Magnesium in PDB 4q4z: Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex

All present enzymatic activity of Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex:
2.7.7.6;

The structure of Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex, PDB code: 4q4z was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.78 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.487, 102.159, 294.719, 90.00, 98.96, 90.00
R / Rfree (%)	25.6 / 27.5

The structure of Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex (pdb code 4q4z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex, PDB code: 4q4z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2003 b:38.9 occ:1.00 OD1 D:ASP741 2.1 20.3 1.0 OD1 D:ASP739 2.1 25.7 1.0 OD1 D:ASP743 2.1 20.1 1.0 O3' C:ATP1201 2.2 51.4 1.0 O D:HOH2123 2.7 69.4 1.0 CG D:ASP741 2.8 20.5 1.0 OD2 D:ASP741 2.8 25.1 1.0 O D:HOH2112 2.9 33.1 1.0 CG D:ASP743 3.1 20.0 1.0 CG D:ASP739 3.1 22.6 1.0 OD2 D:ASP743 3.3 92.4 1.0 C3' C:ATP1201 3.4 43.7 1.0 OD2 D:ASP739 3.4 44.6 1.0 C4' C:ATP1201 3.6 44.4 1.0 C5' C:ATP1201 4.1 41.6 1.0 CB D:ASP741 4.2 20.7 1.0 C5' D:2TM2006 4.4 51.6 1.0 O2' C:ATP1201 4.4 38.9 1.0 CB D:ASP743 4.4 20.2 1.0 O D:ASP739 4.5 52.8 1.0 CB D:ASP739 4.5 20.6 1.0 C2' C:ATP1201 4.5 39.5 1.0 C4' D:2TM2006 4.5 50.1 1.0 N D:ASP743 4.6 20.4 1.0 N D:ASP739 4.6 23.9 1.0 O4' D:2TM2006 4.6 38.9 1.0 C D:ASP739 4.7 20.6 1.0 N D:ASP741 4.7 20.8 1.0 CA D:ASP739 4.8 20.5 1.0 CA D:ASP741 4.8 20.8 1.0 CA D:ASP743 4.8 20.3 1.0 O4' C:ATP1201 4.9 38.9 1.0 C D:ASP741 5.0 20.7 1.0 NH2 D:ARG704 5.0 18.5 1.0

Magnesium binding site 2 out of 3 in the Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2004 b:54.9 occ:1.00 O1G D:2TM2006 3.2 46.1 1.0 O2B D:2TM2006 3.5 69.2 1.0 OD2 D:ASP739 3.5 44.6 1.0 O3B D:2TM2006 3.7 59.9 1.0 PG D:2TM2006 4.0 73.2 1.0 PB D:2TM2006 4.3 66.5 1.0 CG D:ASP739 4.3 22.6 1.0 O2G D:2TM2006 4.3 94.2 1.0 CB D:ASP739 4.6 20.6 1.0 OE2 C:GLU685 4.7 27.6 1.0 OD1 D:ASN737 4.8 20.1 1.0 OE1 C:GLU685 4.9 44.4 1.0 NH2 D:ARG1029 5.0 22.4 1.0

Magnesium binding site 3 out of 3 in the Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Rna Polymerase De Novo Transcription Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2005 b:45.5 occ:1.00 O B:HOH401 1.6 65.6 1.0 O D:LYS840 1.9 54.7 1.0 C D:LYS840 3.0 52.0 1.0 N D:TYR841 3.8 54.4 1.0 OD2 B:ASP168 3.8 47.9 1.0 CA D:TYR841 3.9 54.1 1.0 CA D:LYS840 4.0 54.8 1.0 O D:LEU839 4.0 59.9 1.0 N D:VAL842 4.0 49.5 1.0 OE1 B:GLU154 4.2 66.0 1.0 OD1 B:ASP168 4.2 44.3 1.0 C D:TYR841 4.4 48.1 1.0 CG B:ASP168 4.4 50.4 1.0 OE1 B:GLU64 4.5 86.4 1.0 OE2 B:GLU64 4.6 76.0 1.0 C D:LEU839 4.9 58.2 1.0 N D:LYS840 4.9 53.6 1.0 CG2 D:VAL842 4.9 53.8 1.0

R.S.Basu, B.A.Warner, V.Molodtsov, D.Pupov, D.Esyunina, C.Fernandez-Tornero, A.Kulbachinskiy, K.S.Murakami. Structural Basis of Transcription Initiation By Bacterial Rna Polymerase Holoenzyme. J.Biol.Chem. V. 289 24549 2014.
ISSN: ISSN 0021-9258
PubMed: 24973216
DOI: 10.1074/JBC.M114.584037