Magnesium in PDB 5jji: Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules

The structure of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules, PDB code: 5jji was solved by N.D.Thomsen, M.R.Lawson, L.B.Witkowsky, S.Qu, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.997, 198.567, 111.448, 90.00, 104.36, 90.00
R / Rfree (%)	21.9 / 24.6

The structure of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules also contains other interesting chemical elements:

Fluorine

(F)

18 atoms

The binding sites of Magnesium atom in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules (pdb code 5jji). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules, PDB code: 5jji:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:46.0 occ:1.00 OG1 A:THR185 1.9 39.2 1.0 O A:HOH1103 1.9 30.6 1.0 F3 A:BEF1002 2.0 33.2 1.0 O A:HOH1112 2.0 40.3 1.0 O A:HOH1106 2.1 29.9 1.0 O1B A:ADP1000 2.2 33.4 1.0 CB A:THR185 3.1 34.9 1.0 PB A:ADP1000 3.3 32.9 1.0 BE A:BEF1002 3.3 32.8 1.0 O2B A:ADP1000 3.4 31.9 1.0 OE2 A:GLU215 3.8 45.6 1.0 N A:THR185 3.8 35.4 1.0 NH1 A:ARG212 3.9 30.6 1.0 O1A A:ADP1000 3.9 50.2 1.0 CA A:THR185 4.0 35.8 1.0 OE1 A:GLU215 4.1 65.9 1.0 F2 A:BEF1002 4.1 36.5 1.0 CG2 A:THR185 4.1 35.5 1.0 OD1 A:ASP265 4.3 44.4 1.0 OD2 A:ASP265 4.3 48.2 1.0 CD A:GLU215 4.3 50.3 1.0 OE2 A:GLU211 4.3 67.1 1.0 O3A A:ADP1000 4.4 54.1 1.0 O3B A:ADP1000 4.4 33.0 1.0 F1 A:BEF1002 4.4 30.3 1.0 PA A:ADP1000 4.5 34.1 1.0 O2A A:ADP1000 4.6 35.2 1.0 NH2 B:ARG366 4.6 34.6 1.0 CG A:ASP265 4.7 41.7 1.0 CB A:LYS184 4.9 37.4 1.0 CD A:GLU211 4.9 59.3 1.0 C A:LYS184 4.9 36.0 1.0

Magnesium binding site 2 out of 6 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.0 occ:1.00 OG1 B:THR185 2.0 35.8 1.0 O B:HOH602 2.0 29.9 1.0 O B:HOH642 2.0 29.9 1.0 F3 B:BEF503 2.0 30.6 1.0 O1B B:ADP501 2.2 33.5 1.0 O B:HOH615 2.2 29.9 1.0 CB B:THR185 3.2 22.1 1.0 BE B:BEF503 3.3 20.4 1.0 PB B:ADP501 3.3 27.5 1.0 O2B B:ADP501 3.3 27.9 1.0 NH1 B:ARG212 3.8 30.7 1.0 O2A B:ADP501 3.8 41.0 1.0 N B:THR185 3.9 29.3 1.0 OE2 B:GLU215 3.9 49.4 1.0 F2 B:BEF503 4.0 23.4 1.0 CA B:THR185 4.1 24.6 1.0 OD2 B:ASP265 4.1 27.8 1.0 OE1 B:GLU215 4.1 54.5 1.0 O B:HOH635 4.2 36.6 1.0 CG2 B:THR185 4.2 22.7 1.0 O3B B:ADP501 4.3 27.6 1.0 O3A B:ADP501 4.4 34.3 1.0 OD1 B:ASP265 4.4 47.7 1.0 CD B:GLU215 4.4 40.9 1.0 PA B:ADP501 4.4 28.1 1.0 F1 B:BEF503 4.4 29.1 1.0 OE2 B:GLU211 4.5 51.2 1.0 O1A B:ADP501 4.7 28.2 1.0 CG B:ASP265 4.7 29.6 1.0 NH2 C:ARG366 4.7 21.4 1.0 CD B:GLU211 4.8 54.6 1.0 O C:HOH1133 4.8 29.9 1.0 OE1 B:GLU211 5.0 55.9 1.0

