Atomistry » Magnesium » PDB 4y8o-4yf4 » 4yco
Atomistry »
  Magnesium »
    PDB 4y8o-4yf4 »
      4yco »

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

Protein crystallography data

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

Other elements in 4yco:

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

Manganese (Mn) 3 atoms

Magnesium Binding Sites:

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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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 4yco

Go back to Magnesium Binding Sites List in 4yco
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

Reference:

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
Page generated: Sat Sep 28 23:13:37 2024

Last articles

Mg in 2MSE
Mg in 2MSD
Mg in 2MSC
Mg in 2M2W
Mg in 2M2U
Mg in 2M32
Mg in 2LWI
Mg in 2LVJ
Mg in 2L4I
Mg in 2LCF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy