Zinc in PDB 2d6f: Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln)

The structure of Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln), PDB code: 2d6f was solved by O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.52 / 3.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.812, 140.706, 186.044, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 29.2

The binding sites of Zinc atom in the Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln) (pdb code 2d6f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln), PDB code: 2d6f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn900 b:41.6 occ:1.00 OE1 C:GLU82 1.7 21.8 1.0 SG C:CYS26 2.2 27.3 1.0 SG C:CYS79 2.2 31.9 1.0 SG C:CYS28 2.3 35.2 1.0 CD C:GLU82 2.6 22.6 1.0 CB C:CYS79 2.7 33.0 1.0 CG C:GLU82 3.0 22.7 1.0 N C:CYS79 3.0 34.8 1.0 CA C:CYS79 3.3 33.4 1.0 CB C:CYS28 3.5 34.4 1.0 CB C:CYS26 3.7 30.4 1.0 OE2 C:GLU82 3.8 23.9 1.0 C C:CYS79 3.9 32.1 1.0 C C:THR78 4.0 35.1 1.0 O C:CYS79 4.1 31.4 1.0 N C:GLU82 4.3 24.8 1.0 N C:CYS28 4.4 30.4 1.0 CB C:VAL81 4.5 24.9 1.0 CD C:PRO27 4.5 27.9 1.0 CB C:GLU82 4.5 22.3 1.0 CA C:THR78 4.5 33.4 1.0 N C:VAL81 4.6 27.0 1.0 CA C:CYS28 4.6 34.2 1.0 N C:LEU80 4.7 30.9 1.0 CG2 C:VAL81 4.8 24.8 1.0 NH1 B:ARG427 4.8 29.8 1.0 CA C:CYS26 4.9 30.5 1.0 N C:PRO27 4.9 28.3 1.0 O C:THR78 4.9 35.6 1.0 CA C:VAL81 5.0 25.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Glu-Trna(Gln) Amidotransferase in the Complex with Trna(Gln) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1900 b:35.4 occ:1.00 SG D:CYS79 1.9 20.8 1.0 SG D:CYS28 1.9 21.8 1.0 OE2 D:GLU82 2.1 23.2 1.0 SG D:CYS26 2.1 14.7 1.0 OE1 D:GLU82 2.2 22.0 1.0 CD D:GLU82 2.4 22.3 1.0 CB D:CYS79 3.1 19.4 1.0 CB D:CYS28 3.2 19.1 1.0 N D:CYS79 3.3 20.1 1.0 CB D:CYS26 3.6 16.3 1.0 CA D:CYS79 3.8 17.6 1.0 CG D:GLU82 4.0 20.0 1.0 N D:CYS28 4.0 20.3 1.0 C D:THR78 4.1 22.8 1.0 CA D:CYS28 4.2 19.3 1.0 C D:CYS79 4.4 16.5 1.0 CA D:THR78 4.4 21.2 1.0 CB D:VAL81 4.4 18.1 1.0 N D:GLU82 4.6 18.5 1.0 O D:CYS79 4.6 18.5 1.0 CD D:PRO27 4.6 19.1 1.0 CB D:GLU82 4.7 18.9 1.0 N D:PRO27 4.7 18.8 1.0 CA D:CYS26 4.8 16.9 1.0 CG2 D:VAL81 4.9 18.3 1.0 N D:VAL81 4.9 16.6 1.0 O D:THR78 4.9 26.3 1.0

H.Oshikane, K.Sheppard, S.Fukai, Y.Nakamura, R.Ishitani, T.Numata, R.L.Sherrer, L.Feng, E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam, D.Soll, O.Nureki. Structural Basis of Rna-Dependent Recruitment of Glutamine to the Genetic Code Science V. 312 1950 2006.
ISSN: ISSN 0036-8075
PubMed: 16809540
DOI: 10.1126/SCIENCE.1128470