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Magnesium in PDB 4g7h: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex

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

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex, PDB code: 4g7h 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) 49.27 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.560, 104.570, 297.550, 90.00, 98.32, 90.00
R / Rfree (%) 18.8 / 22.6

Other elements in 4g7h:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex 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 (pdb code 4g7h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex, PDB code: 4g7h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4g7h

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Magnesium binding site 1 out of 10 in the Crystal Structure of Thermus Thermophilus 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 Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:71.0
occ:1.00
 OD2 B:ASP183 2.2 94.2 1.0
OD1 B:ASP193 2.3 75.1 1.0
O B:ASP191 3.1 75.3 1.0
CG B:ASP183 3.4 93.7 1.0
CG B:ASP193 3.5 64.3 1.0
O B:LEU192 3.6 69.3 1.0
OD1 B:ASP191 3.9 96.0 1.0
C B:ASP191 4.0 80.7 1.0
C B:LEU192 4.1 66.3 1.0
OD1 B:ASP183 4.1 0.6 1.0
OD2 B:ASP193 4.2 63.2 1.0
CG B:ARG30 4.4 56.4 1.0
CA B:ASP183 4.4 72.2 1.0
CA B:ASP193 4.5 59.5 1.0
N B:ASP193 4.5 65.8 1.0
CB B:ASP183 4.5 72.8 1.0
CB B:ASP193 4.6 57.6 1.0
N B:LEU192 4.8 79.8 1.0
CA B:ASP191 4.8 77.7 1.0
N B:GLY31 4.8 56.7 1.0
CA B:ARG30 4.9 65.3 1.0
N B:ASP183 4.9 72.7 1.0
CA B:LEU192 4.9 65.3 1.0
CB B:ARG30 4.9 59.3 1.0
CG B:ASP191 5.0 93.9 1.0

Magnesium binding site 2 out of 10 in 4g7h

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Magnesium binding site 2 out of 10 in the Crystal Structure of Thermus Thermophilus 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 Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:32.5
occ:1.00
 OD1 D:ASP739 2.2 45.7 1.0
OD1 D:ASP741 2.2 40.6 1.0
OD1 D:ASP743 2.2 38.9 1.0
OD2 D:ASP741 2.8 45.4 1.0
CG D:ASP741 2.9 41.6 1.0
CG D:ASP743 3.0 34.5 1.0
OD2 D:ASP743 3.0 37.9 1.0
CG D:ASP739 3.1 45.9 1.0
OD2 D:ASP739 3.4 56.6 1.0
O D:HOH2236 4.2 33.5 1.0
CB D:ASP741 4.3 31.9 1.0
CB D:ASP743 4.5 25.9 1.0
CB D:ASP739 4.5 36.4 1.0
O D:ASP739 4.7 43.0 1.0
N D:ASP739 4.7 36.2 1.0
NH2 D:ARG704 4.7 43.4 1.0
N D:ASP743 4.8 35.4 1.0
C D:ASP739 4.8 40.6 1.0
N D:ASP741 4.8 42.6 1.0
CA D:ASP739 4.8 33.5 1.0
CA D:ASP741 4.9 37.6 1.0
CA D:ASP743 5.0 26.7 1.0

Magnesium binding site 3 out of 10 in 4g7h

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Magnesium binding site 3 out of 10 in the Crystal Structure of Thermus Thermophilus 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 Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:67.0
occ:1.00
 O D:LYS840 2.1 67.9 1.0
C D:LYS840 3.3 63.3 1.0
OE2 B:GLU154 3.5 92.2 1.0
OD2 B:ASP168 3.6 81.8 1.0
OD1 B:ASP168 3.9 77.3 1.0
CA D:LYS840 4.1 64.3 1.0
CG B:ASP168 4.2 76.2 1.0
N D:TYR841 4.3 64.3 1.0
O D:LEU839 4.4 69.3 1.0
OE1 B:GLU64 4.4 0.6 1.0
CD B:GLU154 4.5 94.3 1.0
CA D:TYR841 4.5 61.1 1.0
OE1 B:GLU154 4.6 93.0 1.0
OE2 B:GLU64 4.7 0.0 1.0
CG D:LYS840 4.8 63.0 1.0
CB B:ALA153 4.8 73.3 1.0
N D:VAL842 4.8 53.8 1.0
CD B:GLU64 5.0 0.1 1.0