Magnesium binding site 3 out of 6 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:45.6 occ:1.00 OG1 C:THR185 1.9 35.7 1.0 F3 C:BEF1002 1.9 30.3 1.0 O C:HOH1105 1.9 31.1 1.0 O C:HOH1145 2.0 29.9 1.0 O C:HOH1104 2.2 34.2 1.0 O2B C:ADP1000 2.2 39.6 1.0 CB C:THR185 3.1 28.0 1.0 BE C:BEF1002 3.2 32.3 1.0 PB C:ADP1000 3.3 41.1 1.0 O3B C:ADP1000 3.3 39.7 1.0 O2A C:ADP1000 3.8 47.4 1.0 NH1 C:ARG212 3.8 30.9 1.0 N C:THR185 3.9 39.0 1.0 OD2 C:ASP265 3.9 40.9 1.0 OE2 C:GLU215 3.9 42.5 1.0 F2 C:BEF1002 4.0 36.0 1.0 CA C:THR185 4.0 33.0 1.0 CG2 C:THR185 4.1 29.0 1.0 OE2 C:GLU211 4.2 46.0 1.0 O3A C:ADP1000 4.3 29.3 1.0 O1B C:ADP1000 4.4 31.1 1.0 F1 C:BEF1002 4.4 53.3 1.0 OE1 C:GLU215 4.4 57.1 1.0 PA C:ADP1000 4.4 33.7 1.0 O C:HOH1155 4.4 29.9 1.0 NH2 D:ARG366 4.4 30.1 1.0 OD1 C:ASP265 4.4 35.2 1.0 CD C:GLU215 4.5 40.7 1.0 CG C:ASP265 4.6 30.9 1.0 O1A C:ADP1000 4.6 30.7 1.0 O C:HOH1146 4.7 29.9 1.0 CD C:GLU211 4.7 41.6 1.0

Magnesium binding site 4 out of 6 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:46.8 occ:1.00 OG1 D:THR185 2.0 47.3 1.0 F3 D:BEF1002 2.0 39.9 1.0 O D:HOH1126 2.0 29.9 1.0 O D:HOH1111 2.1 29.9 1.0 O D:HOH1133 2.1 36.7 1.0 O2B D:ADP1000 2.2 58.9 1.0 CB D:THR185 3.1 43.1 1.0 PB D:ADP1000 3.2 41.7 1.0 O3B D:ADP1000 3.3 54.2 1.0 BE D:BEF1002 3.3 44.3 1.0 O D:HOH1121 3.8 43.5 1.0 N D:THR185 3.8 47.9 1.0 NH1 D:ARG212 3.8 48.3 1.0 O2A D:ADP1000 4.0 51.8 1.0 CA D:THR185 4.0 42.8 1.0 OD2 D:ASP265 4.0 55.6 1.0 OE2 D:GLU215 4.0 53.8 1.0 CG2 D:THR185 4.2 44.2 1.0 NZ D:LYS184 4.2 54.1 1.0 F2 D:BEF1002 4.2 46.0 1.0 O1B D:ADP1000 4.3 40.6 1.0 OD1 D:ASP265 4.3 57.7 1.0 O3A D:ADP1000 4.4 44.5 1.0 F1 D:BEF1002 4.4 42.0 1.0 OE1 D:GLU215 4.4 53.3 1.0 PA D:ADP1000 4.5 45.7 1.0 CD D:GLU215 4.6 51.9 1.0 CG D:ASP265 4.6 51.3 1.0 OE2 D:GLU211 4.6 65.5 1.0 O1A D:ADP1000 4.7 45.8 1.0 NH2 E:ARG366 4.7 52.3 1.0 OE1 D:GLU211 4.8 55.6 1.0 CD D:GLU211 4.8 57.9 1.0 CB D:LYS184 4.9 39.1 1.0 C D:LYS184 4.9 48.1 1.0

