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Magnesium in PDB 9fxk: Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State

Protein crystallography data

The structure of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State, PDB code: 9fxk was solved by O.Bimai, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.37 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.797, 129.791, 143.877, 90, 90, 90
R / Rfree (%) 22.4 / 25.7

Other elements in 9fxk:

The structure of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State (pdb code 9fxk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State, PDB code: 9fxk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9fxk

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Magnesium binding site 1 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:41.1
occ:1.00
 O1A A:ANP201 1.9 45.4 1.0
O2G A:ANP201 2.1 49.9 1.0
O1B A:DTP200 2.1 50.3 1.0
O1A A:DTP200 2.2 46.8 1.0
O3G A:DTP200 2.2 52.5 1.0
O2B A:ANP201 2.2 45.3 1.0
PB A:DTP200 3.2 49.9 1.0
PA A:ANP201 3.2 45.7 1.0
PB A:ANP201 3.2 46.0 1.0
PG A:ANP201 3.3 50.5 1.0
N3B A:ANP201 3.3 48.3 1.0
PA A:DTP200 3.3 46.5 1.0
O3A A:ANP201 3.4 45.9 1.0
O3A A:DTP200 3.4 48.2 1.0
PG A:DTP200 3.4 52.2 1.0
O3B A:DTP200 3.5 50.6 1.0
O5' A:ANP201 3.8 45.9 1.0
O A:HOH301 3.9 40.8 1.0
O1G A:ANP201 4.0 51.5 1.0
NZ A:LYS53 4.0 53.1 1.0
O5' A:DTP200 4.2 45.2 1.0
O A:HOH317 4.2 62.3 1.0
C5' A:DTP200 4.2 44.5 1.0
O1G A:DTP200 4.3 52.2 1.0
O3G A:ANP201 4.4 50.2 1.0
O2A A:ANP201 4.4 45.6 1.0
NZ B:LYS76 4.5 65.6 1.0
O2G A:DTP200 4.5 53.1 1.0
O2A A:DTP200 4.5 47.1 1.0
O2B A:DTP200 4.5 50.5 1.0
O1B A:ANP201 4.6 46.6 1.0
C8 A:ANP201 4.7 47.6 1.0
CE A:LYS53 5.0 52.8 1.0

Magnesium binding site 2 out of 8 in 9fxk

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Magnesium binding site 2 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:49.0
occ:1.00
 O3G B:DTP200 2.1 48.7 1.0
O2B B:ANP201 2.1 45.9 1.0
O1B B:DTP200 2.1 43.5 1.0
O2G B:ANP201 2.1 47.8 1.0
O1A B:DTP200 2.2 40.4 1.0
O1A B:ANP201 2.3 46.5 1.0
PB B:DTP200 3.1 43.8 1.0
PB B:ANP201 3.1 46.5 1.0
PG B:DTP200 3.3 49.0 1.0
PG B:ANP201 3.3 47.8 1.0
PA B:ANP201 3.3 46.0 1.0
PA B:DTP200 3.3 40.7 1.0
N3B B:ANP201 3.4 47.1 1.0
O3A B:DTP200 3.4 42.3 1.0
O3A B:ANP201 3.4 46.8 1.0
O3B B:DTP200 3.4 46.2 1.0
O B:HOH301 3.6 45.3 1.0
O B:HOH308 3.7 44.8 1.0
NZ B:LYS53 3.8 49.2 1.0
O5' B:ANP201 3.9 45.3 1.0
O1G B:ANP201 4.0 47.9 1.0
O1G B:DTP200 4.2 49.0 1.0
O5' B:DTP200 4.3 39.5 1.0
C5' B:DTP200 4.3 38.9 1.0
NZ A:LYS76 4.4 63.6 1.0
O2G B:DTP200 4.4 50.4 1.0
CE B:LYS53 4.4 49.7 1.0
O3G B:ANP201 4.5 47.8 1.0
O1B B:ANP201 4.5 46.6 1.0
O2B B:DTP200 4.5 42.7 1.0
O2A B:DTP200 4.5 40.6 1.0
C8 B:ANP201 4.6 44.5 1.0
O2A B:ANP201 4.7 45.5 1.0

