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

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

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

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

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of A Protein-Modified Aptamer Complex (pdb code 7mk1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of A Protein-Modified Aptamer Complex, PDB code: 7mk1:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of Structure of A Protein-Modified Aptamer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:6.1 occ:1.00 O A:HOH1104 1.6 27.4 1.0 OE2 A:GLU890 1.7 27.1 1.0 OP1 C:QGJ23 1.8 21.1 1.0 O A:HOH1105 1.9 25.9 1.0 OAS C:QGJ23 2.0 27.3 1.0 N7 C:DG24 2.1 27.5 1.0 CD A:GLU890 2.9 35.0 1.0 C8 C:DG24 3.0 28.9 1.0 CAP C:QGJ23 3.0 26.5 1.0 P C:QGJ23 3.2 27.2 1.0 C5 C:DG24 3.2 30.1 1.0 OE1 A:GLU890 3.4 38.6 1.0 O5' C:QGJ23 3.6 25.4 1.0 O6 C:DG24 3.7 26.5 1.0 C6 C:DG24 3.8 28.3 1.0 NAQ C:QGJ23 3.9 26.9 1.0 C5 C:QGJ23 3.9 27.6 1.0 C6 C:QGJ23 3.9 27.5 1.0 CAR C:QGJ23 4.0 30.1 1.0 O C:HOH161 4.2 25.8 1.0 CG A:GLU890 4.2 36.1 1.0 N9 C:DG24 4.2 29.5 1.0 O3' C:DA22 4.2 27.2 1.0 OP2 C:QGJ23 4.2 27.0 1.0 C2' C:DA22 4.3 27.4 1.0 C3' C:DA22 4.3 27.4 1.0 O A:HOH1198 4.3 35.2 1.0 C4 C:DG24 4.3 29.4 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of Structure of A Protein-Modified Aptamer Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:6.0 occ:1.00 OE2 B:GLU890 1.8 28.1 1.0 O B:HOH1111 1.8 27.4 1.0 O B:HOH1110 1.8 22.7 1.0 OP2 D:QGJ23 1.9 21.9 1.0 OAS D:QGJ23 2.1 28.5 1.0 N7 D:DG24 2.1 31.1 1.0 CD B:GLU890 2.9 30.6 1.0 C8 D:DG24 3.0 34.0 1.0 CAP D:QGJ23 3.0 29.9 1.0 C5 D:DG24 3.2 30.6 1.0 P D:QGJ23 3.3 28.0 1.0 OE1 B:GLU890 3.4 32.1 1.0 O6 D:DG24 3.7 32.2 1.0 O5' D:QGJ23 3.7 27.9 1.0 C6 D:DG24 3.8 30.4 1.0 NAQ D:QGJ23 3.8 31.6 1.0 C5 D:QGJ23 4.0 31.4 1.0 CAR D:QGJ23 4.0 30.1 1.0 C6 D:QGJ23 4.0 33.3 1.0 O B:HOH1131 4.1 26.8 1.0 N9 D:DG24 4.2 32.9 1.0 CG B:GLU890 4.3 30.3 1.0 OP1 D:QGJ23 4.3 27.8 1.0 C2' D:DA22 4.3 27.4 1.0 O B:HOH1187 4.3 38.5 1.0 O3' D:DA22 4.3 27.2 1.0 C3' D:DA22 4.3 26.8 1.0 C4 D:DG24 4.4 32.0 1.0 CAZ D:QGJ25 4.7 42.6 1.0 CB B:SER906 4.9 26.9 1.0 O B:SER906 4.9 27.8 1.0 CAY D:QGJ25 5.0 42.6 1.0

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