Magnesium in PDB 3m0e: Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain

Enzymatic activity of Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain

All present enzymatic activity of Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain:
3.6.1.3;

Protein crystallography data

The structure of Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain, PDB code: 3m0e was solved by B.Chen, T.A.Sysoeva, S.Chowdhury, M.Rusu, S.Birmanns, L.Guo, J.Hanson, H.Yang, B.T.Nixon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.63
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 251.209, 242.586, 40.703, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain (pdb code 3m0e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain, PDB code: 3m0e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3m0e

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Magnesium binding site 1 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:47.0
occ:1.00
 O2G A:ATP400 2.4 28.2 1.0
O1B A:ATP400 2.6 35.4 1.0
O A:HOH416 2.6 57.1 1.0
O A:HOH16 3.0 34.0 1.0
OE1 A:GLU174 3.6 69.8 1.0
O A:HOH98 3.6 45.7 1.0
O B:HOH418 3.7 43.9 1.0
OD2 A:ASP238 3.7 58.9 1.0
NH2 B:ARG299 3.7 37.9 1.0
PG A:ATP400 3.8 39.0 1.0
PB A:ATP400 3.8 30.6 1.0
CB A:GLU174 3.8 42.2 1.0
O3B A:ATP400 4.0 44.3 1.0
OD1 A:ASP238 4.1 49.9 1.0
CG A:ASP238 4.3 48.6 1.0
O1A A:ATP400 4.3 50.6 1.0
N A:GLU174 4.5 33.9 1.0
O1G A:ATP400 4.5 44.3 1.0
CD A:GLU174 4.6 63.1 1.0
CA A:GLU174 4.7 33.3 1.0
NH1 B:ARG253 4.7 54.1 1.0
O3A A:ATP400 4.8 42.5 1.0
CG A:GLU174 4.8 48.6 1.0
O B:HOH46 4.8 46.2 1.0
PA A:ATP400 4.9 39.6 1.0
O2B A:ATP400 4.9 44.6 1.0
O3G A:ATP400 4.9 40.0 1.0

Magnesium binding site 2 out of 7 in 3m0e

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Magnesium binding site 2 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:54.5
occ:1.00
 O3G B:ATP400 2.5 29.5 1.0
O1B B:ATP400 2.6 23.5 1.0
O B:HOH14 2.7 36.8 1.0
OE1 B:GLU174 3.3 68.2 1.0
O1A B:ATP400 3.5 64.0 1.0
O C:HOH99 3.5 39.5 1.0
CB B:GLU174 3.6 36.9 1.0
PG B:ATP400 3.7 40.9 1.0
PB B:ATP400 3.8 30.4 1.0
NH2 C:ARG299 3.8 44.7 1.0
OD2 B:ASP238 3.9 65.2 1.0
O B:HOH114 3.9 39.3 1.0
O3B B:ATP400 3.9 42.8 1.0
O2G B:ATP400 4.3 46.6 1.0
CD B:GLU174 4.3 58.8 1.0
N B:GLU174 4.3 36.7 1.0
OD1 B:ASP238 4.3 49.5 1.0
CG B:ASP238 4.4 51.5 1.0
CA B:GLU174 4.5 33.5 1.0
CG B:GLU174 4.5 46.7 1.0
PA B:ATP400 4.6 35.2 1.0
O B:HOH419 4.6 56.7 1.0
O3A B:ATP400 4.6 42.7 1.0
O C:HOH79 4.8 40.3 1.0
NH1 C:ARG253 4.8 52.8 1.0
O2B B:ATP400 4.9 44.2 1.0
O1G B:ATP400 5.0 34.6 1.0

Magnesium binding site 3 out of 7 in 3m0e

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Magnesium binding site 3 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:54.6
occ:1.00
 O2G C:ATP400 2.5 38.7 1.0
O1B C:ATP400 2.6 39.4 1.0
O C:HOH19 3.0 29.6 1.0
OE1 C:GLU174 3.5 62.5 1.0
OD2 C:ASP238 3.6 58.3 1.0
CB C:GLU174 3.8 37.5 1.0
OD1 C:ASP238 3.9 54.4 1.0
PG C:ATP400 3.9 40.0 1.0
PB C:ATP400 3.9 32.5 1.0
O D:HOH393 3.9 43.9 1.0
NH2 D:ARG299 4.1 41.0 1.0
CG C:ASP238 4.1 50.7 1.0
O3B C:ATP400 4.2 40.0 1.0
N C:GLU174 4.4 37.3 1.0
O1G C:ATP400 4.5 44.8 1.0
CD C:GLU174 4.6 57.2 1.0
CA C:GLU174 4.6 33.8 1.0
O1A C:ATP400 4.7 51.1 1.0
O C:HOH403 4.7 54.8 1.0
NH1 D:ARG253 4.7 48.8 1.0
CG C:GLU174 4.8 50.3 1.0
O3A C:ATP400 4.8 35.3 1.0
CE C:LYS173 5.0 36.5 1.0

