Atomistry » Magnesium » PDB 5k0n-5kft » 5kal
Atomistry »
  Magnesium »
    PDB 5k0n-5kft »
      5kal »

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

Protein crystallography data

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

Magnesium Binding Sites:

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 5kal

Go back to Magnesium Binding Sites List in 5kal
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 5kal

Go back to Magnesium Binding Sites List in 5kal
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 5kal

Go back to Magnesium Binding Sites List in 5kal
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 5kal

Go back to Magnesium Binding Sites List in 5kal
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 5kal

Go back to Magnesium Binding Sites List in 5kal
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

Reference:

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
Page generated: Mon Dec 14 20:37:14 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy