Zinc in PDB 7mk1: Structure of A Protein-Modified Aptamer Complex

Enzymatic activity of Structure of A Protein-Modified Aptamer Complex

All present enzymatic activity of Structure of A Protein-Modified Aptamer Complex:
3.6.4.13;

Protein crystallography data

The structure of Structure of A Protein-Modified Aptamer Complex, PDB code: 7mk1 was solved by X.Ren, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.75 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.126, 86.632, 87.126, 90, 90, 90
R / Rfree (%) 18.8 / 22

Other elements in 7mk1:

The structure of Structure of A Protein-Modified Aptamer Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Protein-Modified Aptamer Complex (pdb code 7mk1). 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 A Protein-Modified Aptamer Complex, PDB code: 7mk1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7mk1

Go back to Zinc Binding Sites List in 7mk1
Zinc binding site 1 out of 2 in the Structure of A Protein-Modified Aptamer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Protein-Modified Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:32.0
occ:1.00
SG A:CYS869 2.2 30.4 1.0
SG A:CYS864 2.3 35.5 1.0
SG A:CYS813 2.4 34.8 1.0
SG A:CYS810 2.4 30.2 1.0
CB A:CYS864 3.1 30.9 1.0
CB A:CYS810 3.2 30.8 1.0
CB A:CYS869 3.2 31.5 1.0
CB A:CYS813 3.4 33.7 1.0
N A:CYS813 3.8 32.9 1.0
CA A:CYS813 4.2 36.1 1.0
CB A:HIS871 4.5 33.0 1.0
CA A:CYS864 4.5 30.0 1.0
CA A:CYS869 4.6 32.4 1.0
CA A:CYS810 4.6 29.7 1.0
CB A:ALA815 4.7 38.2 1.0
CB A:LYS812 4.7 37.2 1.0
NE1 A:TRP873 4.8 29.6 1.0
CZ2 A:TRP873 4.8 29.5 1.0
C A:CYS813 4.8 35.6 1.0
C A:LYS812 4.9 36.7 1.0
CB A:ARG866 4.9 36.9 1.0
N A:HIS871 4.9 28.3 1.0
N A:LYS814 5.0 32.9 1.0

Zinc binding site 2 out of 2 in 7mk1

Go back to Zinc Binding Sites List in 7mk1
Zinc binding site 2 out of 2 in the Structure of A Protein-Modified Aptamer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Protein-Modified Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:38.3
occ:1.00
SG B:CYS869 2.2 38.1 1.0
SG B:CYS813 2.2 41.6 1.0
SG B:CYS864 2.4 39.4 1.0
SG B:CYS810 2.4 36.4 1.0
CB B:CYS869 3.1 43.0 1.0
CB B:CYS810 3.1 31.8 1.0
CB B:CYS864 3.2 35.3 1.0
CB B:CYS813 3.3 44.6 1.0
N B:CYS813 3.7 42.3 1.0
CA B:CYS813 4.0 41.6 1.0
CB B:ARG866 4.5 52.7 1.0
CA B:CYS869 4.5 43.7 1.0
CG B:ARG866 4.6 61.0 1.0
CA B:CYS810 4.6 30.5 1.0
CA B:CYS864 4.6 38.1 1.0
NE1 B:TRP873 4.7 33.9 1.0
C B:CYS813 4.7 42.0 1.0
CB B:HIS871 4.8 39.4 1.0
N B:LYS814 4.8 41.4 1.0
CZ2 B:TRP873 4.8 35.4 1.0
CB B:ALA815 4.8 48.6 1.0
C B:LYS812 4.8 47.0 1.0
CB B:LYS812 4.9 50.3 1.0

Reference:

X.Ren, A.D.Gelinas, M.Linehan, A.Iwasaki, W.Wang, N.Janjic, A.M.Pyle. Evolving A Rig-I Antagonist: A Modified Dna Aptamer Mimics Viral Rna. J.Mol.Biol. V. 433 67227 2021.
ISSN: ESSN 1089-8638
PubMed: 34487794
DOI: 10.1016/J.JMB.2021.167227
Page generated: Fri Nov 5 16:55:00 2021

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