Sodium in PDB 1ve8: X-Ray Analyses of Oligonucleotides Containing 5- Formylcytosine, Suggesting A Structural Reason For Codon- Anticodon Recognition of Mitochondrial Trna-Met; Part 1, D(Cgcgaatt(F5C)Gcg)

The structure of X-Ray Analyses of Oligonucleotides Containing 5- Formylcytosine, Suggesting A Structural Reason For Codon- Anticodon Recognition of Mitochondrial Trna-Met; Part 1, D(Cgcgaatt(F5C)Gcg), PDB code: 1ve8 was solved by K.Kimura, A.Ono, K.Watanabe, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.100, 41.600, 65.500, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.9

The binding sites of Sodium atom in the X-Ray Analyses of Oligonucleotides Containing 5- Formylcytosine, Suggesting A Structural Reason For Codon- Anticodon Recognition of Mitochondrial Trna-Met; Part 1, D(Cgcgaatt(F5C)Gcg) (pdb code 1ve8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Analyses of Oligonucleotides Containing 5- Formylcytosine, Suggesting A Structural Reason For Codon- Anticodon Recognition of Mitochondrial Trna-Met; Part 1, D(Cgcgaatt(F5C)Gcg), PDB code: 1ve8:

Sodium binding site 1 out of 1 in the X-Ray Analyses of Oligonucleotides Containing 5- Formylcytosine, Suggesting A Structural Reason For Codon- Anticodon Recognition of Mitochondrial Trna-Met; Part 1, D(Cgcgaatt(F5C)Gcg)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Analyses of Oligonucleotides Containing 5- Formylcytosine, Suggesting A Structural Reason For Codon- Anticodon Recognition of Mitochondrial Trna-Met; Part 1, D(Cgcgaatt(F5C)Gcg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:45.1 occ:1.00 O2 B:DT7 2.6 32.8 1.0 O A:HOH17 2.8 35.6 1.0 O B:HOH229 2.8 40.5 1.0 O4' B:DT8 2.9 36.7 1.0 O2 A:DT7 2.9 26.2 1.0 O4' A:DT8 3.3 34.0 1.0 C4' B:DT8 3.4 36.7 1.0 C2 B:DT7 3.7 28.4 1.0 C4' A:DT8 3.9 36.5 1.0 C5' B:DT8 3.9 38.3 1.0 C1' B:DT8 4.0 31.4 1.0 C2 A:DT7 4.0 27.1 1.0 C1' B:DT7 4.1 28.6 1.0 C1' A:DT8 4.2 37.4 1.0 C2 A:DA6 4.4 27.0 1.0 N1 B:DT7 4.4 32.1 1.0 C2 B:DA6 4.4 24.4 1.0 C5' A:DT8 4.4 35.4 1.0 C1' A:DT7 4.5 31.5 1.0 N1 B:DT8 4.5 31.5 1.0 O A:HOH63 4.7 31.4 1.0 N1 A:DT8 4.8 29.8 1.0 C3' B:DT8 4.8 39.2 1.0 O4' B:DT7 4.8 31.6 1.0 N3 B:DT7 4.8 23.5 1.0 O A:HOH14 4.8 33.1 1.0 N1 A:DT7 4.8 30.5 1.0 C2 B:DT8 4.8 28.0 1.0 O2 B:DT8 4.8 29.4 1.0 O B:HOH234 4.9 44.0 1.0 N3 A:DT7 5.0 26.0 1.0 O5' B:DT8 5.0 40.7 1.0 O2 A:DT8 5.0 27.7 1.0

K.Kimura, A.Ono, K.Watanabe, A.Takenaka. X-Ray Analyses of Oligonucleotides Containing 5-Formylcytosine, Suggest A Structural Reason For the Codon-Anticodon Recognition of Mitochondrial Trna-Met To Be Published.