Zinc in PDB 1xmo: Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center

The structure of Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center, PDB code: 1xmo was solved by F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.00 / 3.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.811, 400.811, 176.125, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.4

The structure of Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center also contains other interesting chemical elements:

Magnesium

(Mg)

107 atoms

The binding sites of Zinc atom in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center (pdb code 1xmo). 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center, PDB code: 1xmo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center


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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn306 b:23.7 occ:0.81 SG D:CYS9 2.2 26.3 1.0 SG D:CYS31 2.2 29.9 1.0 SG D:CYS26 2.3 36.7 1.0 SG D:CYS12 2.9 84.7 1.0 O D:LEU19 3.1 1.0 1.0 CB D:CYS9 3.5 26.3 1.0 CA D:CYS9 3.7 0.7 1.0 CB D:CYS31 3.8 29.9 1.0 CB D:CYS26 3.9 36.7 1.0 CB D:CYS12 3.9 84.7 1.0 C D:LEU19 4.4 1.0 1.0 N D:CYS9 4.6 0.7 1.0 CA D:CYS31 4.7 0.2 1.0 N D:LEU21 4.8 58.5 1.0 O D:CYS31 4.8 0.2 1.0 N D:LEU19 4.9 1.0 1.0 CA D:CYS26 4.9 0.2 1.0 C D:CYS9 4.9 0.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center


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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn307 b:23.7 occ:0.48 SG N:CYS27 1.8 38.8 1.0 SG N:CYS43 2.0 28.6 1.0 SG N:CYS40 2.2 63.5 1.0 SG N:CYS24 2.3 63.6 1.0 CB N:CYS40 2.9 63.5 1.0 CB N:CYS24 3.0 63.6 1.0 CB N:CYS43 3.0 28.6 1.0 CB N:CYS27 3.1 38.8 1.0 N N:CYS40 3.7 83.5 1.0 N N:CYS27 3.7 81.6 1.0 CA N:CYS40 3.9 83.5 1.0 CA N:CYS27 3.9 81.6 1.0 N N:CYS43 4.0 49.0 1.0 CB N:ARG29 4.0 0.1 1.0 CA N:CYS43 4.1 49.0 1.0 N N:GLY28 4.2 88.8 1.0 N N:ARG29 4.4 0.2 1.0 CA N:CYS24 4.4 0.0 1.0 C N:CYS27 4.6 81.6 1.0 C N:CYS40 4.6 83.5 1.0 N2 A:G1202 4.6 77.0 1.0 O N:CYS40 4.7 83.5 1.0 CA N:ARG29 4.8 0.2 1.0 C N:LEU39 4.9 98.0 1.0 CB N:ARG26 4.9 96.8 1.0 C N:ARG26 4.9 0.5 1.0

F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, P.F.Agris. The Role of Modifications in Codon Discrimination By Trna(Lys)(Uuu). Nat.Struct.Mol.Biol. V. 11 1186 2004.
ISSN: ISSN 1545-9993
PubMed: 15558052
DOI: 10.1038/NSMB861