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

Protein crystallography data

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

Other elements in 1muq:

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

Calcium (Ca) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the X-Ray Crystal Structure of Rattlesnake Venom Complexed with Thiodigalactoside, PDB code: 1muq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 1muq

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Sodium 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 Sodium with other atoms in the Na 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:Na206

b:27.4
occ:1.00
 O A:SER42 2.2 20.0 1.0
O A:HOH306 2.5 38.4 1.0
OG A:SER42 2.6 35.0 1.0
OE1 A:GLN132 2.6 34.5 1.0
OH A:TYR15 2.7 26.5 1.0
C A:SER42 3.1 25.1 1.0
N A:SER42 3.6 19.9 1.0
CD A:GLN132 3.6 25.6 1.0
CD2 A:HIS44 3.6 33.3 1.0
CB A:SER42 3.7 24.0 1.0
CA A:SER42 3.7 22.1 1.0
CZ A:TYR15 3.8 24.7 1.0
NE2 A:HIS44 3.8 38.5 1.0
CE2 A:TYR15 4.0 23.2 1.0
CD1 A:LEU13 4.0 37.1 1.0
N A:PHE43 4.1 24.7 1.0
O A:HOH308 4.1 32.2 1.0
NE2 A:GLN132 4.2 25.6 1.0
OD2 A:ASP83 4.3 35.1 1.0
CA A:PHE43 4.5 27.6 1.0
OE1 A:GLU48 4.5 37.7 1.0
CG A:GLN132 4.7 29.5 1.0
C A:ALA41 4.8 27.1 1.0
CG A:HIS44 4.9 31.0 1.0

Sodium binding site 2 out of 5 in 1muq

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Sodium 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 Sodium with other atoms in the Na 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:Na207

b:31.6
occ:1.00
 O B:SER42 2.3 36.3 1.0
OH B:TYR15 2.4 30.9 1.0
OE1 B:GLN132 2.4 36.3 1.0
OG B:SER42 2.9 36.2 1.0
O B:HOH321 3.2 53.3 1.0
C B:SER42 3.3 34.6 1.0
CD B:GLN132 3.3 27.0 1.0
CZ B:TYR15 3.5 33.9 1.0
N B:SER42 3.6 31.6 1.0
CE2 B:TYR15 3.8 28.3 1.0
CA B:SER42 3.8 32.3 1.0
CD1 B:LEU13 3.9 45.1 1.0
NE2 B:GLN132 3.9 34.0 1.0
CB B:SER42 3.9 31.1 1.0
O B:HOH329 4.0 45.7 1.0
CD2 B:HIS44 4.1 35.2 1.0
N B:PHE43 4.3 36.5 1.0
CG B:GLN132 4.3 31.9 1.0
NE2 B:HIS44 4.4 41.2 1.0
OD2 B:ASP83 4.4 41.0 1.0
CA B:PHE43 4.7 33.9 1.0
CE1 B:TYR15 4.7 32.0 1.0
C B:ALA41 4.8 28.1 1.0
OE2 B:GLU48 4.9 52.1 1.0

Sodium binding site 3 out of 5 in 1muq

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Sodium 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 Sodium with other atoms in the Na 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:Na208

b:39.7
occ:1.00
 OE1 C:GLN132 2.2 33.1 1.0
OH C:TYR15 2.4 33.5 1.0
O C:HOH311 2.5 45.0 1.0
O C:SER42 2.6 29.8 1.0
OG C:SER42 2.8 25.9 1.0
CD C:GLN132 3.2 29.5 1.0
CZ C:TYR15 3.4 28.9 1.0
C C:SER42 3.4 31.2 1.0
CD1 C:LEU13 3.5 37.5 1.0
CE2 C:TYR15 3.7 23.4 1.0
N C:SER42 3.7 28.1 1.0
CB C:SER42 3.9 27.4 1.0
CA C:SER42 3.9 27.5 1.0
NE2 C:GLN132 4.0 23.1 1.0
CD2 C:HIS44 4.1 31.9 1.0
CG C:GLN132 4.2 26.3 1.0
OD2 C:ASP83 4.3 37.0 1.0
NE2 C:HIS44 4.4 31.3 1.0
N C:PHE43 4.5 28.4 1.0
CE1 C:TYR15 4.7 29.3 1.0
CG C:LEU13 4.8 39.6 1.0
CA C:PHE43 4.9 28.3 1.0
C C:ALA41 4.9 29.8 1.0
OE1 C:GLU48 4.9 46.3 1.0
OE2 C:GLU48 4.9 57.1 1.0

Sodium binding site 4 out of 5 in 1muq

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Sodium 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 Sodium with other atoms in the Na 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:Na209

b:56.7
occ:1.00
 OE1 D:GLN132 2.2 47.3 1.0
O D:SER42 2.4 52.3 1.0
OG D:SER42 2.5 45.1 1.0
OH D:TYR15 2.6 37.9 1.0
CD D:GLN132 3.1 42.1 1.0
C D:SER42 3.3 53.8 1.0
N D:SER42 3.5 39.6 1.0
CZ D:TYR15 3.6 32.1 1.0
CD1 D:LEU13 3.6 38.6 1.0
CB D:SER42 3.6 48.8 1.0
NE2 D:GLN132 3.7 43.2 1.0
CA D:SER42 3.7 48.6 1.0
CE2 D:TYR15 3.7 35.6 1.0
NE2 D:HIS44 4.1 97.1 1.0
CD2 D:HIS44 4.1 94.6 1.0
CG D:GLN132 4.2 39.6 1.0
O D:HOH222 4.3 56.8 1.0
OD2 D:ASP83 4.4 75.0 1.0
N D:PHE43 4.4 60.8 1.0
C D:ALA41 4.7 35.5 1.0
CA D:PHE43 4.9 70.7 1.0
CE1 D:TYR15 4.9 35.2 1.0
CG D:LEU13 4.9 37.9 1.0

Sodium binding site 5 out of 5 in 1muq

Go back to Sodium Binding Sites List in 1muq
Sodium 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 Sodium with other atoms in the Na 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:Na210

b:23.5
occ:1.00
 OE1 E:GLN132 2.1 24.9 1.0
O E:HOH314 2.2 48.0 1.0
O E:SER42 2.4 26.5 1.0
OH E:TYR15 2.4 24.1 1.0
OG E:SER42 2.7 27.5 1.0
CD E:GLN132 3.2 25.1 1.0
C E:SER42 3.2 22.1 1.0
CZ E:TYR15 3.5 25.9 1.0
N E:SER42 3.5 22.4 1.0
CE2 E:TYR15 3.7 26.6 1.0
CD1 E:LEU13 3.7 29.2 1.0
CB E:SER42 3.8 25.5 1.0
CA E:SER42 3.8 23.6 1.0
NE2 E:GLN132 3.9 20.6 1.0
CG E:GLN132 4.1 21.9 1.0
CD2 E:HIS44 4.2 20.6 1.0
O E:HOH313 4.2 25.7 1.0
N E:PHE43 4.3 27.2 1.0
OD2 E:ASP83 4.3 33.3 1.0
O E:HOH326 4.5 56.6 1.0
NE2 E:HIS44 4.5 28.9 1.0
CA E:PHE43 4.7 18.9 1.0
C E:ALA41 4.7 22.2 1.0
CE1 E:TYR15 4.7 28.2 1.0
OE1 E:GLU48 4.8 39.5 1.0
CB E:GLN132 4.9 25.4 1.0

Reference:

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
Page generated: Sun Oct 6 20:34:38 2024

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