Magnesium binding site 3 out of 8 in 9fxk

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Magnesium binding site 3 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:45.8
occ:1.00
 O2G C:ANP201 2.0 55.9 1.0
O2B C:ANP201 2.1 54.6 1.0
O1A C:ANP201 2.2 53.9 1.0
O1A C:DTP200 2.2 52.2 1.0
O3G C:DTP200 2.2 55.5 1.0
O1B C:DTP200 2.2 50.3 1.0
PB C:ANP201 3.1 54.6 1.0
PG C:ANP201 3.2 56.1 1.0
PB C:DTP200 3.2 51.3 1.0
PA C:ANP201 3.3 53.6 1.0
N3B C:ANP201 3.3 55.3 1.0
O3A C:ANP201 3.3 54.2 1.0
PA C:DTP200 3.4 51.5 1.0
PG C:DTP200 3.5 54.9 1.0
O3A C:DTP200 3.5 51.1 1.0
O3B C:DTP200 3.6 53.1 1.0
NZ C:LYS53 3.9 68.7 1.0
O5' C:ANP201 3.9 53.1 1.0
O C:HOH308 3.9 56.8 1.0
O1G C:ANP201 4.0 56.4 1.0
O C:HOH301 4.1 54.2 1.0
NZ D:LYS76 4.2 72.1 1.0
O5' C:DTP200 4.2 50.8 1.0
O3G C:ANP201 4.3 56.5 1.0
C5' C:DTP200 4.3 50.7 1.0
O1G C:DTP200 4.3 55.5 1.0
O1B C:ANP201 4.4 55.4 1.0
O2G C:DTP200 4.5 55.0 1.0
O2A C:DTP200 4.5 52.1 1.0
O2A C:ANP201 4.5 53.3 1.0
O2B C:DTP200 4.6 51.5 1.0
CE D:LYS76 4.6 69.4 1.0
C8 C:ANP201 4.7 53.2 1.0
CE C:LYS53 4.7 67.7 1.0

Magnesium binding site 4 out of 8 in 9fxk

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Magnesium binding site 4 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:42.1
occ:1.00
 O2B D:ANP201 2.0 46.5 1.0
O2G D:ANP201 2.1 47.8 1.0
O1A D:ANP201 2.1 44.5 1.0
O1B D:DTP200 2.1 45.1 1.0
O1A D:DTP200 2.2 44.8 1.0
O3G D:DTP200 2.2 46.5 1.0
PB D:ANP201 3.0 46.7 1.0
PA D:ANP201 3.2 44.6 1.0
PB D:DTP200 3.2 45.0 1.0
PG D:ANP201 3.2 48.3 1.0
N3B D:ANP201 3.3 47.9 1.0
O3A D:ANP201 3.3 45.5 1.0
PA D:DTP200 3.4 44.9 1.0
PG D:DTP200 3.5 46.1 1.0
O3A D:DTP200 3.5 44.8 1.0
O3B D:DTP200 3.6 45.5 1.0
O5' D:ANP201 3.8 44.8 1.0
NZ D:LYS53 3.8 57.0 1.0
O D:HOH316 3.9 65.0 1.0
O1G D:ANP201 4.0 48.3 1.0
O D:HOH303 4.1 51.0 1.0
O D:HOH311 4.1 50.7 1.0
O5' D:DTP200 4.3 45.2 1.0
O1G D:DTP200 4.3 46.8 1.0
C5' D:DTP200 4.4 44.8 1.0
O3G D:ANP201 4.4 48.1 1.0
O1B D:ANP201 4.4 46.7 1.0
O2A D:ANP201 4.5 44.7 1.0
O2G D:DTP200 4.6 46.4 1.0
C8 D:ANP201 4.6 46.1 1.0
O2B D:DTP200 4.6 44.4 1.0
O2A D:DTP200 4.6 45.4 1.0
CE D:LYS53 4.7 55.8 1.0
NZ C:LYS76 4.7 71.6 1.0

