Magnesium in PDB 5jjk: Rho Transcription Termination Factor Bound to RA7 and 6 Adp-BEF3 Molecules

The structure of Rho Transcription Termination Factor Bound to RA7 and 6 Adp-BEF3 Molecules, PDB code: 5jjk 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)	49.80 / 3.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.760, 199.210, 112.200, 90.00, 104.83, 90.00
R / Rfree (%)	23.3 / 26.5

The structure of Rho Transcription Termination Factor Bound to RA7 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 RA7 and 6 Adp-BEF3 Molecules (pdb code 5jjk). 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 RA7 and 6 Adp-BEF3 Molecules, PDB code: 5jjk:
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 RA7 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 RA7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:36.5 occ:1.00 O A:HOH1101 1.8 47.1 1.0 OG1 A:THR185 1.9 40.2 1.0 O A:HOH1102 1.9 47.0 1.0 O A:HOH1103 1.9 87.8 1.0 F3 A:BEF1002 2.0 46.1 1.0 O1B A:ADP1000 2.2 40.7 1.0 CB A:THR185 3.1 41.0 1.0 BE A:BEF1002 3.2 45.9 1.0 PB A:ADP1000 3.3 40.4 1.0 O2B A:ADP1000 3.4 39.7 1.0 O1A A:ADP1000 3.6 40.9 1.0 NH1 A:ARG212 3.8 35.5 1.0 N A:THR185 3.8 41.1 1.0 OE2 A:GLU215 3.9 38.3 1.0 CA A:THR185 4.0 41.6 1.0 OE1 A:GLU215 4.0 38.7 1.0 F2 A:BEF1002 4.1 45.9 1.0 CG2 A:THR185 4.1 41.7 1.0 OD2 A:ASP265 4.1 52.6 1.0 OD1 A:ASP265 4.2 52.0 1.0 F1 A:BEF1002 4.3 45.5 1.0 CD A:GLU215 4.3 38.8 1.0 OE2 A:GLU211 4.4 84.6 1.0 O3A A:ADP1000 4.4 40.9 1.0 O3B A:ADP1000 4.4 40.5 1.0 PA A:ADP1000 4.4 41.4 1.0 CG A:ASP265 4.6 52.5 1.0 O2A A:ADP1000 4.7 42.3 1.0 CD A:GLU211 4.8 84.9 1.0 C A:LYS184 4.9 49.4 1.0 CB A:LYS184 4.9 48.4 1.0 CZ A:ARG212 5.0 35.2 1.0 OE1 A:GLU211 5.0 84.9 1.0

Magnesium binding site 2 out of 6 in the Rho Transcription Termination Factor Bound to RA7 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 RA7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:26.4 occ:1.00 O B:HOH1101 1.8 32.6 1.0 OG1 B:THR185 1.9 29.0 1.0 O B:HOH1102 1.9 27.4 1.0 F3 B:BEF1002 2.0 33.3 1.0 O B:HOH1103 2.0 28.8 1.0 O1B B:ADP1000 2.2 36.0 1.0 CB B:THR185 3.1 29.9 1.0 BE B:BEF1002 3.2 33.2 1.0 PB B:ADP1000 3.3 36.0 1.0 O2B B:ADP1000 3.4 36.1 1.0 O2A B:ADP1000 3.6 38.0 1.0 N B:THR185 3.9 29.1 1.0 CA B:THR185 4.0 29.6 1.0 OD2 B:ASP265 4.0 31.2 1.0 NH1 B:ARG212 4.0 28.0 1.0 OE2 B:GLU215 4.0 43.9 1.0 OE1 B:GLU215 4.1 43.2 1.0 F2 B:BEF1002 4.1 32.4 1.0 CG2 B:THR185 4.2 30.8 1.0 OD1 B:ASP265 4.2 29.8 1.0 F1 B:BEF1002 4.3 33.8 1.0 O3A B:ADP1000 4.4 37.1 1.0 O3B B:ADP1000 4.4 35.5 1.0 PA B:ADP1000 4.4 38.1 1.0 OE2 B:GLU211 4.4 48.5 1.0 CD B:GLU215 4.4 44.0 1.0 CG B:ASP265 4.5 30.5 1.0 CD B:GLU211 4.7 48.0 1.0 OE1 B:GLU211 4.7 47.4 1.0 O1A B:ADP1000 4.7 38.3 1.0 NH2 C:ARG366 4.8 29.9 1.0 C B:LYS184 4.9 30.4 1.0 CB B:LYS184 4.9 29.1 1.0

