Magnesium in PDB 6ywo: Cuta in Complex with A3 Rna

The structure of Cuta in Complex with A3 Rna, PDB code: 6ywo was solved by D.Malik, K.Kobylecki, P.Krawczyk, J.Poznanski, A.Jakielaszek, A.Napiorkowska, A.Dziembowski, R.Tomecki, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.26 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.920, 56.950, 149.890, 79.86, 87.12, 75.83
R / Rfree (%)	17.6 / 21.3

The structure of Cuta in Complex with A3 Rna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cuta in Complex with A3 Rna (pdb code 6ywo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cuta in Complex with A3 Rna, PDB code: 6ywo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:47.2 occ:1.00 O A:HOH1024 2.1 57.0 1.0 O A:HOH917 2.1 55.9 1.0 O A:HOH1032 2.2 52.4 1.0 OD1 A:ASP341 2.4 37.5 1.0 OD2 A:ASP341 2.6 46.3 1.0 OP1 F:A0 2.7 59.3 0.9 CG A:ASP341 2.8 43.6 1.0 O3' F:A-1 3.3 63.4 0.9 P F:A0 3.6 62.6 0.9 OD2 A:ASP392 4.1 41.5 1.0 O A:HOH858 4.1 46.2 1.0 CB A:ASP341 4.3 32.2 1.0 CB A:ASP339 4.4 39.6 1.0 C3' F:A-1 4.5 67.3 0.9 O2' F:A-1 4.6 63.5 0.9 CG A:ASP392 4.6 37.0 1.0 OP2 F:A0 4.6 65.7 0.9 O5' F:A0 4.7 62.5 0.9 CB A:ASP392 4.7 28.5 1.0 C5' F:A0 4.8 59.8 0.9 O A:VAL340 4.8 34.2 1.0 CA A:ASP341 4.9 28.5 1.0 N A:ASP341 5.0 28.2 1.0

Magnesium binding site 2 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:38.2 occ:1.00 O A:HOH946 2.3 50.8 1.0 O A:HOH974 2.4 53.2 1.0 O A:HOH886 2.4 37.8 1.0 OD1 A:ASN545 2.4 28.8 1.0 O A:HOH962 2.5 44.9 1.0 O A:HOH1043 3.0 63.7 1.0 CG A:ASN545 3.4 33.1 1.0 ND2 A:ASN545 3.8 30.9 1.0 OE1 A:GLU565 4.2 39.6 0.5 O A:HOH1081 4.2 47.7 1.0 OE1 A:GLU565 4.4 43.7 0.5 O A:LEU542 4.5 26.6 1.0 N A:ASN545 4.7 28.6 1.0 CB A:ASN545 4.7 27.0 1.0 CD A:GLU565 4.8 47.4 0.5 CD A:GLU565 4.9 47.1 0.5 N A:ALA546 5.0 27.5 1.0

Magnesium binding site 3 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:52.1 occ:1.00 O B:HOH1009 2.2 64.8 1.0 OD1 B:ASP341 2.3 47.4 1.0 O B:HOH987 2.4 47.3 1.0 OP1 E:A0 2.5 95.1 0.9 OD2 B:ASP341 2.8 47.7 1.0 CG B:ASP341 2.9 44.9 1.0 O3' E:A-1 3.2 97.9 1.0 P E:A0 3.4 96.2 0.9 O B:HOH833 4.2 44.8 1.0 OD2 B:ASP392 4.2 44.8 1.0 OP2 E:A0 4.4 97.5 0.9 CB B:ASP341 4.4 36.1 1.0 CB B:ASP339 4.5 39.6 1.0 C3' E:A-1 4.5 98.9 1.0 O5' E:A0 4.6 94.4 0.9 CG B:ASP392 4.7 42.6 1.0 C5' E:A0 4.7 92.7 0.9 O2' E:A-1 4.7 98.6 1.0 CB B:ASP392 4.8 36.1 1.0 CA B:ASP341 5.0 30.2 1.0

Magnesium binding site 4 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:41.1 occ:1.00 O B:HOH921 2.3 47.6 1.0 OD1 B:ASN545 2.3 30.6 1.0 O B:HOH911 2.4 39.8 1.0 O B:HOH817 2.5 42.3 1.0 O B:HOH1038 2.5 51.8 1.0 CG B:ASN545 3.3 32.9 1.0 OE2 B:GLU565 3.5 57.9 1.0 ND2 B:ASN545 3.7 31.2 1.0 CD B:GLU565 4.5 48.8 1.0 O B:LEU542 4.5 27.1 1.0 N B:ASN545 4.6 28.9 1.0 CB B:ASN545 4.7 25.4 1.0 N B:ALA546 4.9 28.3 1.0 C B:ASN545 4.9 25.3 1.0 CA B:ASN545 5.0 27.5 1.0

Magnesium binding site 5 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:58.0 occ:1.00 O B:HOH966 2.2 58.0 1.0 OD1 B:ASP289 2.5 54.8 1.0 CG B:ASP289 3.5 48.3 1.0 CD2 B:TYR288 3.6 39.2 1.0 O B:ARG285 3.6 38.2 1.0 OD2 B:ASP289 3.8 54.8 1.0 CB B:ARG285 3.9 50.8 1.0 CE2 B:TYR288 4.2 36.0 1.0 CD B:ARG285 4.3 61.0 1.0 CA B:ARG285 4.3 42.1 1.0 CG B:ARG285 4.3 58.2 1.0 C B:ARG285 4.3 36.9 1.0 NH1 B:ARG285 4.4 58.1 1.0 CG B:TYR288 4.6 34.2 1.0 N B:ASP289 4.6 32.5 1.0 CB B:TYR288 4.7 31.0 1.0 CB B:ASP289 4.8 36.5 1.0 CA B:ASP289 4.9 33.3 1.0

