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Magnesium in PDB 4g7o: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna, PDB code: 4g7o was solved by Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.61 / 2.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.483, 103.883, 297.340, 90.00, 98.23, 90.00
R / Rfree (%) 20.5 / 24.7

Other elements in 4g7o:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna (pdb code 4g7o). 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 Containing 2 Nt of Rna, PDB code: 4g7o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4g7o

Go back to Magnesium Binding Sites List in 4g7o
Magnesium binding site 1 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:40.1
occ:1.00
 OD1 D:ASP739 1.9 53.2 1.0
OD1 D:ASP743 2.0 40.7 1.0
OD1 D:ASP741 2.0 43.0 1.0
O3' I:A2 2.2 50.6 1.0
CG D:ASP739 2.5 47.5 1.0
OD2 D:ASP741 2.6 49.8 1.0
OD2 D:ASP739 2.6 55.2 1.0
CG D:ASP741 2.6 41.4 1.0
CG D:ASP743 3.0 38.1 1.0
OD2 D:ASP743 3.3 41.9 1.0
C3' I:A2 3.5 49.2 1.0
C4' I:A2 4.0 49.3 1.0
CB D:ASP739 4.0 34.4 1.0
CB D:ASP741 4.1 35.9 1.0
N D:ASP741 4.2 40.9 1.0
C5' I:A2 4.2 48.5 1.0
C D:ASP739 4.4 38.1 1.0
CB D:ASP743 4.4 36.6 1.0
O D:ASP739 4.4 39.9 1.0
O D:HOH2136 4.5 51.8 1.0
O2' I:A2 4.5 47.6 1.0
N D:ASP739 4.5 35.3 1.0
CA D:ASP739 4.5 34.9 1.0
C2' I:A2 4.6 46.8 1.0
CA D:ASP741 4.6 41.3 1.0
N D:ASP743 4.6 46.1 1.0
N D:PHE740 4.7 37.2 1.0
C D:ASP741 4.8 43.4 1.0
CA D:ASP743 4.9 36.7 1.0

Magnesium binding site 2 out of 5 in 4g7o

Go back to Magnesium Binding Sites List in 4g7o
Magnesium binding site 2 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:63.9
occ:1.00
 O D:LYS840 2.1 65.8 1.0
C D:LYS840 3.3 64.4 1.0
OD2 B:ASP168 3.4 76.0 1.0
OE2 B:GLU154 3.7 84.6 1.0
OD1 B:ASP168 3.8 75.4 1.0
CG B:ASP168 4.0 74.5 1.0
CA D:LYS840 4.1 66.9 1.0
O D:LEU839 4.2 68.5 1.0
N D:TYR841 4.3 65.3 1.0
OE2 B:GLU64 4.4 1.0 1.0
OE1 B:GLU64 4.5 0.9 1.0
CA D:TYR841 4.6 57.3 1.0
CD B:GLU154 4.7 91.2 1.0
CB B:ALA153 4.8 73.2 1.0
N D:VAL842 4.8 59.2 1.0
CG D:LYS840 4.8 63.5 1.0
OE1 B:GLU154 4.9 93.4 1.0
CD B:GLU64 4.9 0.3 1.0

Magnesium binding site 3 out of 5 in 4g7o

Go back to Magnesium Binding Sites List in 4g7o
Magnesium binding site 3 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1001

b:69.8
occ:1.00
 O K:VAL170 2.7 73.9 1.0
O K:PHE171 3.5 69.2 1.0
O K:SER172 3.5 63.4 1.0
O K:THR51 3.6 79.7 1.0
C K:VAL170 3.8 64.3 1.0
OD2 K:ASP202 3.9 75.5 1.0
C K:PHE171 4.0 68.0 1.0
C K:SER172 4.3 63.6 1.0
CA K:PHE171 4.4 63.4 1.0
C K:THR51 4.6 77.7 1.0
N K:PHE171 4.6 58.6 1.0
CB K:ALA52 4.6 70.4 1.0
N K:SER172 4.7 63.9 1.0
CB K:VAL170 4.7 60.1 1.0
NH2 K:ARG175 4.9 92.7 1.0
N K:PRO173 4.9 67.5 1.0
CA K:VAL170 4.9 61.0 1.0
CA K:PRO173 4.9 65.1 1.0
CA K:ALA52 5.0 70.1 1.0

Magnesium binding site 4 out of 5 in 4g7o

Go back to Magnesium Binding Sites List in 4g7o
Magnesium binding site 4 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2003

b:46.1
occ:1.00
 OD1 N:ASP739 1.9 57.3 1.0
OD1 N:ASP743 1.9 43.0 1.0
OD1 N:ASP741 2.0 53.2 1.0
O3' S:A2 2.2 60.2 1.0
CG N:ASP739 2.6 50.1 1.0
OD2 N:ASP741 2.6 58.7 1.0
CG N:ASP741 2.6 49.9 1.0
OD2 N:ASP739 2.7 57.6 1.0
CG N:ASP743 2.9 43.0 1.0
OD2 N:ASP743 3.2 47.5 1.0
C3' S:A2 3.5 63.2 1.0
C4' S:A2 4.0 59.0 1.0
CB N:ASP739 4.1 42.9 1.0
CB N:ASP741 4.1 40.3 1.0
O2' S:A2 4.2 61.9 1.0
N N:ASP741 4.3 50.4 1.0
CB N:ASP743 4.3 41.5 1.0
C N:ASP739 4.4 44.6 1.0
C2' S:A2 4.4 60.3 1.0
O N:ASP739 4.4 42.6 1.0
C5' S:A2 4.5 56.4 1.0
N N:ASP739 4.5 39.5 1.0
CA N:ASP739 4.6 44.6 1.0
N N:ASP743 4.6 45.3 1.0
CA N:ASP741 4.6 45.6 1.0
N N:PHE740 4.7 48.3 1.0
C N:ASP741 4.8 45.4 1.0
CA N:ASP743 4.8 39.9 1.0

Magnesium binding site 5 out of 5 in 4g7o

Go back to Magnesium Binding Sites List in 4g7o
Magnesium binding site 5 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2004

b:66.0
occ:1.00
 O N:LYS840 2.2 71.3 1.0
C N:LYS840 3.4 68.5 1.0
OD2 L:ASP168 3.4 72.2 1.0
OE2 L:GLU154 3.6 87.0 1.0
OD1 L:ASP168 3.6 70.5 1.0
CG L:ASP168 3.9 67.4 1.0
CA N:LYS840 4.2 72.1 1.0
N N:TYR841 4.4 70.6 1.0
O N:LEU839 4.4 72.8 1.0
CD L:GLU154 4.5 93.3 1.0
CA N:TYR841 4.6 66.1 1.0
OE1 L:GLU64 4.6 0.6 1.0
CB L:ALA153 4.6 74.9 1.0
OE1 L:GLU154 4.6 95.1 1.0
N N:VAL842 4.8 67.3 1.0
CG N:LYS840 4.9 64.2 1.0

Reference:

Y.Zhang, Y.Feng, S.Chatterjee, S.Tuske, M.X.Ho, E.Arnold, R.H.Ebright. Structural Basis of Transcription Initiation. Science V. 338 1076 2012.
ISSN: ISSN 0036-8075
PubMed: 23086998
DOI: 10.1126/SCIENCE.1227786
Page generated: Fri Aug 16 15:27:26 2024

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