Magnesium in PDB 3ice: Rho Transcription Termination Factor Bound to Rna and Adp-BEF3

The structure of Rho Transcription Termination Factor Bound to Rna and Adp-BEF3, PDB code: 3ice was solved by N.D.Thomsen, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.88 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.230, 127.030, 127.170, 60.48, 90.26, 89.77
R / Rfree (%)	27 / 29.5

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

Fluorine

(F)

18 atoms

The binding sites of Magnesium atom in the Rho Transcription Termination Factor Bound to Rna and Adp-BEF3 (pdb code 3ice). 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 Rna and Adp-BEF3, PDB code: 3ice:
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 Rna and Adp-BEF3


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:37.8 occ:1.00 O A:HOH1102 1.8 32.9 1.0 OG1 A:THR185 1.8 39.6 1.0 O2B A:ADP1000 1.9 48.6 1.0 O A:HOH1109 2.0 40.6 1.0 F3 A:BEF1002 2.1 28.4 1.0 O A:HOH1101 2.1 22.0 1.0 CB A:THR185 2.9 30.3 1.0 PB A:ADP1000 3.2 32.0 1.0 BE A:BEF1002 3.4 30.6 1.0 OE2 A:GLU211 3.5 47.5 1.0 O3A A:ADP1000 3.6 21.0 1.0 O1B A:ADP1000 3.7 28.6 1.0 O A:HOH1108 3.7 26.8 1.0 OE2 A:GLU215 3.7 41.0 1.0 CA A:THR185 3.9 28.4 1.0 OD2 A:ASP265 3.9 38.0 1.0 CG2 A:THR185 3.9 23.9 1.0 N A:THR185 4.0 33.9 1.0 NH1 A:ARG212 4.1 28.5 1.0 F2 A:BEF1002 4.1 38.3 1.0 OD1 A:ASP265 4.3 48.5 1.0 O3B A:ADP1000 4.5 27.7 1.0 CD A:GLU211 4.5 49.7 1.0 CG A:ASP265 4.5 45.1 1.0 F1 A:BEF1002 4.5 26.2 1.0 NH2 B:ARG366 4.6 22.4 1.0 CD A:GLU215 4.6 40.0 1.0 CG A:GLU211 4.7 45.9 1.0 PA A:ADP1000 4.7 24.4 1.0 OE1 A:GLU215 4.8 37.0 1.0 NZ A:LYS184 4.8 34.9 1.0 O2A A:ADP1000 4.9 21.2 1.0 O1A A:ADP1000 5.0 23.6 1.0 CB A:LYS184 5.0 21.4 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:25.8 occ:1.00 O B:HOH1101 1.8 16.3 1.0 OG1 B:THR185 1.8 30.4 1.0 O2B B:ADP1000 1.8 31.6 1.0 F3 B:BEF1002 2.0 29.5 1.0 O B:HOH1102 2.2 33.7 1.0 CB B:THR185 2.7 20.5 1.0 PB B:ADP1000 3.0 25.1 1.0 BE B:BEF1002 3.2 32.3 1.0 O3A B:ADP1000 3.4 32.5 1.0 OE2 B:GLU211 3.5 42.0 1.0 O1B B:ADP1000 3.5 27.5 1.0 F2 B:BEF1002 3.6 45.3 1.0 O B:HOH1108 3.7 32.4 1.0 CA B:THR185 3.8 30.1 1.0 CG2 B:THR185 3.8 21.2 1.0 N B:THR185 3.8 37.1 1.0 OD2 B:ASP265 3.9 35.3 1.0 OE2 B:GLU215 4.1 31.6 1.0 NH1 B:ARG212 4.2 24.8 1.0 O3B B:ADP1000 4.3 23.5 1.0 OD1 B:ASP265 4.3 52.9 1.0 CD B:GLU211 4.4 30.1 1.0 OE1 B:GLU215 4.4 30.0 1.0 NH2 C:ARG366 4.4 15.0 1.0 F1 B:BEF1002 4.5 25.0 1.0 PA B:ADP1000 4.5 23.6 1.0 NZ B:LYS184 4.5 31.5 1.0 CG B:ASP265 4.5 29.5 1.0 CD B:GLU215 4.7 32.4 1.0 O1A B:ADP1000 4.8 17.6 1.0 O2A B:ADP1000 4.8 22.3 1.0 CE B:LYS184 5.0 24.6 1.0 CB B:LYS184 5.0 22.1 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:45.5 occ:1.00 O C:HOH1116 1.7 46.1 1.0 O2B C:ADP1000 1.8 48.7 1.0 OG1 C:THR185 1.8 24.8 1.0 F3 C:BEF1002 2.0 26.9 1.0 O C:HOH1101 2.0 18.5 1.0 PB C:ADP1000 2.7 32.8 1.0 O3A C:ADP1000 2.9 54.5 1.0 CB C:THR185 3.0 31.6 1.0 BE C:BEF1002 3.1 37.9 1.0 O1B C:ADP1000 3.2 32.5 1.0 NH1 C:ARG212 3.6 40.3 1.0 OE2 C:GLU215 3.8 50.5 1.0 F2 C:BEF1002 3.8 47.5 1.0 CG2 C:THR185 3.9 39.1 1.0 OD2 C:ASP265 