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Magnesium in PDB 5x22: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp, PDB code: 5x22 was solved by Y.Zhang, R.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 3.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 186.410, 104.320, 297.290, 90.00, 98.36, 90.00
R / Rfree (%) 20.8 / 25

Other elements in 5x22:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp (pdb code 5x22). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp, PDB code: 5x22:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 5x22

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Magnesium binding site 1 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:65.2
occ:1.00
 OD1 B:ASP191 2.1 67.2 1.0
OD1 B:ASP193 2.2 52.5 1.0
OD1 B:ASP183 2.2 66.0 1.0
O B:LEU192 3.0 46.8 1.0
C B:LEU192 3.3 47.0 1.0
CG B:ASP191 3.4 65.2 1.0
CG B:ASP183 3.4 61.4 1.0
CG B:ASP193 3.4 43.5 1.0
N B:LEU192 3.5 52.6 1.0
N B:ASP193 3.9 43.2 1.0
CA B:LEU192 3.9 49.4 1.0
C B:ASP191 4.0 52.3 1.0
OD2 B:ASP191 4.1 62.4 1.0
CA B:ASP193 4.1 39.6 1.0
OD2 B:ASP183 4.2 60.5 1.0
OD2 B:ASP193 4.2 35.3 1.0
CA B:ASP191 4.2 54.7 1.0
CG B:ARG30 4.3 42.5 1.0
CB B:ASP193 4.4 42.6 1.0
CB B:ASP183 4.4 50.8 1.0
CB B:ASP191 4.4 57.3 1.0
CA B:ASP183 4.4 46.3 1.0
CA B:ARG30 4.6 38.6 1.0
CB B:ARG30 4.6 42.0 1.0
O B:ASP191 4.6 51.4 1.0

Magnesium binding site 2 out of 14 in 5x22

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Magnesium binding site 2 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:13.9
occ:1.00
 O3' I:A2 1.8 16.2 1.0
OD1 D:ASP739 2.0 15.2 1.0
OD1 D:ASP743 2.1 14.1 1.0
OD1 D:ASP741 2.1 13.1 1.0
CG D:ASP743 2.7 13.3 1.0
OD2 D:ASP743 2.8 12.3 1.0
CG D:ASP741 2.8 14.8 1.0
OD2 D:ASP741 2.9 17.8 1.0
CG D:ASP739 3.1 16.8 1.0
C3' I:A2 3.2 15.9 1.0
OD2 D:ASP739 3.4 17.6 1.0
O2' I:A2 3.7 17.8 1.0
C4' I:A2 3.9 15.1 1.0
C2' I:A2 4.0 16.4 1.0
C5' D:2TM2007 4.1 18.5 0.6
CB D:ASP743 4.2 12.2 1.0
CB D:ASP741 4.3 13.4 1.0
O D:ASP739 4.4 11.3 1.0
CB D:ASP739 4.4 14.2 1.0
C5' I:A2 4.4 15.6 1.0
O2A D:2TM2007 4.4 16.6 0.6
O5' D:2TM2007 4.5 19.7 0.5
N D:ASP743 4.5 12.8 1.0
N D:ASP739 4.5 14.2 1.0
C D:ASP739 4.6 11.1 1.0
N D:ASP741 4.6 13.0 1.0
CA D:ASP739 4.7 12.4 1.0
C4' D:2TM2007 4.7 17.1 0.6
CA D:ASP743 4.7 12.6 1.0
CA D:ASP741 4.8 12.6 1.0
O4' D:2TM2007 4.9 16.3 0.6
NH2 D:ARG704 4.9 13.6 1.0
O4' D:2TM2007 5.0 17.0 0.5

