.2 31.6 1.0 N E:ASP98 4.2 39.1 1.0 C2 E:GAL305 4.3 48.5 1.0 C E:ASN119 4.4 29.5 1.0 CG E:GLN96 4.5 30.3 1.0 CB E:ASN119 4.5 25.9 1.0 CG E:GLU104 4.6 33.8 1.0 N E:GLN121 4.6 23.6 1.0 CB E:TYR100 4.6 42.7 1.0 CB E:GLU104 4.7 33.0 1.0 CB E:ASP98 4.7 42.8 1.0 CA E:ASN119 4.7 29.2 1.0 CB E:GLN96 4.8 30.3 1.0 N E:TYR100 4.9 34.6 1.0 N E:HIS99 4.9 40.2 1.0 C5 E:GAL305 4.9 50.7 1.0 CA E:ASP98 4.9 41.7 1.0

J.R.Walker, B.Nagar, N.M.Young, T.Hirama, J.M.Rini. X-Ray Crystal Structure of A Galactose-Specific C-Type Lectin Possessing A Novel Decameric Quaternary Structure. Biochemistry V. 43 3783 2004.
ISSN: ISSN 0006-2960
PubMed: 15049685
DOI: 10.1021/BI035871A