Magnesium in PDB 1tra: Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles

The structure of Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles, PDB code: 1tra was solved by E.Westhof, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.000, 33.300, 63.000, 90.00, 90.40, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles (pdb code 1tra). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles, PDB code: 1tra:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg77 b:32.1 occ:1.00 O A:HOH126 2.0 34.4 1.0 OP1 A:G20 2.2 0.1 1.0 OP2 A:A21 3.0 4.8 1.0 P A:G20 3.6 2.0 1.0 OP2 A:G20 4.1 1.2 1.0 P A:A21 4.3 11.2 1.0 O5' A:G20 4.6 3.8 1.0 OP1 A:A21 4.6 1.1 1.0 O3' A:G19 4.6 1.5 1.0 C5' A:G20 4.8 5.9 1.0

Magnesium binding site 2 out of 5 in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg78 b:37.0 occ:1.00 OP1 A:U8 3.2 14.1 1.0 OP2 A:U12 3.6 13.0 1.0 OP1 A:A9 4.0 8.8 1.0 OP2 A:C11 4.1 20.5 1.0 OP2 A:U8 4.2 0.3 1.0 P A:U8 4.3 5.7 1.0 O A:HOH139 4.4 34.8 1.0 OP1 A:C11 4.7 11.8 1.0 OP2 A:A9 4.7 1.3 1.0 P A:C11 4.7 17.4 1.0 O5' A:C11 4.8 15.7 1.0 P A:A9 5.0 0.5 1.0

Magnesium binding site 3 out of 5 in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg79 b:33.6 occ:1.00 OP1 A:G19 1.7 8.4 1.0 O A:HOH177 2.0 32.5 1.0 O A:HOH176 2.0 34.6 1.0 O A:HOH179 2.0 33.5 1.0 O A:HOH175 2.0 35.4 1.0 O A:HOH178 2.0 34.6 1.0 P A:G19 3.2 3.6 1.0 OP2 A:G19 3.8 4.6 1.0 C5' A:G19 3.9 2.9 1.0 O4 A:U59 3.9 16.6 1.0 O5' A:G19 4.0 0.6 1.0 O3' A:G18 4.3 0.0 1.0 N7 A:G20 4.3 5.3 1.0 N3 A:C60 4.3 9.1 1.0 O A:HOH123 4.3 30.9 1.0 N4 A:C60 4.6 13.8 1.0 O6 A:G20 4.7 6.7 1.0 O2' A:H2U17 4.7 27.9 0.7 O A:HOH166 4.9 32.3 0.8 C4 A:C60 4.9 6.1 1.0 O A:HOH101 5.0 29.3 1.0

Magnesium binding site 4 out of 5 in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg80 b:30.6 occ:0.50 O A:HOH182 2.0 30.6 0.5 O A:HOH181 2.0 29.2 0.5 O A:HOH185 2.0 30.5 0.5 O A:HOH184 2.0 29.8 0.5 O A:HOH183 2.0 31.3 0.5 O A:HOH180 2.0 31.0 0.5 O4 A:U41 4.5 26.0 1.0 O A:HOH92 4.5 31.0 1.0 C5 A:U41 4.8 27.4 1.0 C4 A:U41 4.9 24.0 1.0 N7 A:G42 4.9 28.0 1.0 O6 A:G42 4.9 35.1 1.0

Magnesium binding site 5 out of 5 in the Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg81 b:31.4 occ:0.50 O A:HOH186 2.0 30.7 0.5 O A:HOH188 2.0 30.4 0.5 O A:HOH190 2.0 29.7 0.5 O A:HOH189 2.0 30.6 0.5 O A:HOH191 2.0 30.4 0.5 O A:HOH187 2.0 30.4 0.5 O2 A:PSU39 4.3 34.9 1.0 N6 A:A31 4.5 38.5 1.0 OP2 A:A38 4.5 40.9 1.0 O6 A:G30 4.7 34.1 1.0 N4 A:5MC40 4.9 26.9 1.0

E.Westhof, M.Sundaralingam. Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer Rna. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles. Biochemistry V. 25 4868 1986.
ISSN: ISSN 0006-2960
PubMed: 3533142
DOI: 10.1021/BI00365A022