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Magnesium in PDB 4oin: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077, PDB code: 4oin was solved by Y.Zhang, R.H.Ebright, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.50 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.770, 103.200, 294.770, 90.00, 99.18, 90.00
R / Rfree (%) 20.6 / 25.2

Other elements in 4oin:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 (pdb code 4oin). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077, PDB code: 4oin:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4oin

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Magnesium binding site 1 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:50.2
occ:1.00
 OD1 B:ASP193 2.5 41.3 1.0
O B:ASP191 3.0 47.4 1.0
OD1 B:ASP191 3.2 57.6 1.0
OD1 B:ASP183 3.3 46.2 1.0
CG B:ASP193 3.6 37.3 1.0
OD2 B:ASP193 4.0 28.4 1.0
C B:ASP191 4.1 54.6 1.0
CG B:ASP183 4.2 49.4 1.0
CG B:ARG30 4.2 30.4 1.0
O B:LEU192 4.3 35.1 1.0
CG B:ASP191 4.3 68.0 1.0
N B:GLY31 4.5 26.3 1.0
C B:LEU192 4.6 32.7 1.0
CA B:ARG30 4.7 26.9 1.0
CA B:ASP191 4.8 57.5 1.0
O C:HOH1367 4.8 27.9 1.0
CB B:ASP193 4.8 30.2 1.0
OD2 B:ASP183 4.9 52.1 1.0
CA B:ASP193 4.9 27.2 1.0
CB B:ARG30 4.9 28.5 1.0
N B:ASP193 4.9 28.1 1.0
CB B:ASP191 5.0 61.6 1.0

Magnesium binding site 2 out of 5 in 4oin

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Magnesium binding site 2 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:5.5
occ:1.00
 OD1 D:ASP739 2.0 4.8 1.0
O D:HOH2106 2.1 6.9 1.0
O D:HOH2107 2.1 6.0 1.0
OD1 D:ASP743 2.1 9.0 1.0
O D:HOH2105 2.1 8.5 1.0
OD1 D:ASP741 2.1 8.3 1.0
CG D:ASP741 2.8 8.2 1.0
OD2 D:ASP741 2.8 9.7 1.0
CG D:ASP743 3.0 7.9 1.0
CG D:ASP739 3.0 6.7 1.0
OD2 D:ASP743 3.3 7.8 1.0
OD2 D:ASP739 3.4 9.7 1.0
O D:HOH2116 4.1 8.4 1.0
O I:HOH208 4.2 7.2 1.0
CB D:ASP741 4.2 4.5 1.0
O D:HOH2191 4.3 5.5 1.0
O I:R2T4 4.3 8.2 1.0
CB D:ASP743 4.4 4.0 1.0
O D:ASP739 4.4 5.7 1.0
CB D:ASP739 4.4 5.4 1.0
N D:ASP743 4.5 5.3 1.0
N D:ASP739 4.5 6.8 1.0
C D:ASP739 4.6 4.6 1.0
CB I:R2T4 4.7 8.1 1.0
N D:ASP741 4.7 5.1 1.0
CA D:ASP739 4.7 4.7 1.0
CA D:ASP741 4.8 4.3 1.0
CA D:ASP743 4.8 5.0 1.0
O D:HOH2104 4.9 12.2 1.0
NH2 D:ARG704 4.9 6.1 1.0
C D:ASP741 5.0 5.8 1.0
O C:HOH1380 5.0 11.9 1.0
C I:R2T4 5.0 7.9 1.0
O D:HOH2328 5.0 15.1 1.0

Magnesium binding site 3 out of 5 in 4oin

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Magnesium binding site 3 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:31.0
occ:1.00
 O D:HOH2109 2.0 29.8 1.0
O D:LYS840 2.1 26.8 1.0
O B:HOH2103 2.2 31.4 1.0
O B:HOH2102 2.3 28.4 1.0
O D:HOH2108 2.3 26.3 1.0
O B:HOH2101 2.8 27.0 1.0
C D:LYS840 3.1 27.6 1.0
OD2 B:ASP168 3.8 27.0 1.0
N D:TYR841 3.9 28.0 1.0
CA D:TYR841 3.9 24.8 1.0
N D:VAL842 4.0 28.3 1.0
O D:LEU839 4.1 30.6 1.0
CA D:LYS840 4.1 28.2 1.0
OD1 B:ASP168 4.3 30.2 1.0
OE1 B:GLU154 4.3 44.3 1.0
CG B:ASP168 4.4 27.8 1.0
C D:TYR841 4.4 29.1 1.0
OE1 B:GLU64 4.5 46.5 1.0
O B:HOH2105 4.5 24.6 1.0
OE2 B:GLU64 4.7 53.8 1.0
CG2 D:VAL842 4.9 27.4 1.0
C D:LEU839 4.9 29.9 1.0
CB D:VAL842 5.0 24.4 1.0

Magnesium binding site 4 out of 5 in 4oin

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Magnesium binding site 4 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:31.1
occ:1.00
 O D:GLU898 3.0 30.8 1.0
O D:TRP897 3.1 28.7 1.0
O D:ILE900 3.1 27.5 1.0
O D:HOH2171 3.6 27.3 1.0
C D:GLU898 3.6 27.7 1.0
CA D:GLU898 3.8 22.0 1.0
C D:TRP897 4.1 26.1 1.0
C D:ILE900 4.3 21.0 1.0
N D:GLU898 4.5 23.4 1.0
N D:LEU899 4.6 26.1 1.0
N D:ILE900 4.8 27.2 1.0
C D:LEU899 4.9 25.4 1.0

Magnesium binding site 5 out of 5 in 4oin

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Magnesium binding site 5 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Soaked with GE23077 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:22.8
occ:1.00
 O F:TRP299 2.5 31.5 1.0
O F:HOH2105 2.5 36.1 1.0
O F:GLY296 2.9 39.0 1.0
O F:ALA292 2.9 33.2 1.0
C F:ALA292 3.6 34.1 1.0
C F:TRP299 3.6 31.2 1.0
C F:GLY296 3.8 45.3 1.0
N F:GLU293 4.1 32.0 1.0
CA F:GLU293 4.1 30.9 1.0
CA F:TRP299 4.4 34.7 1.0
N F:TRP299 4.4 40.0 1.0
CB F:ALA292 4.4 31.6 1.0
CB F:TRP299 4.5 32.1 1.0
N F:PRO297 4.5 44.6 1.0
CA F:ALA292 4.5 29.9 1.0
CA F:PRO297 4.5 44.5 1.0
N F:ASP300 4.7 33.0 1.0
O F:GLU293 4.7 31.6 1.0
CA F:GLY296 4.7 42.0 1.0
N F:GLY296 4.7 33.4 1.0
C F:GLU293 4.8 27.5 1.0
CA F:ASP300 4.9 31.3 1.0

Reference:

Y.Zhang, D.Degen, M.X.Ho, E.Sineva, K.Y.Ebright, Y.W.Ebright, V.Mekler, H.Vahedian-Movahed, Y.Feng, R.Yin, S.Tuske, H.Irschik, R.Jansen, S.Maffioli, S.Donadio, E.Arnold, R.H.Ebright. GE23077 Binds to the Rna Polymerase 'I' and 'I+1' Sites and Prevents the Binding of Initiating Nucleotides. Elife V. 3 02450 2014.
ISSN: ESSN 2050-084X
PubMed: 24755292
Page generated: Tue Aug 20 00:51:10 2024

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