Magnesium binding site 6 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:25.3 occ:1.00 O B:HOH1008 2.3 45.8 1.0 O B:HOH1003 2.5 45.2 1.0 OE1 B:GLU359 2.5 35.8 1.0 O B:HOH1035 2.6 42.9 1.0 CD B:GLU359 3.4 33.9 1.0 O D:HOH979 3.8 53.9 1.0 CG B:GLU359 3.9 29.7 1.0 OE2 B:GLU359 4.3 29.7 1.0 O D:HOH821 4.4 42.5 1.0 NE B:ARG363 4.5 36.4 1.0 O D:HOH827 4.7 28.1 1.0 O D:HOH831 4.8 40.1 1.0

Magnesium binding site 7 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:58.5 occ:1.00 O C:HOH946 1.9 59.0 1.0 OP1 I:A0 2.5 96.6 0.9 O C:HOH971 2.5 51.4 1.0 OD1 C:ASP341 2.7 45.0 1.0 OD2 C:ASP341 2.8 47.9 1.0 O C:HOH969 2.8 55.4 1.0 CG C:ASP341 3.1 45.5 1.0 O3' I:A-1 3.6 0.9 1.0 P I:A0 3.6 95.7 0.9 O C:HOH813 4.1 44.9 1.0 CB C:ASP339 4.4 41.7 1.0 OP2 I:A0 4.5 94.7 0.9 CB C:ASP341 4.6 32.3 1.0 O C:HOH911 4.6 45.0 1.0 OD2 C:ASP392 4.8 50.9 1.0 O5' I:A0 4.8 92.2 0.9 O C:ASP339 4.8 36.6 1.0 C C:ASP339 4.9 40.3 1.0 O C:HOH805 4.9 42.8 1.0 C5' I:A0 4.9 91.0 0.9 C3' I:A-1 4.9 0.6 1.0

Magnesium binding site 8 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:49.7 occ:1.00 OD1 C:ASN545 2.3 31.4 1.0 O C:HOH892 2.5 45.0 1.0 O C:HOH951 2.5 46.0 1.0 O C:HOH936 2.6 45.8 1.0 O C:HOH854 2.7 44.5 1.0 O C:HOH954 2.8 60.4 1.0 CG C:ASN545 3.3 31.1 1.0 O C:HOH907 3.6 47.7 1.0 ND2 C:ASN545 3.7 29.9 1.0 OE2 C:GLU565 4.1 54.7 1.0 O C:HOH827 4.2 51.6 1.0 O C:LEU542 4.4 30.0 1.0 CD C:GLU565 4.5 53.9 1.0 OE1 C:GLU565 4.5 67.2 1.0 N C:ASN545 4.6 27.3 1.0 CB C:ASN545 4.6 25.0 1.0 N C:ALA546 4.9 27.7 1.0 C C:ASN545 4.9 26.7 1.0 CA C:ASN545 5.0 27.2 1.0

Magnesium binding site 9 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:44.1 occ:1.00 O D:HOH891 2.4 48.9 1.0 O D:HOH862 2.4 41.0 1.0 OD1 D:ASN545 2.5 32.9 1.0 O D:HOH993 2.5 55.5 1.0 O D:HOH916 2.6 47.1 1.0 CG D:ASN545 3.5 37.6 1.0 ND2 D:ASN545 3.8 30.3 1.0 OE2 D:GLU565 4.1 57.8 1.0 O D:HOH957 4.4 50.1 1.0 CD D:GLU565 4.5 58.8 1.0 O D:LEU542 4.7 31.8 1.0 N D:ASN545 4.7 29.8 1.0 OE1 D:GLU565 4.7 71.9 1.0 CB D:ASN545 4.8 28.8 1.0 N D:ALA546 4.9 31.0 1.0 O D:HOH990 4.9 48.8 1.0

Magnesium binding site 10 out of 12 in the Cuta in Complex with A3 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cuta in Complex with A3 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:52.1 occ:1.00 O D:HOH958 2.1 50.5 1.0 O D:HOH972 2.2 63.7 1.0 OD1 D:ASP341 2.5 46.4 1.0 O D:HOH860 2.5 61.6 1.0 OP1 K:A0 2.8 75.1 1.0 O3' K:A-1 3.1 76.6 0.7 CG D:ASP341 3.2 47.2 1.0 OD2 D:ASP341 3.3 49.5 1.0 P K:A0 3.5 93.9 1.0 OD2 D:ASP392 3.6 47.9 1.0 CG D:ASP392 4.2 41.8 1.0 C3' K:A-1 4.3 76.0 0.7 CB D:ASP392 4.4 31.5 1.0 O2' K:A-1 4.4 70.7 0.7 OP2 K:A0 4.4 82.9 1.0 CB D:ASP339 4.6 45.5 1.0 CB D:ASP341 4.6 37.5 1.0 C4' K:A-1 4.7 75.4 0.7 O5' K:A0 4.7 82.9 1.0 C2' K:A-1 5.0 74.0 0.7 OD2 D:ASP339 5.0 69.9 1.0

D.Malik, K.Kobylecki, P.Krawczyk, J.Poznanski, A.Jakielaszek, A.Napiorkowska, A.Dziembowski, R.Tomecki, M.Nowotny. Structure and Mechanism of Cuta, Rna Nucleotidyl Transferase with An Unusual Preference For Cytosine. Nucleic Acids Res. V. 48 9387 2020.
ISSN: ESSN 1362-4962
PubMed: 32785623
DOI: 10.1093/NAR/GKAA647