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Sodium in PDB 3o1c: High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine

Protein crystallography data

The structure of High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine, PDB code: 3o1c was solved by R.M.Dolot, M.Ozga, A.K.Krakowiak, B.Nawrot, W.J.Stec, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.26 / 1.08
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 39.965, 39.965, 141.700, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.3

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine (pdb code 3o1c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine, PDB code: 3o1c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3o1c

Go back to Sodium Binding Sites List in 3o1c
Sodium binding site 1 out of 2 in the High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na128

b:65.8
occ:1.00
N A:HIS59 2.9 15.4 0.5
N A:HIS59 2.9 14.3 0.5
O A:HOH308 3.1 39.5 1.0
O A:HOH192 3.3 51.4 1.0
CB A:HIS59 3.5 15.4 0.5
O A:HOH311 3.6 45.6 1.0
CA A:LYS58 3.7 16.7 1.0
CA A:HIS59 3.7 16.0 0.5
C A:LYS58 3.7 14.0 1.0
CB A:HIS59 3.8 16.5 0.5
CA A:HIS59 3.8 14.7 0.5
N A:GLY14 3.9 28.9 1.0
O A:LYS57 4.2 16.6 1.0
CG A:LYS58 4.2 20.0 1.0
O A:HIS59 4.3 14.0 0.5
CB A:LYS58 4.5 17.9 1.0
C A:HIS59 4.6 13.2 0.5
CA A:PRO13 4.7 38.0 1.0
O A:ARG12 4.7 40.1 1.0
O A:HOH304 4.7 38.7 1.0
CA A:GLY14 4.7 25.8 1.0
N A:LYS58 4.7 15.4 1.0
C A:HIS59 4.7 14.9 0.5
C A:PRO13 4.8 34.9 1.0
O A:HIS59 4.9 17.6 0.5
N A:GLY15 4.9 20.3 1.0
CG A:HIS59 4.9 16.6 0.5
C A:LYS57 4.9 14.7 1.0
O A:LYS58 4.9 14.7 1.0
C A:GLY14 5.0 19.7 1.0

Sodium binding site 2 out of 2 in 3o1c

Go back to Sodium Binding Sites List in 3o1c
Sodium binding site 2 out of 2 in the High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of Histidine Triad Nucleotide- Binding Protein 1 (HINT1) C38A Mutant From Rabbit Complexed with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na129

b:34.0
occ:1.00
O A:GLN120 2.8 11.8 1.0
O A:HOH242 3.1 33.0 1.0
C A:GLN120 3.8 10.7 1.0
CD A:ARG119 3.8 13.5 1.0
NH1 A:ARG119 3.9 13.0 1.0
O A:HOH324 3.9 36.3 1.0
N A:GLN120 4.0 12.4 1.0
CB A:GLN120 4.0 13.0 1.0
CB A:ARG119 4.1 12.4 1.0
CA A:GLN120 4.1 12.2 1.0
O A:HOH224 4.1 17.4 1.0
CG A:ARG119 4.2 12.2 1.0
C A:ARG119 4.7 11.3 1.0
NE A:ARG119 4.7 13.6 1.0
CZ A:ARG119 4.7 11.8 1.0
CG A:GLN120 4.9 13.4 1.0
CA A:ARG119 5.0 11.6 1.0
N A:MET121 5.0 10.6 1.0

Reference:

M.Ozga, R.Dolot, M.Janicka, R.Kaczmarek, A.Krakowiak. Histidine Triad Nucleotide-Binding Protein 1 (Hint-1) Phosphoramidase Transforms Nucleoside 5'-O-Phosphorothioates to Nucleoside 5'-O-Phosphates. J.Biol.Chem. V. 285 40809 2010.
ISSN: ISSN 0021-9258
PubMed: 20940308
DOI: 10.1074/JBC.M110.162065
Page generated: Tue Dec 15 06:19:32 2020

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