Magnesium in PDB 4tra: Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals

The structure of Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals, PDB code: 4tra was solved by E.Westhof, P.Dumas, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.00
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	33.000, 56.000, 161.000, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals (pdb code 4tra). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals, PDB code: 4tra:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals


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 Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg77 b:38.6 occ:1.00 O A:HOH185 2.0 36.1 1.0 O A:HOH187 2.0 37.2 1.0 O A:HOH188 2.0 38.9 0.9 O A:HOH189 2.0 38.6 0.7 O A:HOH186 2.0 39.7 1.0 OP1 A:G19 2.4 2.0 1.0 OP2 A:G19 3.2 1.4 1.0 P A:G19 3.3 0.0 1.0 O A:HOH145 4.2 37.2 1.0 O A:HOH149 4.3 37.1 1.0 N7 A:G20 4.3 0.0 1.0 O5' A:G19 4.3 0.0 1.0 O2' A:H2U17 4.3 12.7 0.6 C5' A:G19 4.5 0.0 1.0 O A:HOH113 4.6 37.6 1.0 O3' A:G18 4.6 0.0 1.0 O4 A:U59 4.7 16.9 1.0 O A:HOH162 4.8 37.1 0.7 N4 A:C60 5.0 0.0 1.0 N3 A:C60 5.0 0.0 1.0

Magnesium binding site 2 out of 4 in the Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals


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 Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg78 b:39.9 occ:0.93 O A:HOH190 2.0 37.4 1.0 O A:HOH192 2.0 39.0 0.9 O A:HOH191 2.0 39.1 1.0 OP2 A:A21 2.1 2.0 1.0 OP1 A:G20 2.8 1.9 1.0 P A:A21 3.2 0.0 1.0 OP1 A:A21 3.6 0.0 1.0 O5' A:A21 3.7 0.0 1.0 C5' A:G20 4.0 0.0 1.0 P A:G20 4.0 2.5 1.0 O5' A:G20 4.4 0.0 1.0 O3' A:G20 4.5 1.6 1.0 OP2 A:G20 4.7 0.0 1.0 O A:HOH141 4.7 37.0 1.0 C3' A:G20 4.9 0.0 1.0 C4' A:G20 5.0 0.0 1.0

Magnesium binding site 3 out of 4 in the Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals


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 Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg79 b:38.7 occ:0.86 O A:HOH198 2.0 37.3 1.0 O A:HOH193 2.0 37.9 0.9 O A:HOH195 2.0 39.9 0.8 O A:HOH196 2.0 39.7 0.6 O A:HOH197 2.0 39.6 0.9 O A:HOH194 2.0 40.1 0.7 OP2 A:U8 3.6 10.9 1.0 OP2 A:U12 3.6 6.8 1.0 OP1 A:U8 3.7 11.0 1.0 P A:U8 4.2 6.4 1.0 OP2 A:C11 4.4 7.4 1.0 OP1 A:A9 4.5 13.0 1.0 OP2 A:A9 4.7 6.3 1.0 O A:HOH104 4.7 36.0 1.0 O A:HOH165 4.7 36.7 1.0 O A:HOH116 4.8 36.4 1.0

Magnesium binding site 4 out of 4 in the Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals


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 Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg80 b:39.2 occ:0.86 O A:HOH202 2.0 39.6 0.9 O A:HOH199 2.0 39.4 0.9 O A:HOH200 2.0 39.5 0.6 O A:HOH201 2.0 39.0 0.9 O A:HOH203 2.0 38.5 1.0 OP2 A:YG37 2.6 39.5 1.0 P A:YG37 3.7 45.5 1.0 N7 A:A38 3.7 24.7 1.0 O5' A:YG37 3.8 34.4 1.0 O2 A:OMC32 3.9 34.9 1.0 OP2 A:A38 4.0 39.4 1.0 N6 A:A31 4.0 21.3 1.0 O2 A:PSU39 4.0 32.9 1.0 C8 A:YG37 4.1 33.2 0.7 N7 A:YG37 4.1 34.6 0.7 C3' A:A36 4.3 31.2 1.0 C8 A:A38 4.5 26.0 1.0 N3 A:OMC32 4.5 36.9 1.0 O3' A:A36 4.5 34.7 1.0 C2 A:PSU39 4.6 31.3 1.0 C5' A:A36 4.6 29.4 1.0 C2 A:OMC32 4.6 35.8 1.0 N6 A:A38 4.7 31.0 1.0 C5 A:A38 4.8 26.5 1.0 OP1 A:YG37 4.8 43.6 1.0 C6 A:A31 4.9 20.8 1.0

E.Westhof, P.Dumas, D.Moras. Restrained Refinement of Two Crystalline Forms of Yeast Aspartic Acid and Phenylalanine Transfer Rna Crystals. Acta Crystallogr.,Sect.A V. 44 112 1988.
ISSN: ISSN 0108-7673
PubMed: 3272146
DOI: 10.1107/S010876738700446X