Magnesium binding site 3 out of 6 in the Rho Transcription Termination Factor Bound to RA7 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 RA7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:37.0 occ:1.00 O C:HOH1101 1.8 37.5 1.0 O C:HOH1102 1.9 42.0 1.0 O C:HOH1103 1.9 50.2 1.0 OG1 C:THR185 1.9 49.9 1.0 F3 C:BEF1002 2.0 44.9 1.0 O2B C:ADP1000 2.2 45.9 1.0 CB C:THR185 3.1 51.6 1.0 BE C:BEF1002 3.2 45.0 1.0 PB C:ADP1000 3.3 46.4 1.0 O3B C:ADP1000 3.4 46.8 1.0 O2A C:ADP1000 3.6 50.2 1.0 NH1 C:ARG212 3.8 35.2 1.0 OD2 C:ASP265 3.9 45.2 1.0 N C:THR185 4.0 50.2 1.0 OE2 C:GLU215 4.0 50.2 1.0 CA C:THR185 4.1 50.9 1.0 F2 C:BEF1002 4.1 43.2 1.0 CG2 C:THR185 4.2 52.7 1.0 OE2 C:GLU211 4.3 53.1 1.0 OD1 C:ASP265 4.3 42.8 1.0 F1 C:BEF1002 4.3 46.3 1.0 O3A C:ADP1000 4.4 48.6 1.0 OE1 C:GLU215 4.4 48.2 1.0 O1B C:ADP1000 4.4 45.3 1.0 PA C:ADP1000 4.4 50.4 1.0 CG C:ASP265 4.5 43.7 1.0 CD C:GLU215 4.6 50.0 1.0 CD C:GLU211 4.7 51.8 1.0 NH2 D:ARG366 4.7 41.4 1.0 O1A C:ADP1000 4.7 50.4 1.0 OE1 C:GLU211 4.9 50.6 1.0 CZ C:ARG212 5.0 36.5 1.0

Magnesium binding site 4 out of 6 in the Rho Transcription Termination Factor Bound to RA7 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 RA7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:97.6 occ:1.00 O D:HOH1101 1.8 70.8 1.0 OG1 D:THR185 1.8 58.9 1.0 F3 D:BEF1002 2.0 81.1 1.0 O D:HOH1102 2.0 68.9 1.0 O D:HOH1103 2.2 70.1 1.0 O2B D:ADP1000 2.2 61.6 1.0 CB D:THR185 3.0 61.2 1.0 BE D:BEF1002 3.2 81.3 1.0 PB D:ADP1000 3.3 62.4 1.0 O3B D:ADP1000 3.4 63.0 1.0 O2A D:ADP1000 3.6 68.1 1.0 NH1 D:ARG212 3.8 79.6 1.0 N D:THR185 3.8 59.4 1.0 NZ D:LYS184 4.0 53.2 1.0 CA D:THR185 4.0 60.1 1.0 OE2 D:GLU215 4.0 77.7 1.0 CG2 D:THR185 4.1 62.2 1.0 OD2 D:ASP265 4.1 61.6 1.0 F2 D:BEF1002 4.1 78.2 1.0 OD1 D:ASP265 4.3 57.9 1.0 OE1 D:GLU215 4.3 74.1 1.0 F1 D:BEF1002 4.3 83.2 1.0 O3A D:ADP1000 4.4 65.9 1.0 O1B D:ADP1000 4.4 60.7 1.0 PA D:ADP1000 4.4 68.4 1.0 CD D:GLU215 4.6 76.9 1.0 OE2 D:GLU211 4.6 74.4 1.0 CG D:ASP265 4.6 59.1 1.0 O1A D:ADP1000 4.8 68.3 1.0 CD D:GLU211 4.8 72.2 1.0 OE1 D:GLU211 4.9 70.4 1.0 C D:LYS184 5.0 58.4 1.0 CB D:LYS184 5.0 54.9 1.0