4.1 39.8 1.0 O3B C:ADP1000 4.1 33.3 1.0 CA C:THR185 4.1 39.5 1.0 N C:THR185 4.1 41.0 1.0 F1 C:BEF1002 4.3 32.8 1.0 OE1 C:GLU215 4.3 70.0 1.0 OE1 C:GLU211 4.4 55.7 1.0 PA C:ADP1000 4.4 36.0 1.0 CD C:GLU211 4.4 52.7 1.0 CD C:GLU215 4.5 50.1 1.0 OE2 C:GLU211 4.6 53.7 1.0 NZ C:LYS184 4.7 22.1 1.0 CZ C:ARG212 4.8 35.6 1.0 CG C:GLU211 4.9 44.7 1.0 O1A C:ADP1000 4.9 34.5 1.0 O2A C:ADP1000 4.9 53.8 1.0 CG C:ASP265 5.0 49.6 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:58.3 occ:1.00 O2B D:ADP1000 1.8 59.6 1.0 O D:HOH1112 1.9 43.6 1.0 F3 D:BEF1002 1.9 37.7 1.0 OG1 D:THR185 2.0 44.1 1.0 OE2 D:GLU211 2.7 57.5 1.0 PB D:ADP1000 3.1 67.0 1.0 BE D:BEF1002 3.1 57.7 1.0 CB D:THR185 3.2 43.1 1.0 O1B D:ADP1000 3.4 60.5 1.0 CD D:GLU211 3.5 51.8 1.0 NZ D:LYS184 3.7 55.2 1.0 NH1 D:ARG212 3.8 59.9 1.0 OD2 D:ASP265 3.8 51.4 1.0 CG D:GLU211 3.8 51.6 1.0 F2 D:BEF1002 4.0 67.0 1.0 O3A D:ADP1000 4.0 51.0 1.0 CA D:THR185 4.1 51.9 1.0 N D:THR185 4.2 54.3 1.0 O3B D:ADP1000 4.2 56.9 1.0 OE2 D:GLU215 4.2 74.3 1.0 CG2 D:THR185 4.2 53.6 1.0 F1 D:BEF1002 4.3 74.4 1.0 OE1 D:GLU215 4.5 60.2 1.0 OE1 D:GLU211 4.5 49.6 1.0 CE D:LYS184 4.7 51.3 1.0 O2A D:ADP1000 4.7 70.2 1.0 CG D:ASP265 4.8 48.9 1.0 PA D:ADP1000 4.8 51.2 1.0 CD D:GLU215 4.8 60.6 1.0 O1A D:ADP1000 4.9 47.3 1.0 OD1 D:ASP265 5.0 48.7 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:95.1 occ:1.00 O2B E:ADP501 1.8 88.8 1.0 OG1 E:THR185 2.0 78.5 1.0 O E:HOH604 2.1 75.2 1.0 OE2 E:GLU211 2.1 89.2 1.0 F3 E:BEF503 2.1 91.9 1.0 O E:HOH605 2.1 55.5 1.0 PB E:ADP501 3.0 0.9 1.0 CB E:THR185 3.0 86.5 1.0 CD E:GLU211 3.3 81.7 1.0 O1B E:ADP501 3.4 93.1 1.0 BE E:BEF503 3.5 85.5 1.0 O3A E:ADP501 3.6 0.3 1.0 NH1 E:ARG212 3.7 78.6 1.0 NZ E:LYS184 3.9 97.5 1.0 CG2 E:THR185 3.9 84.5 1.0 OE2 E:GLU215 4.1 96.1 1.0 CG E:GLU211 4.1 91.1 1.0 CA E:THR185 4.1 88.0 1.0 OE1 E:GLU211 4.2 83.2 1.0 O3B E:ADP501 4.3 94.3 1.0 F2 E:BEF503 4.3 83.2 1.0 N E:THR185 4.4 86.7 1.0 CE E:LYS184 4.5 98.7 1.0 OD1 E:ASP265 4.5 67.5 1.0 F1 E:BEF503 4.6 70.8 1.0 CG E:LYS184 4.7 86.8 1.0 OD2 E:ASP265 4.7 82.8 1.0 PA E:ADP501 4.7 0.9 1.0 O1A E:ADP501 4.8 0.8 1.0 CD E:GLU215 5.0 84.6 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1001 b:72.5 occ:1.00 O2B F:ADP1000 1.7 91.8 1.0 OG1 F:THR185 2.0 74.8 1.0 F3 F:BEF1002 2.1 74.8 1.0 PB F:ADP1000 2.7 88.2 1.0 O3A F:ADP1000 2.7 77.3 1.0 CB F:THR185 2.8 70.8 1.0 BE F:BEF1002 3.0 71.5 1.0 F2 F:BEF1002 3.2 66.6 1.0 O1B F:ADP1000 3.2 75.8 1.0 CG2 F:THR185 3.7 72.0 1.0 PA F:ADP1000 3.9 67.3 1.0 O3B F:ADP1000 4.0 71.5 1.0 OE2 F:GLU215 4.0 96.9 1.0 O2A F:ADP1000 4.1 72.2 1.0 CA F:THR185 4.1 75.6 1.0 N F:THR185 4.2 83.8 1.0 NH2 A:ARG366 4.2 64.7 1.0 OE1 F:GLU215 4.3 72.9 1.0 F1 F:BEF1002 4.4 77.2 1.0 OE2 F:GLU211 4.4 0.3 1.0 O1A F:ADP1000 4.4 62.4 1.0 OD1 F:ASP265 4.5 90.7 1.0 CD F:GLU215 4.6 89.2 1.0 CD F:GLU211 4.9 100.0 1.0 NE F:ARG212 4.9 74.3 1.0

N.D.Thomsen, J.M.Berger. Running in Reverse: the Structural Basis For Translocation Polarity in Hexameric Helicases. Cell(Cambridge,Mass.) V. 139 523 2009.
ISSN: ISSN 0092-8674
PubMed: 19879839
DOI: 10.1016/J.CELL.2009.08.043