Manganese in PDB 1ehz: The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution

The structure of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution, PDB code: 1ehz was solved by H.Shi, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.981, 33.389, 61.921, 90.00, 90.20, 90.00
R / Rfree (%)	23.3 / 25.3

The structure of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Manganese atom in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution (pdb code 1ehz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution, PDB code: 1ehz:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn530 b:34.2 occ:1.00 O A:HOH710 2.0 34.5 1.0 O A:HOH708 2.0 37.6 1.0 O A:HOH709 2.0 40.1 1.0 O A:HOH711 2.0 37.9 1.0 OP1 A:G19 2.2 31.5 1.0 O2' A:H2U16 2.3 88.2 1.0 P A:G19 3.4 34.6 1.0 O3' A:H2U16 3.6 84.1 1.0 C2' A:H2U16 3.6 86.7 1.0 OP2 A:G19 3.9 35.1 1.0 N7 A:G20 4.0 27.6 1.0 N4 A:C60 4.1 31.2 1.0 O4 A:U59 4.1 34.5 1.0 O5' A:G19 4.1 30.9 1.0 O6 A:G20 4.2 30.1 1.0 C3' A:H2U16 4.3 84.3 1.0 O A:HOH105 4.3 34.9 1.0 O A:HOH145 4.4 39.5 1.0 C5' A:G19 4.4 35.5 1.0 N3 A:C60 4.5 27.8 1.0 O A:HOH118 4.7 42.1 1.0 O3' A:G18 4.7 28.0 1.0 C5' A:H2U17 4.7 76.1 1.0 C1' A:H2U16 4.8 88.1 1.0 C4 A:C60 4.8 31.4 1.0 P A:H2U17 4.8 82.8 1.0 C5 A:G20 4.8 26.9 1.0 OP1 A:H2U17 4.8 83.7 1.0 C6 A:G20 4.9 29.1 1.0 O5' A:H2U17 4.9 81.7 1.0

Manganese binding site 2 out of 3 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn520 b:89.2 occ:1.00 O A:HOH719 2.0 89.3 1.0 O A:HOH717 2.0 90.1 1.0 O A:HOH721 2.0 88.9 1.0 O A:HOH718 2.0 88.2 1.0 O A:HOH720 2.0 89.3 1.0 N7 A:G1 2.3 91.2 1.0 C8 A:G1 3.1 92.6 1.0 C5 A:G1 3.4 91.5 1.0 O6 A:G1 3.8 90.4 1.0 C6 A:G1 4.0 90.7 1.0 N1 A:A73 4.2 53.7 1.0 N9 A:G1 4.3 93.7 1.0 C4 A:G1 4.5 92.6 1.0 OP1 A:G1 4.5 0.2 1.0 C2 A:A73 4.7 55.5 1.0

Manganese binding site 3 out of 3 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn550 b:56.5 occ:1.00 O A:HOH740 2.0 61.5 1.0 O A:HOH742 2.0 61.0 1.0 O A:HOH739 2.0 58.7 1.0 O A:HOH738 2.0 58.5 1.0 O A:HOH741 2.0 60.6 1.0 N7 A:G15 2.5 28.3 1.0 C8 A:G15 3.4 30.4 1.0 C5 A:G15 3.4 27.4 1.0 O6 A:G15 3.6 26.5 1.0 C6 A:G15 3.9 24.9 1.0 OP2 A:G15 4.2 36.1 1.0 OP1 A:U7 4.5 48.1 1.0 N9 A:G15 4.5 30.4 1.0 C4 A:G15 4.6 29.3 1.0 C4 A:U8 4.7 27.4 1.0 O4 A:U8 4.8 32.6 1.0 MG A:MG580 4.8 61.7 1.0 O A:HOH611 5.0 59.1 1.0

H.Shi, P.B.Moore. The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution: A Classic Structure Revisited Rna V. 6 1091 2000.
ISSN: ISSN 1355-8382
PubMed: 10943889
DOI: 10.1017/S1355838200000364