Magnesium binding site 5 out of 6 in the Rho Transcription Termination Factor Bound to RA7 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 RA7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:0.7 occ:1.00 O E:HOH1102 1.9 0.5 1.0 O E:HOH1101 1.9 0.6 1.0 OG1 E:THR185 1.9 0.7 1.0 F3 E:BEF1002 2.0 0.2 1.0 O E:HOH1103 2.1 0.7 1.0 O2B E:ADP1000 2.2 0.1 1.0 CB E:THR185 3.0 0.9 1.0 BE E:BEF1002 3.2 0.7 1.0 PB E:ADP1000 3.3 0.9 1.0 O1B E:ADP1000 3.4 0.6 1.0 O1A E:ADP1000 3.6 0.2 1.0 OE1 E:GLU215 3.9 0.0 1.0 OD2 E:ASP265 3.9 0.8 1.0 OD1 E:ASP265 4.0 0.4 1.0 N E:THR185 4.0 0.8 1.0 CG2 E:THR185 4.0 0.7 1.0 CA E:THR185 4.0 0.1 1.0 F2 E:BEF1002 4.1 0.8 1.0 OE2 E:GLU215 4.3 0.2 1.0 F1 E:BEF1002 4.3 0.6 1.0 CG E:ASP265 4.3 0.8 1.0 NH1 E:ARG269 4.4 97.6 1.0 O3A E:ADP1000 4.4 0.8 1.0 O3B E:ADP1000 4.4 0.2 1.0 PA E:ADP1000 4.4 0.4 1.0 NZ E:LYS184 4.4 0.8 1.0 NH2 E:ARG212 4.4 0.6 1.0 CD E:GLU215 4.5 0.5 1.0 O2A E:ADP1000 4.7 0.9 1.0 OE2 E:GLU211 4.8 96.4 1.0 NH1 E:ARG212 4.8 0.4 1.0 NH2 F:ARG366 4.9 0.8 1.0 OE1 E:GLU211 4.9 97.0 1.0

Magnesium binding site 6 out of 6 in the Rho Transcription Termination Factor Bound to RA7 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 RA7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1001 b:64.8 occ:1.00 O F:HOH1101 1.8 80.2 1.0 O F:HOH1102 1.9 99.3 1.0 O F:HOH1103 1.9 79.9 1.0 OG1 F:THR185 1.9 67.7 1.0 F3 F:BEF1002 2.0 64.8 1.0 O2B F:ADP1000 2.2 79.0 1.0 CB F:THR185 3.1 68.2 1.0 BE F:BEF1002 3.2 64.8 1.0 PB F:ADP1000 3.3 79.1 1.0 O1B F:ADP1000 3.4 79.1 1.0 O1A F:ADP1000 3.6 79.7 1.0 N F:THR185 3.8 68.0 1.0 OD2 F:ASP265 3.9 65.5 1.0 CA F:THR185 4.0 68.3 1.0 F2 F:BEF1002 4.1 64.9 1.0 OE2 F:GLU215 4.1 66.2 1.0 NH1 F:ARG212 4.1 65.3 1.0 OD1 F:ASP265 4.1 65.1 1.0 CG2 F:THR185 4.2 68.7 1.0 OE1 F:GLU215 4.3 66.3 1.0 F1 F:BEF1002 4.3 65.1 1.0 O3A F:ADP1000 4.4 79.6 1.0 O3B F:ADP1000 4.4 79.1 1.0 PA F:ADP1000 4.4 79.9 1.0 CG F:ASP265 4.4 65.4 1.0 CD F:GLU215 4.5 66.4 1.0 OE2 F:GLU211 4.5 91.4 1.0 O2A F:ADP1000 4.7 80.3 1.0 CD F:GLU211 4.8 91.5 1.0 OE1 F:GLU211 4.8 91.4 1.0 CB F:LYS184 4.9 64.9 1.0 C F:LYS184 4.9 65.6 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