Magnesium binding site 3 out of 14 in 5x22

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Magnesium binding site 3 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:22.1
occ:0.55
 MG D:MG2004 0.0 22.1 0.6
PB D:2TM2007 1.2 20.3 0.5
O3B D:2TM2007 1.5 22.1 0.5
O1B D:2TM2007 1.6 19.4 0.5
PG D:2TM2007 1.9 21.6 0.5
O3G D:2TM2007 2.0 21.8 0.5
C1 D:2TM2007 2.0 21.0 0.5
O1G D:2TM2007 2.3 21.7 0.6
O1B D:2TM2007 2.3 21.1 0.6
O1G D:2TM2007 2.5 19.5 0.5
O2B D:2TM2007 2.7 18.8 0.5
MG D:MG2004 2.8 18.3 0.5
PA D:2TM2007 3.2 20.9 0.5
O2G D:2TM2007 3.3 22.2 0.5
O2A D:2TM2007 3.3 20.8 0.5
PG D:2TM2007 3.5 20.3 0.6
PB D:2TM2007 3.6 21.6 0.6
O2G D:2TM2007 3.9 20.6 0.6
OD2 D:ASP739 3.9 17.6 1.0
O3B D:2TM2007 4.0 22.4 0.6
O5' D:2TM2007 4.0 19.7 0.5
NH1 D:ARG1239 4.4 33.5 1.0
C1 D:2TM2007 4.4 19.6 0.6
O1A D:2TM2007 4.5 20.1 0.5
O3G D:2TM2007 4.7 20.7 0.6
O2B D:2TM2007 4.8 21.4 0.6
NH1 C:ARG879 5.0 28.2 1.0

Magnesium binding site 4 out of 14 in 5x22

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Magnesium binding site 4 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:18.3
occ:0.45
 MG D:MG2004 0.0 18.3 0.5
OD2 D:ASP739 2.1 17.6 1.0
O1G D:2TM2007 2.1 19.5 0.5
O1B D:2TM2007 2.1 19.4 0.5
MG D:MG2004 2.8 22.1 0.6
CG D:ASP739 3.1 16.8 1.0
PG D:2TM2007 3.1 21.6 0.5
O3G D:2TM2007 3.3 21.8 0.5
CB D:ASP739 3.4 14.2 1.0
PB D:2TM2007 3.4 20.3 0.5
O3B D:2TM2007 3.6 22.1 0.5
NH1 C:ARG879 3.7 28.2 1.0
OE1 C:GLU685 3.9 25.7 1.0
NH2 D:ARG1029 4.0 24.7 1.0
O1G D:2TM2007 4.1 21.7 0.6
O2A D:2TM2007 4.2 20.8 0.5
OD1 D:ASP739 4.2 15.2 1.0
OD1 C:ASP686 4.4 32.3 1.0
O2G D:2TM2007 4.4 22.2 0.5
O2B D:2TM2007 4.5 18.8 0.5
C1 D:2TM2007 4.5 21.0 0.5
O2G D:2TM2007 4.6 20.6 0.6
CD C:GLU685 4.6 22.7 1.0
O1B D:2TM2007 4.7 21.1 0.6
OD2 D:ASP741 4.7 17.8 1.0
OE2 C:GLU685 4.8 19.4 1.0
CA D:ASP739 4.8 12.4 1.0
NH1 D:ARG1029 4.9 24.8 1.0
CZ D:ARG1029 4.9 25.9 1.0
PA D:2TM2007 4.9 20.9 0.5
CG C:ASP686 4.9 25.5 1.0
CZ C:ARG879 4.9 22.6 1.0
PG D:2TM2007 5.0 20.3 0.6

Magnesium binding site 5 out of 14 in 5x22

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Magnesium binding site 5 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:29.8
occ:1.00
 O D:LYS840 2.0 35.1 1.0
C D:LYS840 3.2 36.6 1.0
OD2 B:ASP168 3.7 40.8 1.0
OE1 B:GLU154 3.7 51.0 1.0
OD1 B:ASP168 3.9 43.9 1.0
OE1 B:GLU64 4.0 70.7 1.0
CA D:LYS840 4.1 36.7 1.0
OE2 B:GLU64 4.2 67.2 1.0
O D:LEU839 4.2 35.3 1.0
N D:TYR841 4.2 37.6 1.0
CG B:ASP168 4.2 38.9 1.0
CA D:TYR841 4.4 35.8 1.0
CD B:GLU64 4.5 67.2 1.0
N D:VAL842 4.6 34.7 1.0
CD B:GLU154 4.8 60.7 1.0
C D:TYR841 4.9 34.0 1.0
CG D:LYS840 4.9 36.5 1.0

Magnesium binding site 6 out of 14 in 5x22

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Magnesium binding site 6 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2006

b:42.4
occ:1.00
 O D:ILE900 2.4 36.2 1.0
O D:TRP897 2.4 34.8 1.0
O D:GLU898 3.0 34.6 1.0
C D:GLU898 3.4 34.8 1.0
C D:TRP897 3.5 35.6 1.0
C D:ILE900 3.5 30.8 1.0
CA D:GLU898 3.7 37.7 1.0
N D:ILE900 4.0 25.8 1.0
N D:GLU898 4.1 34.2 1.0
CA D:ILE900 4.2 26.1 1.0
C D:LEU899 4.2 28.2 1.0
N D:LEU899 4.3 31.3 1.0
O D:LEU899 4.5 30.9 1.0
CB D:ILE900 4.6 27.3 1.0
N D:GLN901 4.6 30.1 1.0
CA D:TRP897 4.8 37.5 1.0
CA D:GLN901 4.8 32.2 1.0
CA D:LEU899 4.8 29.4 1.0
CD1 D:TRP897 4.9 40.1 1.0
N D:LEU902 4.9 33.8 1.0
NE1 D:TRP897 5.0 41.2 1.0

Magnesium binding site 7 out of 14 in 5x22

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Magnesium binding site 7 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:68.3
occ:1.00
 O F:ALA292 2.2 71.5 1.0
O F:TRP299 2.3 72.5 1.0
C F:ALA292 2.9 72.8 1.0
O F:GLY296 3.2 69.8 1.0
C F:TRP299 3.4 72.0 1.0
CB F:ALA292 3.6 64.5 1.0
CA F:ALA292 3.7 67.2 1.0
N F:GLU293 3.7 75.0 1.0
CA F:GLU293 4.0 72.0 1.0
CB F:TRP299 4.1 71.6 1.0
CA F:TRP299 4.2 70.9 1.0
C F:GLY296 4.4 72.0 1.0
N F:ASP300 4.4 69.7 1.0
N F:TRP299 4.4 69.3 1.0
CA F:ASP300 4.5 69.7 1.0
C F:GLU293 4.7 70.2 1.0
O F:GLU293 4.7 73.8 1.0
N F:GLY296 4.8 75.5 1.0

Magnesium binding site 8 out of 14 in 5x22

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Magnesium binding site 8 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg2001

b:54.5
occ:1.00
 OD1 L:ASP191 2.1 63.5 1.0
OD1 L:ASP183 2.2 68.5 1.0
OD1 L:ASP193 2.2 52.7 1.0
O L:LEU192 3.0 45.4 1.0
CG L:ASP191 3.3 62.2 1.0
CG L:ASP193 3.4 42.7 1.0
CG L:ASP183 3.4 61.9 1.0
C L:LEU192 3.5 42.2 1.0
N L:LEU192 3.7 46.2 1.0
OD2 L:ASP191 4.0 59.6 1.0
N L:ASP193 4.0 35.4 1.0
CA L:LEU192 4.1 44.2 1.0
C L:ASP191 4.1 49.4 1.0
CA L:ASP193 4.2 35.0 1.0
CA L:ASP183 4.2 44.4 1.0
OD2 L:ASP193 4.2 33.8 1.0
CB L:ASP183 4.3 48.3 1.0
OD2 L:ASP183 4.3 60.0 1.0
CA L:ASP191 4.3 51.8 1.0
CB L:ASP193 4.4 37.5 1.0
CB L:ASP191 4.4 55.1 1.0
CG L:ARG30 4.6 38.8 1.0
O L:ASP191 4.8 55.1 1.0
CA L:ARG30 4.9 34.4 1.0
N L:THR184 5.0 44.9 1.0

