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Sodium in PDB 5obg: Crystal Structure of Glycine Binding Protein in Complex with Strychnine

Protein crystallography data

The structure of Crystal Structure of Glycine Binding Protein in Complex with Strychnine, PDB code: 5obg was solved by A.Dawson, W.N.Hunter, M.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 2.00
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.353, 100.040, 163.752, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine (pdb code 5obg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine, PDB code: 5obg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5obg

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Sodium binding site 1 out of 5 in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Glycine Binding Protein in Complex with Strychnine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:19.5
occ:1.00
 O A:ALA109 2.3 16.5 1.0
OG1 A:THR108 2.4 17.5 1.0
O A:HOH807 2.4 21.9 1.0
O B:LEU119 2.5 17.0 1.0
OXT A:ACT607 2.6 19.9 1.0
O2 A:EDO608 2.6 23.3 1.0
C A:ALA109 3.4 16.5 1.0
OG A:SER112 3.5 18.1 1.0
C B:LEU119 3.6 17.8 1.0
C2 A:EDO608 3.7 25.3 1.0
CB A:THR108 3.7 18.1 1.0
C A:ACT607 3.7 18.3 1.0
N A:ALA109 3.9 15.1 1.0
CG2 A:THR108 3.9 19.4 1.0
CA A:ALA109 4.1 15.3 1.0
O A:ACT607 4.2 19.1 1.0
O A:HOH761 4.2 19.8 1.0
C1 A:EDO608 4.2 23.5 1.0
O A:HOH775 4.3 36.3 1.0
C A:THR108 4.3 15.3 1.0
CB B:LEU119 4.4 17.2 1.0
CA B:SER120 4.4 17.2 1.0
N A:ALA110 4.4 15.8 1.0
N B:SER120 4.4 16.9 1.0
CB A:ALA109 4.5 15.7 1.0
CA A:THR108 4.5 16.6 1.0
CB A:SER112 4.5 18.0 1.0
CA B:LEU119 4.6 16.1 1.0
CA A:ALA110 4.6 17.4 1.0
CB B:SER120 4.8 18.2 1.0
C A:ALA110 4.8 18.7 1.0
CH3 A:ACT607 4.8 14.1 1.0

Sodium binding site 2 out of 5 in 5obg

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Sodium binding site 2 out of 5 in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Glycine Binding Protein in Complex with Strychnine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:24.4
occ:1.00
 O B:HOH737 2.3 30.7 1.0
OG1 B:THR108 2.4 19.8 1.0
O C:LEU119 2.4 19.8 1.0
O B:ALA109 2.4 21.3 1.0
OXT B:ACT608 2.6 17.9 1.0
O2 B:EDO609 2.8 23.0 1.0
C B:ALA109 3.5 19.2 1.0
C C:LEU119 3.6 19.9 1.0
C B:ACT608 3.6 19.0 1.0
CB B:THR108 3.6 19.9 1.0
OG B:SER112 3.6 17.9 1.0
CG2 B:THR108 3.8 19.0 1.0
O B:ACT608 3.9 21.4 1.0
C2 B:EDO609 3.9 27.7 1.0
N B:ALA109 4.1 17.8 1.0
O B:HOH754 4.2 18.1 1.0
CB C:LEU119 4.3 16.6 1.0
CA B:ALA109 4.3 19.1 1.0
CA C:SER120 4.4 18.9 1.0
C B:THR108 4.4 18.5 1.0
N C:SER120 4.4 19.1 1.0
CA C:LEU119 4.5 17.2 1.0
N B:ALA110 4.5 18.6 1.0
C1 B:EDO609 4.5 28.8 1.0
CA B:THR108 4.6 19.2 1.0
CA B:ALA110 4.6 19.6 1.0
O B:HOH803 4.7 38.0 1.0
CB B:ALA109 4.7 18.6 1.0
CB C:SER120 4.7 16.9 1.0
CB B:SER112 4.8 18.5 1.0
CH3 B:ACT608 4.9 16.9 1.0
C B:ALA110 4.9 18.6 1.0

Sodium binding site 3 out of 5 in 5obg

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Sodium binding site 3 out of 5 in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Glycine Binding Protein in Complex with Strychnine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na609

