Atomistry » Magnesium » PDB 5wti-5x7u » 5x22
Atomistry »
  Magnesium »
    PDB 5wti-5x7u »
      5x22 »

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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Go back to Magnesium Binding Sites List in 5x22
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy