Magnesium in PDB 5kal: Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu

The structure of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu, PDB code: 5kal was solved by J.R.Stagno, H.Luecke, R.Afasizhev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.13 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.688, 42.876, 109.618, 90.00, 94.05, 90.00
R / Rfree (%)	21.4 / 25.9

The binding sites of Magnesium atom in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu (pdb code 5kal). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu, PDB code: 5kal:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.9 occ:1.00 O A:HOH602 2.2 35.8 1.0 O3G A:UTP501 2.2 20.7 1.0 OD1 A:ASP66 2.2 30.8 1.0 O A:HOH638 2.3 36.9 1.0 O1B A:UTP501 2.5 16.5 1.0 O1A A:UTP501 2.6 26.6 1.0 OD2 A:ASP68 2.7 29.7 1.0 CG A:ASP66 3.2 32.0 1.0 OD2 A:ASP66 3.5 31.0 1.0 PG A:UTP501 3.6 21.8 1.0 H5'2 A:UTP501 3.6 33.7 1.0 O A:HOH649 3.7 30.8 1.0 PB A:UTP501 3.7 19.1 1.0 O A:HOH624 3.7 23.7 1.0 CG A:ASP68 3.8 28.1 1.0 PA A:UTP501 3.8 19.5 1.0 MG Y:MG101 3.9 17.7 1.0 HG A:SER54 4.0 35.7 1.0 O3B A:UTP501 4.0 25.4 1.0 OD1 A:ASP68 4.0 27.8 1.0 H A:ASP66 4.1 43.1 1.0 H5'1 A:UTP501 4.1 33.7 1.0 H A:SER54 4.1 35.8 1.0 O A:HOH610 4.2 16.4 1.0 O3A A:UTP501 4.2 22.0 1.0 C5' A:UTP501 4.2 28.0 1.0 O1G A:UTP501 4.5 21.2 1.0 O5' A:UTP501 4.5 16.6 1.0 HA3 A:GLY53 4.6 33.7 1.0 O2G A:UTP501 4.6 24.7 1.0 O A:ASP66 4.6 28.2 1.0 CB A:ASP66 4.6 34.2 1.0 O A:HOH665 4.7 17.6 1.0 OG A:SER54 4.7 29.6 1.0 C A:ASP66 4.7 31.3 1.0 N A:ASP66 4.7 35.8 1.0 HB3 A:SER65 4.8 54.9 1.0 CA A:ASP66 4.9 34.1 1.0 O2B A:UTP501 4.9 20.4 1.0 HB3 A:SER54 5.0 37.1 1.0 O3' Y:U2 5.0 23.0 1.0 N A:SER54 5.0 29.7 1.0

Magnesium binding site 2 out of 5 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:31.7 occ:1.00 O3G B:UTP401 2.2 38.2 1.0 O B:HOH507 2.2 37.0 1.0 O B:HOH508 2.2 32.5 1.0 O1B B:UTP401 2.3 31.6 1.0 O1A B:UTP401 2.3 42.5 1.0 OD2 B:ASP68 2.8 51.0 1.0 OD1 B:ASP66 2.8 63.8 1.0 H5'2 B:UTP401 3.2 54.9 1.0 PB B:UTP401 3.4 33.0 1.0 PG B:UTP401 3.4 38.9 1.0 PA B:UTP401 3.5 38.7 1.0 MG Z:MG101 3.5 40.9 1.0 H5'1 B:UTP401 3.6 54.9 1.0 CG B:ASP68 3.7 52.1 1.0 C5' B:UTP401 3.7 45.7 1.0 O3B B:UTP401 3.8 37.3 1.0 O B:HOH527 3.8 39.1 1.0 O3A B:UTP401 3.8 32.5 1.0 CG B:ASP66 3.8 64.6 1.0 OD1 B:ASP68 3.9 51.9 1.0 O5' B:UTP401 4.0 42.2 1.0 O B:HOH505 4.1 36.3 1.0 O1G B:UTP401 4.1 36.8 1.0 OD2 B:ASP66 4.1 66.2 1.0 H B:SER54 4.2 46.0 1.0 HA3 B:GLY53 4.5 47.9 1.0 H B:ASP66 4.6 71.3 1.0 O2G B:UTP401 4.6 38.5 1.0 O2B B:UTP401 4.6 32.4 1.0 O2A B:UTP401 4.7 39.4 1.0 HO3' Z:U2 4.7 67.7 1.0 OG B:SER54 4.9 42.7 1.0 O B:ASP66 5.0 55.6 1.0

Magnesium binding site 3 out of 5 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:66.7 occ:1.00 OD2 B:ASP66 2.1 66.2 1.0 OD1 B:ASP136 2.1 69.9 1.0 CG B:ASP136 2.9 67.0 1.0 CG B:ASP66 3.0 64.6 1.0 HB3 B:ASP66 3.0 77.6 1.0 HB2 B:ASP66 3.0 77.6 1.0 HE B:ARG126 3.1 0.4 1.0 OD2 B:ASP136 3.2 66.0 1.0 HG3 B:ARG126 3.2 0.8 1.0 CB B:ASP66 3.2 64.6 1.0 NE B:ARG126 3.5 0.9 1.0 HD3 B:ARG126 3.6 0.9 1.0 O B:HOH527 3.8 39.1 1.0 CD B:ARG126 3.9 0.2 1.0 CG B:ARG126 4.0 0.4 1.0 HA B:PHE135 4.0 67.4 1.0 C B:PHE135 4.1 58.0 1.0 N B:ASP136 4.1 67.0 1.0 H B:ASP136 4.2 80.6 1.0 OD1 B:ASP66 4.2 63.8 1.0 CB B:ASP136 4.2 67.1 1.0 CZ B:ARG126 4.3 0.1 1.0 HH21 B:ARG126 4.4 0.3 1.0 HG2 B:ARG126 4.4 0.8 1.0 O B:PHE135 4.4 54.0 1.0 CA B:PHE135 4.4 56.1 1.0 HB2 B:ASP136 4.5 80.6 1.0 N B:PHE135 4.5 66.5 1.0 H B:PHE135 4.6 79.9 1.0 NH2 B:ARG126 4.6 0.5 1.0 HB3 B:ASP134 4.6 0.6 1.0 CA B:ASP136 4.6 70.2 1.0 CA B:ASP66 4.7 61.3 1.0 HA B:ASP136 4.8 84.4 1.0 O B:HOH507 4.8 37.0 1.0 HD2 B:ARG126 4.8 0.9 1.0 H B:VAL67 4.9 70.9 1.0 HB3 B:ASP136 4.9 80.6 1.0 O B:HOH558 4.9 37.5 1.0 C B:ASP134 5.0 79.9 1.0 HB2 B:ASP134 5.0 0.6 1.0