b:27.2
occ:1.00
 O C:HOH755 2.3 27.0 1.0
O C:ALA109 2.4 18.4 1.0
O C:ACT610 2.5 19.5 1.0
O D:LEU119 2.5 19.7 1.0
OG1 C:THR108 2.5 22.9 1.0
O2 C:EDO611 2.7 28.6 1.0
OG C:SER112 3.4 17.1 1.0
C C:ALA109 3.6 19.8 1.0
C C:ACT610 3.6 24.0 1.0
C D:LEU119 3.6 20.4 1.0
CB C:THR108 3.7 21.3 1.0
C2 C:EDO611 3.9 27.2 1.0
CG2 C:THR108 3.9 21.8 1.0
OXT C:ACT610 4.0 26.0 1.0
N C:ALA109 4.1 19.9 1.0
O C:HOH740 4.2 41.9 1.0
O C:HOH745 4.2 26.5 1.0
CB D:LEU119 4.2 18.2 1.0
CA D:SER120 4.3 18.9 1.0
CA C:ALA109 4.4 20.4 1.0
N D:SER120 4.4 19.5 1.0
CB C:SER112 4.4 16.9 1.0
C1 C:EDO611 4.5 27.4 1.0
C C:THR108 4.5 20.9 1.0
N C:ALA110 4.5 18.7 1.0
CA D:LEU119 4.5 18.1 1.0
CA C:ALA110 4.6 18.4 1.0
CB D:SER120 4.6 16.8 1.0
CA C:THR108 4.6 19.2 1.0
C C:ALA110 4.8 19.3 1.0
CB C:ALA109 4.8 21.2 1.0
CH3 C:ACT610 4.8 18.1 1.0
N C:SER112 4.9 17.5 1.0

Sodium binding site 4 out of 5 in 5obg

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Sodium binding site 4 out of 5 in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Glycine Binding Protein in Complex with Strychnine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na609

b:25.3
occ:1.00
 O D:ALA109 2.3 19.2 1.0
O E:HOH782 2.3 18.0 1.0
O E:LEU119 2.4 16.9 1.0
OG1 D:THR108 2.4 18.7 1.0
O E:ACT606 2.5 19.2 1.0
O2 E:EDO608 2.9 23.9 1.0
C D:ALA109 3.5 17.8 1.0
OG D:SER112 3.5 16.9 1.0
C E:ACT606 3.6 19.3 1.0
C E:LEU119 3.6 16.6 1.0
CB D:THR108 3.7 18.8 1.0
CG2 D:THR108 3.8 19.5 1.0
N D:ALA109 3.9 16.4 1.0
C2 E:EDO608 4.0 27.8 1.0
OXT E:ACT606 4.0 18.2 1.0
O D:HOH735 4.2 32.2 1.0
CA D:ALA109 4.3 16.9 1.0
O E:HOH770 4.3 19.1 1.0
CB E:LEU119 4.3 15.8 1.0
N D:ALA110 4.3 19.3 1.0
C D:THR108 4.4 16.5 1.0
CA E:SER120 4.4 15.8 1.0
CA D:ALA110 4.4 19.0 1.0
N E:SER120 4.4 15.9 1.0
CA D:THR108 4.5 16.4 1.0
CA E:LEU119 4.5 16.2 1.0
C1 E:EDO608 4.5 30.0 1.0
CB D:SER112 4.6 15.3 1.0
CB D:ALA109 4.7 17.6 1.0
CB E:SER120 4.7 16.7 1.0
C D:ALA110 4.8 18.7 1.0
CH3 E:ACT606 4.8 15.9 1.0

Sodium binding site 5 out of 5 in 5obg

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Sodium binding site 5 out of 5 in the Crystal Structure of Glycine Binding Protein in Complex with Strychnine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Glycine Binding Protein in Complex with Strychnine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na604

b:23.1
occ:1.00
 O A:LEU119 2.3 19.9 1.0
O E:ALA109 2.4 16.1 1.0
OXT E:ACT602 2.5 19.6 1.0
OG1 E:THR108 2.6 19.0 1.0
O E:HOH794 2.6 24.0 1.0
O2 A:EDO602 2.9 21.3 1.0
OG E:SER112 3.4 16.4 1.0
C E:ACT602 3.5 19.3 1.0
C A:LEU119 3.5 18.2 1.0
C E:ALA109 3.5 14.7 1.0
CB E:THR108 3.7 17.4 1.0
CG2 E:THR108 3.7 20.3 1.0
O E:ACT602 3.9 16.1 1.0
N E:ALA109 4.0 15.9 1.0
C2 A:EDO602 4.0 24.5 1.0
CB A:LEU119 4.3 14.9 1.0
O A:HOH756 4.3 21.4 1.0
CA A:SER120 4.3 17.3 1.0
N A:SER120 4.3 16.9 1.0
CA E:ALA109 4.4 14.8 1.0
CA A:LEU119 4.4 15.2 1.0
N E:ALA110 4.5 14.6 1.0
O E:HOH767 4.5 39.4 1.0
C E:THR108 4.5 16.9 1.0
CA E:ALA110 4.5 14.9 1.0
CB E:SER112 4.5 15.8 1.0
CA E:THR108 4.6 17.4 1.0
C1 A:EDO602 4.6 26.6 1.0
CB A:SER120 4.7 17.4 1.0
CH3 E:ACT602 4.7 14.7 1.0
C E:ALA110 4.8 16.0 1.0
CB E:ALA109 4.9 14.3 1.0

Reference:

A.Dawson, W.N.Hunter, M.Jones. Crystal Structure of Glycine Binding Protein in Complex with Strychnine To Be Published.
Page generated: Mon Aug 18 01:30:13 2025

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