Magnesium binding site 4 out of 10 in 4g7h

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Magnesium binding site 4 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:71.5
occ:1.00
 O D:ILE900 3.0 73.8 1.0
O D:TRP897 3.0 63.3 1.0
O D:GLU898 3.3 60.0 1.0
O D:HOH2187 3.3 64.7 1.0
C D:GLU898 3.9 63.9 1.0
CA D:GLU898 4.2 65.4 1.0
C D:TRP897 4.2 67.7 1.0
C D:ILE900 4.2 62.7 1.0
N D:GLU898 4.7 67.7 1.0
NE1 D:TRP897 4.9 85.7 1.0
N D:ILE900 4.9 60.8 1.0
CD1 D:TRP897 4.9 86.9 1.0
N D:LEU899 5.0 58.7 1.0

Magnesium binding site 5 out of 10 in 4g7h

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Magnesium binding site 5 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:63.8
occ:1.00
 O F:GLY296 2.3 69.1 1.0
O F:ALA292 2.4 63.6 1.0
O F:TRP299 2.5 63.0 1.0
C F:ALA292 3.2 60.3 1.0
C F:GLY296 3.3 77.5 1.0
C F:TRP299 3.6 59.1 1.0
CA F:GLU293 3.8 67.1 1.0
N F:GLU293 3.8 62.7 1.0
CB F:TRP299 4.1 60.7 1.0
N F:GLY296 4.1 74.8 1.0
CA F:GLY296 4.1 73.9 1.0
CA F:TRP299 4.2 60.9 1.0
N F:PRO297 4.2 82.3 1.0
N F:TRP299 4.2 67.0 1.0
O F:GLU293 4.2 61.1 1.0
CA F:ALA292 4.3 54.9 1.0
CB F:ALA292 4.4 56.4 1.0
C F:GLU293 4.4 59.5 1.0
CA F:PRO297 4.4 73.2 1.0
N F:ASP300 4.7 59.0 1.0
C F:PRO297 4.9 70.3 1.0
C F:MET295 5.0 65.9 1.0

Magnesium binding site 6 out of 10 in 4g7h

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Magnesium binding site 6 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1001

b:67.2
occ:1.00
 O K:VAL170 3.0 68.7 1.0
O K:THR51 3.1 72.5 1.0
O K:PHE171 3.3 64.8 1.0
O K:SER172 3.4 59.9 1.0
OD2 K:ASP202 3.6 70.0 1.0
C K:PHE171 3.9 64.1 1.0
C K:SER172 4.1 60.0 1.0
C K:VAL170 4.2 59.6 1.0
C K:THR51 4.2 68.3 1.0
CA K:PHE171 4.4 61.0 1.0
N K:SER172 4.6 61.1 1.0
N K:PRO173 4.6 62.4 1.0
CB K:ALA52 4.6 63.2 1.0
CA K:PRO173 4.6 60.9 1.0
N K:PHE171 4.7 56.8 1.0
CG K:ASP202 4.8 71.1 1.0
CA K:ALA52 4.9 64.8 1.0
N K:THR51 4.9 62.6 1.0
CA K:SER172 5.0 60.2 1.0