Magnesium binding site 9 out of 14 in 5x22

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Magnesium binding site 9 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2003

b:11.7
occ:1.00
 O3' S:A2 1.8 14.6 1.0
OD1 N:ASP739 2.0 12.4 1.0
OD1 N:ASP741 2.1 12.4 1.0
OD1 N:ASP743 2.1 14.3 1.0
OD2 N:ASP743 2.8 12.8 1.0
CG N:ASP743 2.8 12.6 1.0
CG N:ASP741 2.8 13.3 1.0
OD2 N:ASP741 2.8 16.1 1.0
CG N:ASP739 3.1 15.4 1.0
C3' S:A2 3.2 13.6 1.0
OD2 N:ASP739 3.5 21.4 1.0
O2' S:A2 3.6 16.1 1.0
C4' S:A2 3.8 12.3 1.0
C2' S:A2 3.9 15.4 1.0
CB N:ASP743 4.3 10.3 1.0
CB N:ASP741 4.3 12.0 1.0
O5' N:2TM2007 4.3 20.4 0.5
O N:ASP739 4.3 12.0 1.0
CB N:ASP739 4.4 11.6 1.0
N N:ASP739 4.4 11.0 1.0
C5' S:A2 4.5 13.7 1.0
O5' N:2TM2007 4.5 19.5 0.6
C N:ASP739 4.5 11.0 1.0
NH2 N:ARG704 4.6 14.7 1.0
N N:ASP743 4.6 11.8 1.0
CA N:ASP739 4.6 10.3 1.0
N N:ASP741 4.7 10.2 1.0
C5' N:2TM2007 4.8 19.1 0.5
CA N:ASP743 4.8 10.6 1.0
C4' N:2TM2007 4.8 16.9 0.5
O4' N:2TM2007 4.9 14.1 0.5
O4' N:2TM2007 4.9 14.3 0.6
CA N:ASP741 4.9 9.9 1.0
C5' N:2TM2007 4.9 19.1 0.6
C4' N:2TM2007 5.0 17.0 0.6

Magnesium binding site 10 out of 14 in 5x22

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Magnesium binding site 10 out of 14 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2004

b:25.4
occ:0.55
 MG N:MG2004 0.0 25.4 0.6
O2B N:2TM2007 1.7 22.3 0.5
O3G N:2TM2007 2.0 25.5 0.5
PG N:2TM2007 2.0 26.0 0.5
O2G N:2TM2007 2.0 23.0 0.5
PB N:2TM2007 2.0 22.7 0.5
O2G N:2TM2007 2.1 25.1 0.6
MG N:MG2004 2.2 19.7 0.5
O3B N:2TM2007 2.3 25.4 0.5
O2B N:2TM2007 2.4 24.0 0.6
C1 N:2TM2007 2.6 23.8 0.5
PG N:2TM2007 3.2 24.9 0.6
O1A N:2TM2007 3.3 22.0 0.5
O1G N:2TM2007 3.3 22.9 0.6
O1B N:2TM2007 3.5 20.1 0.5
O1G N:2TM2007 3.5 24.9 0.5
PA N:2TM2007 3.5 22.4 0.5
OD2 N:ASP739 3.6 21.4 1.0
PB N:2TM2007 3.6 25.6 0.6
O3B N:2TM2007 3.8 24.2 0.6
NH1 M:ARG879 4.1 27.9 1.0
O5' N:2TM2007 4.3 20.4 0.5
C1 N:2TM2007 4.4 22.1 0.6
O3G N:2TM2007 4.4 26.6 0.6
NH2 N:ARG1029 4.5 29.7 1.0
O2A N:2TM2007 4.8 22.2 0.5
CG N:ASP739 4.8 15.4 1.0
O1B N:2TM2007 4.8 23.8 0.6
NH1 N:ARG1029 4.9 27.0 1.0

Reference:

S.I.Maffioli, Y.Zhang, D.Degen, T.Carzaniga, G.Del Gatto, S.Serina, P.Monciardini, C.Mazzetti, P.Guglierame, G.Candiani, A.I.Chiriac, G.Facchetti, P.Kaltofen, H.G.Sahl, G.Deho, S.Donadio, R.H.Ebright. Antibacterial Nucleoside-Analog Inhibitor of Bacterial Rna Polymerase. Cell V. 169 1240 2017.
ISSN: ISSN 1097-4172
PubMed: 28622509
DOI: 10.1016/J.CELL.2017.05.042
Page generated: Mon Sep 30 09:00:25 2024

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