Magnesium in PDB 6tna: Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement

The structure of Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement, PDB code: 6tna was solved by J.L.Sussman, S.R.Holbrook, R.W.Warrant, G.M.Church, S.-H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.70
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 (%)	19.8 / n/a

The binding sites of Magnesium atom in the Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement (pdb code 6tna). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement, PDB code: 6tna:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg77 b:10.0 occ:1.00 OP1 A:G19 1.9 10.0 1.0 O A:HOH147 2.0 10.0 1.0 O A:HOH145 2.0 10.0 1.0 O A:HOH149 2.0 10.0 1.0 O A:HOH146 2.0 10.0 1.0 O A:HOH148 2.0 10.0 1.0 P A:G19 3.1 10.0 1.0 OP2 A:G19 3.5 10.0 1.0 O5' A:G19 3.8 10.0 1.0 N7 A:G20 4.1 10.0 1.0 C5' A:G19 4.2 10.0 1.0 O3' A:G18 4.3 10.0 1.0 O4 A:U59 4.5 10.0 1.0 O2' A:H2U17 4.5 10.0 1.0 N4 A:C60 4.7 10.0 1.0 O6 A:G20 4.7 10.0 1.0 N3 A:C60 4.9 10.0 1.0 C3' A:G18 5.0 10.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg78 b:10.0 occ:1.00 OP2 A:A21 1.8 10.0 1.0 O A:HOH153 2.0 10.0 1.0 O A:HOH151 2.0 10.0 1.0 O A:HOH152 2.0 10.0 1.0 O A:HOH150 2.0 10.0 1.0 OP1 A:G20 2.3 10.0 1.0 P A:A21 3.1 10.0 1.0 O5' A:A21 3.7 10.0 1.0 P A:G20 3.7 10.0 1.0 OP1 A:A21 3.8 10.0 1.0 C5' A:G20 4.1 10.0 1.0 O3' A:G20 4.3 10.0 1.0 O5' A:G20 4.4 10.0 1.0 OP2 A:G20 4.4 10.0 1.0 C3' A:G20 4.7 10.0 1.0 C5' A:A21 4.9 10.0 1.0 O3' A:G19 4.9 10.0 1.0 C4' A:G20 4.9 10.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg79 b:10.0 occ:1.00 O A:HOH154 2.0 10.0 1.0 O A:HOH157 2.0 10.0 1.0 O A:HOH155 2.0 10.0 1.0 O A:HOH156 2.0 10.0 1.0 O A:HOH159 2.0 10.0 1.0 O A:HOH158 2.0 10.0 1.0 O A:HOH133 3.1 10.0 1.0 OP2 A:U12 3.3 10.0 1.0 OP2 A:U8 3.5 10.0 1.0 OP1 A:U8 3.9 10.0 1.0 OP2 A:C11 4.3 10.0 1.0 P A:U8 4.3 10.0 1.0 P A:U12 4.7 10.0 1.0 OP2 A:A9 4.7 10.0 1.0 OP1 A:A9 4.8 10.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Yeast Phenylalanine T-Rna. I.Crystallographic Refinement within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg80 b:10.0 occ:1.00 O A:HOH161 2.0 10.0 1.0 O A:HOH164 2.0 10.0 1.0 O A:HOH160 2.0 10.0 1.0 O A:HOH162 2.0 10.0 1.0 O A:HOH163 2.0 10.0 1.0 OP2 A:YG37 2.3 10.0 1.0 P A:YG37 3.7 10.0 1.0 N7 A:YG37 3.8 10.0 1.0 C8 A:YG37 3.9 10.0 1.0 O2 A:OMC32 3.9 10.0 1.0 N7 A:A38 4.0 10.0 1.0 C3' A:A36 4.2 10.0 1.0 O2 A:PSU39 4.2 10.0 1.0 N6 A:A31 4.3 10.0 1.0 N6 A:A38 4.4 10.0 1.0 O3' A:A36 4.4 10.0 1.0 N3 A:OMC32 4.4 10.0 1.0 OP1 A:YG37 4.5 10.0 1.0 C2 A:OMC32 4.6 10.0 1.0 O5' A:YG37 4.7 10.0 1.0 C5' A:A36 4.7 10.0 1.0 C2 A:PSU39 4.8 10.0 1.0 C5 A:A38 4.9 10.0 1.0 C5 A:YG37 4.9 10.0 1.0

J.L.Sussman, S.R.Holbrook, R.W.Warrant, G.M.Church, S.H.Kim. Crystal Structure of Yeast Phenylalanine Transfer Rna. I. Crystallographic Refinement. J.Mol.Biol. V. 123 607 1978.
ISSN: ISSN 0022-2836
PubMed: 357742
DOI: 10.1016/0022-2836(78)90209-7