Magnesium binding site 7 out of 10 in 4g7h

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Magnesium binding site 7 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2003

b:38.1
occ:1.00
 OD1 N:ASP739 2.2 48.8 1.0
OD1 N:ASP741 2.2 47.2 1.0
OD1 N:ASP743 2.3 36.7 1.0
OD2 N:ASP741 2.9 55.1 1.0
CG N:ASP741 2.9 48.4 1.0
CG N:ASP743 3.0 38.2 1.0
OD2 N:ASP743 3.1 37.9 1.0
CG N:ASP739 3.2 47.5 1.0
OD2 N:ASP739 3.4 57.1 1.0
CB N:ASP741 4.4 33.5 1.0
CB N:ASP743 4.5 32.4 1.0
CB N:ASP739 4.5 40.3 1.0
N N:ASP739 4.7 39.9 1.0
NH2 N:ARG704 4.7 37.1 1.0
O N:ASP739 4.7 43.7 1.0
N N:ASP743 4.8 32.6 1.0
C N:ASP739 4.8 41.6 1.0
N N:ASP741 4.9 45.2 1.0
CA N:ASP739 4.9 36.9 1.0

Magnesium binding site 8 out of 10 in 4g7h

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Magnesium binding site 8 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2004

b:66.8
occ:1.00
 O N:LYS840 2.1 67.8 1.0
C N:LYS840 3.3 63.5 1.0
OE2 L:GLU154 3.7 95.2 1.0
OD2 L:ASP168 3.7 72.0 1.0
CA N:LYS840 4.1 65.5 1.0
OD1 L:ASP168 4.1 69.7 1.0
O N:LEU839 4.2 65.4 1.0
OE1 L:GLU64 4.2 0.8 1.0
N N:TYR841 4.3 67.8 1.0
CG L:ASP168 4.4 68.3 1.0
CA N:TYR841 4.5 63.4 1.0
OE2 L:GLU64 4.5 0.9 1.0
N N:VAL842 4.7 58.3 1.0
CD L:GLU154 4.7 0.8 1.0
CD L:GLU64 4.8 0.6 1.0
OE1 L:GLU154 4.9 0.1 1.0
CG N:LYS840 4.9 57.4 1.0

Magnesium binding site 9 out of 10 in 4g7h

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Magnesium binding site 9 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2005

b:67.3
occ:1.00
 O N:ILE900 2.5 78.9 1.0
O N:TRP897 3.0 67.9 1.0
O N:GLU898 3.0 67.9 1.0
C N:GLU898 3.7 70.1 1.0
C N:ILE900 3.7 63.4 1.0
C N:TRP897 4.1 69.7 1.0
CA N:GLU898 4.1 69.9 1.0
N N:ILE900 4.5 60.7 1.0
CA N:ILE900 4.6 61.2 1.0
C N:LEU899 4.6 62.6 1.0
N N:GLU898 4.6 67.0 1.0
N N:LEU899 4.7 65.3 1.0
N N:GLN901 4.7 63.0 1.0
O N:LEU899 4.8 65.3 1.0
CA N:GLN901 4.8 69.7 1.0
CB N:ILE900 4.9 67.5 1.0

Magnesium binding site 10 out of 10 in 4g7h

Go back to Magnesium Binding Sites List in 4g7h
Magnesium binding site 10 out of 10 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg2001

b:71.3
occ:1.00
 O P:TRP299 2.9 82.8 1.0
O P:GLY296 3.0 85.3 1.0
O P:ALA292 3.0 76.7 1.0
C P:ALA292 3.7 78.4 1.0
CA P:GLU293 3.9 78.7 1.0
C P:GLY296 4.0 93.3 1.0
C P:TRP299 4.1 78.3 1.0
N P:GLU293 4.1 81.8 1.0
O P:GLU293 4.5 79.8 1.0
CA P:PRO297 4.6 97.9 1.0
C P:GLU293 4.7 73.4 1.0
N P:PRO297 4.7 97.8 1.0
N P:TRP299 4.7 84.9 1.0
CB P:ALA292 4.7 62.7 1.0
CA P:TRP299 4.8 78.0 1.0
CA P:ALA292 4.8 70.0 1.0
CB P:TRP299 4.9 79.3 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: Mon Aug 11 13:10:34 2025

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