Magnesium binding site 4 out of 5 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg101 b:17.7 occ:1.00 O A:HOH649 2.2 30.8 1.0 O A:HOH613 2.2 21.2 1.0 O A:HOH610 2.2 16.4 1.0 O3' Y:U2 2.2 23.0 1.0 O A:HOH602 2.2 35.8 1.0 O Y:HOH205 2.3 15.9 1.0 O1A A:UTP501 2.5 26.6 1.0 PA A:UTP501 3.4 19.5 1.0 O2A A:UTP501 3.5 18.8 1.0 C3' Y:U2 3.5 24.7 1.0 H3' Y:U2 3.7 29.7 1.0 H5'' Y:U2 3.8 49.1 1.0 MG A:MG502 3.9 17.9 1.0 O5' A:UTP501 4.0 16.6 1.0 OD2 A:ASP66 4.0 31.0 1.0 C4' Y:U2 4.3 30.8 1.0 H4' Y:U2 4.3 37.1 1.0 OD1 A:ASP68 4.3 27.8 1.0 H5'2 A:UTP501 4.4 33.7 1.0 HO2' Y:U2 4.4 21.9 1.0 OD2 A:ASP136 4.5 37.4 1.0 C5' Y:U2 4.5 40.9 1.0 O3G A:UTP501 4.6 20.7 1.0 OP1 Y:U2 4.7 57.5 1.0 C2' Y:U2 4.7 22.9 1.0 C5' A:UTP501 4.8 28.0 1.0 O A:HOH716 4.8 45.6 1.0 HH21 A:ARG126 4.8 87.1 1.0 O2' Y:U2 4.9 18.2 1.0 O A:HOH691 4.9 16.5 1.0 O3A A:UTP501 4.9 22.0 1.0 CG A:ASP66 4.9 32.0 1.0 OD1 A:ASP66 4.9 30.8 1.0 H2' Y:U2 4.9 27.6 1.0 OD2 A:ASP68 5.0 29.7 1.0

Magnesium binding site 5 out of 5 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Upu within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg101 b:40.9 occ:1.00 HO3' Z:U2 1.8 67.7 1.0 O B:HOH506 2.2 42.2 1.0 O B:HOH505 2.2 36.3 1.0 O B:HOH527 2.2 39.1 1.0 O B:HOH507 2.2 37.0 1.0 O Z:HOH202 2.2 54.0 1.0 O1A B:UTP401 2.3 42.5 1.0 O3' Z:U2 2.3 56.3 1.0 PA B:UTP401 3.3 38.7 1.0 MG B:MG402 3.5 31.7 1.0 O2A B:UTP401 3.6 39.4 1.0 O5' B:UTP401 3.7 42.2 1.0 C3' Z:U2 3.7 55.3 1.0 H3' Z:U2 3.9 66.4 1.0 H5'2 B:UTP401 4.0 54.9 1.0 HO2' Z:U2 4.1 60.9 1.0 O5' Z:U2 4.2 60.2 1.0 OD1 B:ASP68 4.3 51.9 1.0 OD2 B:ASP66 4.4 66.2 1.0 C5' B:UTP401 4.4 45.7 1.0 O B:HOH558 4.4 37.5 1.0 OD2 B:ASP136 4.5 66.0 1.0 H4' Z:U2 4.6 70.1 1.0 O3G B:UTP401 4.6 38.2 1.0 C2' Z:U2 4.6 51.5 1.0 HH21 B:ARG126 4.7 0.3 1.0 C4' Z:U2 4.7 58.3 1.0 O2' Z:U2 4.7 50.6 1.0 OP1 Z:U2 4.7 55.3 1.0 O B:HOH546 4.7 48.8 1.0 H2' Z:U2 4.8 61.9 1.0 O3A B:UTP401 4.8 32.5 1.0 O1G B:UTP401 4.8 36.8 1.0 OD1 B:ASP66 4.9 63.8 1.0 H5'1 B:UTP401 4.9 54.9 1.0 OD2 B:ASP68 5.0 51.0 1.0 H6 B:UTP401 5.0 52.1 1.0

L.Rajappa-Titu, T.Suematsu, P.Munoz-Tello, M.Long, O.Demir, K.J.Cheng, J.R.Stagno, H.Luecke, R.E.Amaro, I.Aphasizheva, R.Aphasizhev, S.Thore. Rna Editing Tutase 1: Structural Foundation of Substrate Recognition, Complex Interactions and Drug Targeting. Nucleic Acids Res. V. 44 10862 2016.
ISSN: ESSN 1362-4962
PubMed: 27744351
DOI: 10.1093/NAR/GKW917