Magnesium binding site 5 out of 8 in 9fxk

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Magnesium binding site 5 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:45.4
occ:1.00
 O2G E:ANP201 2.0 53.7 1.0
O2B E:ANP201 2.1 51.1 1.0
O1A E:ANP201 2.1 51.3 1.0
O1A E:DTP200 2.2 47.7 1.0
O3G E:DTP200 2.2 52.8 1.0
O1B E:DTP200 2.2 49.0 1.0
PB E:ANP201 3.1 51.2 1.0
PG E:ANP201 3.2 53.7 1.0
PB E:DTP200 3.2 48.8 1.0
PA E:ANP201 3.2 51.0 1.0
N3B E:ANP201 3.3 52.5 1.0
O3A E:ANP201 3.4 51.1 1.0
PA E:DTP200 3.4 47.2 1.0
PG E:DTP200 3.5 52.8 1.0
O3A E:DTP200 3.5 47.9 1.0
O3B E:DTP200 3.6 50.6 1.0
O5' E:ANP201 3.9 50.4 1.0
NZ E:LYS53 3.9 71.6 1.0
O1G E:ANP201 4.0 54.0 1.0
O E:HOH320 4.2 55.5 1.0
O5' E:DTP200 4.2 46.0 1.0
O1G E:DTP200 4.3 53.1 1.0
C5' E:DTP200 4.3 45.7 1.0
O3G E:ANP201 4.3 54.0 1.0
NZ F:LYS76 4.3 68.0 1.0
O1B E:ANP201 4.4 51.3 1.0
O2A E:DTP200 4.5 47.9 1.0
O2A E:ANP201 4.5 51.5 1.0
O2G E:DTP200 4.6 53.6 1.0
O2B E:DTP200 4.6 48.3 1.0
C8 E:ANP201 4.7 51.2 1.0
CE E:LYS53 4.7 70.4 1.0

Magnesium binding site 6 out of 8 in 9fxk

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Magnesium binding site 6 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:49.2
occ:1.00
 O1B F:DTP200 2.0 48.9 1.0
O2B F:ANP201 2.1 54.7 1.0
O1A F:DTP200 2.1 45.3 1.0
O3G F:DTP200 2.1 52.3 1.0
O2G F:ANP201 2.2 57.1 1.0
O1A F:ANP201 2.2 53.6 1.0
PB F:DTP200 3.0 48.6 1.0
PB F:ANP201 3.2 54.9 1.0
PA F:DTP200 3.3 45.5 1.0
PA F:ANP201 3.3 53.4 1.0
O3A F:DTP200 3.3 46.8 1.0
PG F:DTP200 3.4 52.2 1.0
PG F:ANP201 3.4 57.4 1.0
O3B F:DTP200 3.4 50.5 1.0
N3B F:ANP201 3.4 56.4 1.0
O3A F:ANP201 3.4 54.3 1.0
NZ F:LYS53 3.8 58.4 1.0
O5' F:ANP201 3.9 52.8 1.0
O1G F:ANP201 4.1 58.2 1.0
O5' F:DTP200 4.1 44.8 1.0
O F:HOH311 4.2 56.8 1.0
C5' F:DTP200 4.2 44.8 1.0
O1G F:DTP200 4.3 52.3 1.0
O2B F:DTP200 4.4 48.9 1.0
O2G F:DTP200 4.4 53.2 1.0
O2A F:DTP200 4.5 45.8 1.0
O1B F:ANP201 4.5 54.6 1.0
O3G F:ANP201 4.5 57.0 1.0
C8 F:ANP201 4.6 49.3 1.0
O2A F:ANP201 4.7 53.4 1.0
NZ E:LYS76 4.7 70.3 1.0
CE F:LYS53 4.8 58.9 1.0