Magnesium binding site 5 out of 6 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:63.9 occ:1.00 OG1 E:THR185 1.9 67.2 1.0 O2B E:ADP1000 1.9 68.5 1.0 F3 E:BEF1002 1.9 63.4 1.0 O E:HOH1110 2.1 43.5 1.0 O E:HOH1104 2.2 48.3 1.0 O E:HOH1115 2.2 52.3 1.0 CB E:THR185 3.0 66.4 1.0 BE E:BEF1002 3.1 63.3 1.0 PB E:ADP1000 3.2 66.1 1.0 O1B E:ADP1000 3.5 69.0 1.0 F2 E:BEF1002 3.7 71.5 1.0 CG2 E:THR185 3.9 70.4 1.0 OE1 E:GLU215 4.0 67.0 1.0 N E:THR185 4.0 66.2 1.0 CA E:THR185 4.1 66.5 1.0 O3A E:ADP1000 4.1 68.3 1.0 OD1 E:ASP265 4.2 61.5 1.0 OE2 E:GLU215 4.2 69.4 1.0 NZ E:LYS184 4.3 66.9 1.0 O1A E:ADP1000 4.3 71.0 1.0 O3B E:ADP1000 4.3 66.2 1.0 F1 E:BEF1002 4.3 63.5 1.0 NH1 E:ARG269 4.3 71.7 1.0 OD2 E:ASP265 4.4 90.9 1.0 NH2 E:ARG212 4.4 73.3 1.0 NH1 E:ARG212 4.5 75.8 1.0 CD E:GLU215 4.5 68.7 1.0 PA E:ADP1000 4.5 69.8 1.0 O2A E:ADP1000 4.6 69.4 1.0 CG E:ASP265 4.7 71.1 1.0 CZ E:ARG212 5.0 71.0 1.0 OE1 E:GLU211 5.0 89.3 1.0

Magnesium binding site 6 out of 6 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1001 b:67.8 occ:1.00 OG1 F:THR185 1.9 66.9 1.0 O F:HOH1105 2.0 30.2 1.0 O2B F:ADP1000 2.0 66.8 1.0 O F:HOH1101 2.0 29.9 1.0 F3 F:BEF1002 2.0 66.5 1.0 O F:HOH1103 2.2 62.1 1.0 BE F:BEF1002 3.1 66.7 1.0 CB F:THR185 3.1 67.5 1.0 PB F:ADP1000 3.2 67.1 1.0 O1B F:ADP1000 3.7 67.9 1.0 O3A F:ADP1000 3.7 70.1 1.0 O1A F:ADP1000 3.9 74.8 1.0 N F:THR185 3.9 67.3 1.0 NH1 F:ARG212 4.0 67.2 1.0 O F:HOH1108 4.0 41.3 1.0 CA F:THR185 4.1 67.5 1.0 OE2 F:GLU215 4.1 67.7 1.0 CG2 F:THR185 4.1 67.7 1.0 OD2 F:ASP265 4.1 66.5 1.0 F2 F:BEF1002 4.1 66.3 1.0 F1 F:BEF1002 4.2 67.2 1.0 OE1 F:GLU215 4.3 67.2 1.0 PA F:ADP1000 4.3 69.0 1.0 OD1 F:ASP265 4.4 70.7 1.0 OE2 F:GLU211 4.4 79.7 1.0 O3B F:ADP1000 4.5 67.4 1.0 CD F:GLU215 4.5 67.6 1.0 CG F:ASP265 4.7 66.2 1.0 O2A F:ADP1000 4.7 68.3 1.0 CD F:GLU211 4.8 75.6 1.0 NZ F:LYS184 5.0 66.2 1.0 CB F:LYS184 5.0 66.5 1.0

N.D.Thomsen, M.R.Lawson, L.B.Witkowsky, S.Qu, J.M.Berger. Molecular Mechanisms of Substrate-Controlled Ring Dynamics and Substepping in A Nucleic Acid-Dependent Hexameric Motor. Proc. Natl. Acad. Sci. V. 113 E7691 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27856760
DOI: 10.1073/PNAS.1616745113