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Magnesium in PDB 5x21: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum):
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum), PDB code: 5x21 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) 39.67 / 3.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 186.790, 103.090, 296.230, 90.00, 98.71, 90.00
R / Rfree (%) 23.2 / 28

Other elements in 5x21:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum) 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 with Gpa and Pseudouridimycin (Pum) (pdb code 5x21). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum), PDB code: 5x21:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5x21

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Magnesium binding site 1 out of 6 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)


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 Pseudouridimycin (Pum) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:43.7
occ:1.00
 NH2 A:ARG175 2.2 62.7 1.0
O A:VAL170 2.5 58.4 1.0
O A:THR51 3.3 58.7 1.0
CZ A:ARG175 3.3 69.3 1.0
O A:PHE171 3.5 59.8 1.0
C A:VAL170 3.7 52.0 1.0
O A:SER172 3.7 58.8 1.0
NH1 A:ARG175 3.8 62.4 1.0
OD2 A:ASP202 3.8 59.8 1.0
C A:PHE171 3.9 58.3 1.0
C A:SER172 4.1 56.9 1.0
CA A:PHE171 4.3 55.6 1.0
N A:PHE171 4.4 52.1 1.0
NE A:ARG175 4.4 75.5 1.0
C A:THR51 4.5 60.5 1.0
CA A:PRO173 4.5 65.2 1.0
N A:PRO173 4.5 62.3 1.0
N A:SER172 4.5 59.1 1.0
CB A:VAL170 4.6 39.6 1.0
CG1 A:VAL170 4.6 47.8 1.0
CB A:ALA52 4.7 60.2 1.0
CA A:VAL170 4.7 44.4 1.0
CA A:SER172 5.0 54.9 1.0
CG A:ASP202 5.0 60.0 1.0

Magnesium binding site 2 out of 6 in 5x21

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Magnesium binding site 2 out of 6 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)


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 Pseudouridimycin (Pum) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2000

b:31.6
occ:1.00
 O C:SER389 2.2 41.5 1.0
O C:SER392 3.0 29.8 1.0
O C:SER387 3.2 41.0 1.0
C C:SER389 3.3 43.0 1.0
C C:ARG388 3.8 48.9 1.0
N C:SER389 3.9 41.4 1.0
O C:ARG388 4.1 48.2 1.0
NH1 C:ARG134 4.2 32.1 1.0
CA C:ARG388 4.2 56.2 1.0
N C:GLN390 4.2 40.2 1.0
C C:SER392 4.2 25.7 1.0
CA C:GLN390 4.2 38.7 1.0
CA C:SER389 4.2 45.0 1.0
C C:SER387 4.3 40.2 1.0
O C:GLN390 4.6 44.2 1.0
NH2 C:ARG134 4.6 51.6 1.0
C C:GLN390 4.6 38.5 1.0
CB C:SER392 4.7 31.8 1.0
N C:ARG388 4.7 43.3 1.0
CZ C:ARG134 4.8 35.2 1.0
CA C:SER392 4.9 24.8 1.0
OD1 F:ASP323 5.0 67.7 1.0
N C:SER392 5.0 28.3 1.0

Magnesium binding site 3 out of 6 in 5x21

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Magnesium binding site 3 out of 6 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)


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 Pseudouridimycin (Pum) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:39.3
occ:1.00
 O D:LYS840 2.1 51.7 1.0
OD2 B:ASP168 3.1 46.4 1.0
C D:LYS840 3.3 55.1 1.0
OE2 B:GLU154 3.4 72.8 1.0
OD1 B:ASP168 3.6 50.9 1.0
CG B:ASP168 3.7 52.0 1.0
CA D:TYR841 4.1 52.6 1.0
OE1 B:GLU154 4.1 77.3 1.0
N D:TYR841 4.1 60.1 1.0
CD B:GLU154 4.2 75.2 1.0
CA D:LYS840 4.4 48.3 1.0
OE1 B:GLU64 4.4 96.4 1.0
N D:VAL842 4.4 49.8 1.0
CB B:ALA153 4.5 61.9 1.0
O D:LEU839 4.5 43.0 1.0
C D:TYR841 4.7 48.4 1.0
OE2 B:GLU64 4.8 87.3 1.0

Magnesium binding site 4 out of 6 in 5x21

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Magnesium binding site 4 out of 6 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)


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 Pseudouridimycin (Pum) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:21.9
occ:1.00
 OD1 D:ASP741 2.1 15.3 1.0
O3' I:A2 2.1 24.1 1.0
OD1 D:ASP743 2.1 22.2 1.0
OD1 D:ASP739 2.1 22.6 1.0
OD2 D:ASP743 2.6 21.0 1.0
CG D:ASP743 2.7 20.7 1.0
CG D:ASP739 2.7 22.1 1.0
CG D:ASP741 2.8 15.6 1.0
OD2 D:ASP741 2.8 21.9 1.0
OD2 D:ASP739 2.9 22.7 1.0
C3' I:A2 3.3 23.2 1.0
O2' I:A2 3.3 27.3 1.0
C4' I:A2 3.8 22.8 1.0
C2' I:A2 3.9 25.8 1.0
O D:ASP739 3.9 17.0 1.0
CB D:ASP739 4.0 22.6 1.0
NH2 D:ARG704 4.0 24.3 1.0
N D:ASP739 4.1 20.1 1.0
CB D:ASP743 4.1 22.9 1.0
C D:ASP739 4.2 14.3 1.0
CAP I:PUM101 4.2 29.0 1.0
CB D:ASP741 4.3 14.7 1.0
CA D:ASP739 4.3 14.9 1.0
N D:ASP741 4.4 19.3 1.0
C5' I:A2 4.5 22.7 1.0
NAR I:PUM101 4.5 24.9 1.0
N D:ASP743 4.7 21.8 1.0
CA D:ASP741 4.8 15.5 1.0
CA D:ASP743 4.9 24.4 1.0
N D:PHE740 5.0 13.4 1.0
O4' I:A2 5.0 27.4 1.0

Magnesium binding site 5 out of 6 in 5x21

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Magnesium binding site 5 out of 6 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)


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

b:45.2
occ:1.00
 O F:GLY296 2.3 54.0 1.0
O F:ALA292 2.3 56.6 1.0
O F:TRP299 2.4 51.2 1.0
C F:ALA292 3.3 54.5 1.0
C F:GLY296 3.4 56.9 1.0
C F:TRP299 3.5 49.1 1.0
CB F:TRP299 3.9 54.4 1.0
N F:TRP299 3.9 53.9 1.0
CA F:TRP299 4.0 50.2 1.0
CA F:GLU293 4.1 59.0 1.0
N F:GLU293 4.1 56.3 1.0
N F:GLY296 4.2 65.8 1.0
N F:PRO297 4.3 62.5 1.0
CA F:GLY296 4.3 67.8 1.0
O F:GLU293 4.3 57.0 1.0
CA F:ALA292 4.3 51.1 1.0
CA F:PRO297 4.4 74.4 1.0
CB F:ALA292 4.5 55.2 1.0
C F:GLU293 4.6 56.0 1.0
C F:PRO297 4.7 74.1 1.0
N F:ASP300 4.7 50.6 1.0
N F:GLY298 4.8 71.0 1.0

Magnesium binding site 6 out of 6 in 5x21

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Magnesium binding site 6 out of 6 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Pseudouridimycin (Pum)


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 Pseudouridimycin (Pum) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2001

b:50.9
occ:1.00
 O6 H:DG20 3.7 74.4 1.0
N7 H:DG19 3.7 56.5 1.0
O6 H:DG19 4.0 66.1 1.0
C5 H:DC18 4.4 55.7 1.0
N4 G:DC8 4.5 83.8 1.0
C5 H:DG19 4.6 59.1 1.0
C6 H:DG19 4.7 63.3 1.0
O4 G:DT7 4.7 96.6 1.0
C8 H:DG19 4.7 57.9 1.0
C6 H:DG20 4.8 73.8 1.0
C4 H:DC18 4.8 57.1 1.0
N4 H:DC18 4.9 54.2 1.0
C6 H:DC18 4.9 58.7 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 08:59:46 2024

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