Magnesium binding site 7 out of 8 in 9fxk

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Magnesium binding site 7 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg204

b:59.6
occ:1.00
 O2G G:ANP202 2.0 68.4 1.0
O1A G:ANP202 2.1 64.5 1.0
O2B G:ANP202 2.1 66.0 1.0
O1A G:DTP201 2.2 60.0 1.0
O3G G:DTP201 2.3 61.6 1.0
O1B G:DTP201 2.3 60.3 1.0
PB G:ANP202 3.0 65.8 1.0
PG G:ANP202 3.1 68.0 1.0
PA G:ANP202 3.2 64.3 1.0
N3B G:ANP202 3.2 67.1 1.0
O3A G:ANP202 3.3 65.0 1.0
PB G:DTP201 3.3 60.6 1.0
PA G:DTP201 3.4 60.2 1.0
PG G:DTP201 3.6 61.4 1.0
O3A G:DTP201 3.6 60.3 1.0
O3B G:DTP201 3.7 61.1 1.0
O5' G:ANP202 3.8 63.9 1.0
O1G G:ANP202 3.9 68.2 1.0
O3G G:ANP202 4.2 68.2 1.0
NZ G:LYS53 4.3 83.6 1.0
O5' G:DTP201 4.3 59.9 1.0
NZ H:LYS76 4.3 87.6 1.0
C5' G:DTP201 4.3 59.5 1.0
O1B G:ANP202 4.4 65.7 1.0
O2A G:ANP202 4.4 64.4 1.0
O1G G:DTP201 4.4 61.1 1.0
CE G:LYS53 4.4 83.1 1.0
O2A G:DTP201 4.6 60.3 1.0
O2G G:DTP201 4.6 61.8 1.0
O2B G:DTP201 4.7 60.6 1.0
C8 G:ANP202 4.7 65.1 1.0
CE H:LYS76 4.8 85.9 1.0

Magnesium binding site 8 out of 8 in 9fxk

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Magnesium binding site 8 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg205

b:48.3
occ:1.00
 O3G H:DTP200 2.0 55.8 1.0
O1B H:DTP200 2.0 55.6 1.0
O1A H:DTP200 2.1 54.3 1.0
O2B H:ANP201 2.1 59.5 1.0
O2G H:ANP201 2.2 62.8 1.0
O1A H:ANP201 2.4 58.7 1.0
PB H:DTP200 3.0 55.5 1.0
PB H:ANP201 3.2 59.9 1.0
PA H:DTP200 3.2 54.6 1.0
PG H:DTP200 3.2 56.2 1.0
O3A H:DTP200 3.3 54.8 1.0
O3B H:DTP200 3.3 55.9 1.0
PG H:ANP201 3.4 63.0 1.0
PA H:ANP201 3.5 58.0 1.0
N3B H:ANP201 3.5 61.8 1.0
O3A H:ANP201 3.6 58.6 1.0
NZ H:LYS53 3.8 68.3 1.0
O H:HOH309 3.9 62.6 1.0
O5' H:ANP201 4.0 57.1 1.0
O1G H:ANP201 4.1 63.4 1.0
O1G H:DTP200 4.2 55.8 1.0
O5' H:DTP200 4.2 54.6 1.0
C5' H:DTP200 4.3 54.2 1.0
O2G H:DTP200 4.3 57.0 1.0
O2A H:DTP200 4.4 54.6 1.0
O2B H:DTP200 4.4 55.7 1.0
CE H:LYS53 4.4 67.0 1.0
NZ G:LYS76 4.4 84.6 1.0
O3G H:ANP201 4.5 63.4 1.0
O H:HOH310 4.5 60.2 1.0
O1B H:ANP201 4.6 60.0 1.0
C8 H:ANP201 4.6 53.4 1.0
O2A H:ANP201 4.8 58.3 1.0
CE G:LYS76 4.9 82.3 1.0

Reference:

I.Rozman Grinberg, O.Bimai, S.Shahid, L.Philipp, M.Martinez-Carranza, I.Banerjee, D.Lundin, P.Stenmark, B.M.Sjoberg, D.T.Logan. Bacterial Transcriptional Repressor Nrdr - A Flexible Multifactorial Nucleotide Sensor. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40029022
DOI: 10.1111/FEBS.70037
Page generated: Sat Aug 16 02:28:08 2025

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