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Zinc in PDB 1xnq: Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center

Protein crystallography data

The structure of Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center, PDB code: 1xnq was solved by F.V.Murphy, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.00 / 3.05
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.135, 401.135, 175.193, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27

Other elements in 1xnq:

The structure of Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center also contains other interesting chemical elements:

Magnesium (Mg) 107 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center (pdb code 1xnq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center, PDB code: 1xnq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1xnq

Go back to Zinc Binding Sites List in 1xnq
Zinc binding site 1 out of 2 in the Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of 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 Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn306

b:67.7
occ:1.00
SG D:CYS31 2.2 56.3 1.0
SG D:CYS9 2.3 51.0 1.0
SG D:CYS26 2.4 55.8 1.0
SG D:CYS12 2.9 79.7 1.0
O D:LEU19 3.4 0.2 1.0
CB D:CYS9 3.7 51.0 1.0
O D:CYS31 3.8 0.9 1.0
CB D:CYS31 3.9 56.3 1.0
CB D:CYS26 3.9 55.8 1.0
CA D:CYS9 4.0 1.0 1.0
CB D:CYS12 4.1 79.7 1.0
CG D:LYS22 4.2 0.5 1.0
CA D:CYS31 4.4 0.9 1.0
CB D:LYS22 4.5 0.5 1.0
C D:CYS31 4.5 0.9 1.0
CA D:CYS26 4.6 0.9 1.0
C D:LEU19 4.6 0.2 1.0
N D:CYS9 4.9 1.0 1.0
N D:LYS22 5.0 0.4 1.0

Zinc binding site 2 out of 2 in 1xnq

Go back to Zinc Binding Sites List in 1xnq
Zinc binding site 2 out of 2 in the Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of 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 Structure of An Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn307

b:67.7
occ:0.98
SG N:CYS27 2.0 74.9 1.0
SG N:CYS43 2.1 46.5 1.0
SG N:CYS24 2.5 81.1 1.0
SG N:CYS40 2.5 62.6 1.0
CB N:CYS27 2.7 74.9 1.0
CB N:CYS24 3.3 81.1 1.0
CB N:CYS40 3.5 62.6 1.0
N N:CYS27 3.6 78.1 1.0
CA N:CYS27 3.7 78.1 1.0
CB N:CYS43 3.7 46.5 1.0
CB N:ARG29 4.2 0.6 1.0
C N:ARG26 4.3 92.0 1.0
N N:CYS40 4.3 79.4 1.0
N2 A:G1202 4.3 71.3 1.0
N N:CYS43 4.3 56.5 1.0
C N:CYS27 4.5 78.1 1.0
CA N:CYS40 4.5 79.4 1.0
CB N:ARG26 4.6 74.4 1.0
CA N:CYS43 4.7 56.5 1.0
N N:GLY28 4.7 0.8 1.0
N3 A:G1202 4.7 71.3 1.0
CA N:CYS24 4.7 99.9 1.0
N N:ARG29 4.8 0.9 1.0
CA N:ARG26 4.8 92.0 1.0
O N:ARG26 5.0 92.0 1.0
C2 A:G1202 5.0 71.3 1.0
CB N:ILE42 5.0 50.8 1.0

Reference:

F.V.Murphy, V.Ramakrishnan. Structure of A Purine-Purine Wobble Base Pair in the Decoding Center of the Ribosome. Nat.Struct.Mol.Biol. V. 11 1251 2004.
ISSN: ISSN 1545-9993
PubMed: 15558050
DOI: 10.1038/NSMB866
Page generated: Wed Dec 16 03:12:44 2020

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