Magnesium in PDB 4yco: E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe

The structure of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe, PDB code: 4yco was solved by R.T.Byrne, H.T.Jenkins, D.T.Peters, F.Whelan, J.Stowell, N.Aziz, P.Kasatsky, M.V.Rodnina, E.V.Koonin, A.L.Konevega, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.21 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.585, 176.895, 238.413, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.3

The structure of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Magnesium atom in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe (pdb code 4yco). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 25 binding sites of Magnesium where determined in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe, PDB code: 4yco:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:69.8 occ:1.00 O E:HOH213 2.2 71.2 1.0 O B:HOH514 2.2 53.4 1.0 O B:HOH513 2.2 65.9 1.0 O E:HOH212 2.2 65.4 1.0 OP2 E:U20 4.1 81.9 1.0 CD1 B:TYR268 4.1 41.9 1.0 OP1 E:A21 4.2 79.7 1.0 CB B:TYR268 4.6 44.7 1.0 CA B:TYR268 4.8 45.5 1.0 O5' E:U20 4.8 77.8 1.0 CG B:TYR268 4.8 42.7 1.0 O2' E:U20 5.0 85.6 1.0

Magnesium binding site 2 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:51.0 occ:1.00 O D:HOH218 2.2 54.8 1.0 O D:HOH220 2.2 48.6 1.0 O D:HOH217 2.2 52.5 1.0 O D:HOH215 2.2 45.9 1.0 O D:HOH219 2.2 54.3 1.0 O D:HOH216 2.2 49.1 1.0 O D:HOH225 3.9 59.7 1.0 O6 D:G53 4.1 37.3 1.0 O4 D:U54 4.2 36.9 1.0 O2' D:A58 4.3 33.7 1.0 OP1 D:A58 4.3 37.2 1.0 N7 D:G53 4.4 41.7 1.0 C2' D:A58 4.7 33.7 1.0 C6 D:G53 4.9 38.4 1.0 OP2 D:A58 5.0 37.3 1.0

Magnesium binding site 3 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg103 b:66.5 occ:1.00 O D:HOH224 2.2 56.0 1.0 O D:HOH225 2.2 59.7 1.0 O D:HOH221 2.2 60.9 1.0 O D:HOH222 2.2 63.6 1.0 O D:HOH223 2.2 61.2 1.0 O4 D:U51 2.5 44.0 1.0 C4 D:U51 3.4 45.7 1.0 O6 D:G52 3.9 39.1 1.0 C5 D:U51 3.9 45.6 1.0 O D:HOH220 4.4 48.6 1.0 OP1 D:U60 4.4 38.2 1.0 N3 D:U51 4.4 46.3 1.0 O D:HOH218 4.5 54.8 1.0 C6 D:G52 4.9 41.0 1.0 N7 D:G52 4.9 42.4 1.0

Magnesium binding site 4 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg104 b:58.4 occ:1.00 O D:HOH230 2.2 58.7 1.0 O D:HOH226 2.2 60.1 1.0 O D:HOH227 2.2 59.6 1.0 O D:HOH229 2.2 61.9 1.0 O D:HOH231 2.2 55.0 1.0 O D:HOH228 2.2 48.4 1.0 OP2 D:U55 4.1 48.4 1.0 C5 D:U55 4.2 39.4 1.0 OP2 D:G57 4.2 39.5 1.0 OP1 D:G57 4.5 41.4 1.0 OP2 D:C56 4.5 45.5 1.0 C6 D:U55 4.6 39.3 1.0 P D:G57 4.8 40.3 1.0

Magnesium binding site 5 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg105 b:61.5 occ:1.00 O D:HOH237 2.2 58.8 1.0 O D:HOH233 2.2 50.1 1.0 O D:HOH232 2.2 62.2 1.0 O D:HOH236 2.2 56.9 1.0 O D:HOH234 2.2 54.5 1.0 O D:HOH235 2.2 57.2 1.0 N7 D:G27 3.9 49.6 1.0 O6 D:G28 4.2 57.1 1.0 O6 D:G27 4.3 48.9 1.0 O D:HOH284 4.5 53.8 1.0 C5 D:G27 4.6 49.3 1.0 OP2 D:A26 4.6 45.1 1.0 N7 D:G28 4.6 58.8 1.0 C6 D:G27 4.7 49.0 1.0 C8 D:G27 4.7 49.4 1.0 OP2 D:G27 5.0 51.9 1.0

Magnesium binding site 6 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg106 b:48.5 occ:1.00 O D:HOH214 2.2 56.9 1.0 O D:HOH239 2.2 58.2 1.0 O D:HOH201 2.2 58.3 1.0 O D:HOH238 2.2 53.9 1.0 O D:HOH212 2.2 62.7 1.0 N7 D:G18 2.2 38.1 1.0 C8 D:G18 3.1 37.9 1.0 C5 D:G18 3.3 37.3 1.0 O6 D:G18 3.7 38.7 1.0 C6 D:G18 3.9 37.5 1.0 N9 D:G18 4.3 36.9 1.0 O6 D:G57 4.4 36.1 1.0 O D:HOH262 4.4 38.1 1.0 C4 D:G18 4.5 36.4 1.0 O D:HOH259 4.5 39.5 1.0 OP1 D:G18 4.9 42.7 1.0

Magnesium binding site 7 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg107 b:39.7 occ:1.00 OP2 D:C17 2.0 38.1 1.0 OP2 D:G19 2.1 36.0 1.0 O D:HOH241 2.1 44.0 1.0 O D:HOH240 2.1 42.1 1.0 O D:HOH242 2.1 43.8 1.0 O A:HOH501 2.2 37.5 1.0 P D:G19 3.3 35.5 1.0 P D:C17 3.4 38.2 1.0 O D:HOH278 3.5 43.3 1.0 OP1 D:G19 3.7 35.0 1.0 OP1 D:C17 3.9 38.3 1.0 O D:HOH273 4.0 34.9 1.0 O3' D:U16 4.1 39.3 1.0 OE1 A:GLU9 4.1 49.8 1.0 O5' D:G19 4.1 34.7 1.0 C3' D:U16 4.2 39.0 1.0 O D:HOH252 4.3 37.9 1.0 O A:GLU9 4.4 31.3 1.0 O2' D:U16 4.4 39.6 1.0 O D:HOH245 4.5 31.8 1.0 O3' D:G18 4.5 35.8 1.0 O5' D:C17 4.5 39.8 1.0 OE1 A:GLN275 4.7 33.6 1.0 C3' D:G18 4.7 36.7 1.0 C2' D:U16 4.7 39.1 1.0 O A:HOH518 4.9 38.0 1.0

Magnesium binding site 8 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg108 b:56.4 occ:1.00 O D:HOH211 2.2 56.6 1.0 O D:HOH207 3.6 55.2 1.0 O2 D:C61 3.9 38.6 1.0 O2' D:C61 3.9 42.0 1.0 N6 D:A58 4.3 34.4 1.0 O2 D:U54 4.3 39.4 1.0 C1' D:C61 4.6 38.5 1.0 C2' D:C61 4.8 40.0 1.0 O D:HOH201 4.8 58.3 1.0 O2' D:U54 4.8 42.9 1.0 C2 D:C61 5.0 37.0 1.0

Magnesium binding site 9 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg109 b:53.7 occ:1.00 N7 D:G46 2.2 73.8 1.0 O D:HOH243 2.2 53.7 1.0 OP2 D:U45 2.5 78.6 1.0 C8 D:G46 2.9 77.1 1.0 O4' D:U45 3.3 86.0 1.0 C5 D:G46 3.4 73.2 1.0 O2 D:U45 3.6 84.3 1.0 C5' D:U45 3.7 85.2 1.0 P D:U45 3.7 79.9 1.0 C4' D:U45 3.8 87.3 1.0 O6 D:G46 4.0 68.7 1.0 O5' D:U45 4.1 82.9 1.0 C6 D:G46 4.1 70.7 1.0 N9 D:G46 4.2 79.1 1.0 N7 D:A21 4.3 37.3 1.0 C2 D:U45 4.4 85.8 1.0 C4 D:G46 4.4 76.2 1.0 C1' D:U45 4.5 88.6 1.0 OP1 D:U45 4.5 79.2 1.0 C8 D:A21 4.6 37.1 1.0 N1 D:U45 4.9 88.0 1.0 O3' D:G44 4.9 78.9 1.0

Magnesium binding site 10 out of 25 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnaphe within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:64.9 occ:1.00 O E:HOH211 2.2 61.5 1.0 O E:HOH206 2.2 64.0 1.0 O E:HOH207 2.2 60.3 1.0 O E:HOH210 2.2 63.1 1.0 O E:HOH208 2.2 62.8 1.0 O E:HOH209 2.2 60.3 1.0 O E:HOH229 3.7 73.4 1.0 O4 E:U54 3.9 53.6 1.0 O6 E:G53 4.1 49.5 1.0 O2' E:A58 4.3 45.5 1.0 O E:HOH251 4.4 51.5 1.0 N7 E:G53 4.5 52.9 1.0 O E:HOH233 4.6 79.3 1.0 OP1 E:A58 4.7 50.9 1.0 C2' E:A58 4.8 45.9 1.0 C6 E:G53 4.9 51.8 1.0 O E:HOH232 5.0 75.3 1.0

R.T.Byrne, H.T.Jenkins, D.T.Peters, F.Whelan, J.Stowell, N.Aziz, P.Kasatsky, M.V.Rodnina, E.V.Koonin, A.L.Konevega, A.A.Antson. Major Reorientation of Trna Substrates Defines Specificity of Dihydrouridine Synthases. Proc.Natl.Acad.Sci.Usa V. 112 6033 2015.
ISSN: ESSN 1091-6490
PubMed: 25902496
DOI: 10.1073/PNAS.1500161112