Magnesium binding site 4 out of 7 in 3m0e

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Magnesium binding site 4 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:55.0
occ:1.00
 O1B D:ATP400 2.6 27.8 1.0
O2G D:ATP400 2.7 29.5 1.0
O E:HOH8 2.8 32.2 1.0
OE1 D:GLU174 3.5 72.2 1.0
OD2 D:ASP238 3.5 65.2 1.0
CB D:GLU174 3.8 38.4 1.0
OD1 D:ASP238 3.8 49.6 1.0
PG D:ATP400 3.9 44.1 1.0
PB D:ATP400 3.9 31.6 1.0
CG D:ASP238 4.0 48.8 1.0
O E:HOH389 4.1 38.0 1.0
O1G D:ATP400 4.2 34.4 1.0
NH2 E:ARG299 4.2 41.1 1.0
O3B D:ATP400 4.2 37.7 1.0
N D:GLU174 4.3 38.0 1.0
CA D:GLU174 4.5 35.2 1.0
CD D:GLU174 4.5 62.0 1.0
O1A D:ATP400 4.7 36.3 1.0
CG D:GLU174 4.8 46.7 1.0
O D:HOH389 4.8 45.9 1.0
O E:HOH390 4.8 50.0 1.0
CE D:LYS173 4.9 31.4 1.0
NH1 E:ARG253 4.9 51.8 1.0
O2B D:ATP400 4.9 37.7 1.0
O3A D:ATP400 4.9 43.8 1.0
CB D:LYS173 4.9 33.0 1.0

Magnesium binding site 5 out of 7 in 3m0e

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Magnesium binding site 5 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:45.9
occ:1.00
 O1G E:ATP400 2.4 33.3 1.0
O E:HOH405 2.5 53.1 1.0
O1B E:ATP400 2.6 37.5 1.0
O E:HOH6 2.6 33.7 1.0
NH2 F:ARG299 3.5 42.7 1.0
OE1 E:GLU174 3.6 65.1 1.0
PG E:ATP400 3.7 42.6 1.0
PB E:ATP400 3.8 34.2 1.0
OD2 E:ASP238 3.8 55.6 1.0
CB E:GLU174 3.8 39.7 1.0
O3B E:ATP400 3.9 41.2 1.0
O F:HOH45 4.1 44.5 1.0
O1A E:ATP400 4.2 39.0 1.0
O3G E:ATP400 4.4 38.5 1.0
OD1 E:ASP238 4.4 49.0 1.0
CG E:ASP238 4.5 48.6 1.0
N E:GLU174 4.5 35.8 1.0
CD E:GLU174 4.5 61.1 1.0
O E:HOH414 4.7 62.3 1.0
O3A E:ATP400 4.7 35.3 1.0
CA E:GLU174 4.7 34.3 1.0
PA E:ATP400 4.7 39.1 1.0
CG E:GLU174 4.8 50.4 1.0
CZ F:ARG299 4.8 38.7 1.0
NH1 F:ARG253 4.8 52.0 1.0
O2A E:ATP400 4.8 32.7 1.0
O2G E:ATP400 4.9 30.2 1.0
O2B E:ATP400 4.9 38.3 1.0

Magnesium binding site 6 out of 7 in 3m0e

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Magnesium binding site 6 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:51.3
occ:1.00
 O1B F:ATP400 2.6 20.9 1.0
O1G F:ATP400 2.6 35.7 1.0
O F:HOH419 3.0 51.0 1.0
O F:HOH18 3.1 40.6 1.0
OE1 F:GLU174 3.4 64.3 1.0
CB F:GLU174 3.6 35.1 1.0
OD2 F:ASP238 3.7 62.5 1.0
O1A F:ATP400 3.8 65.1 1.0
PG F:ATP400 3.9 41.7 1.0
PB F:ATP400 3.9 33.0 1.0
NH2 G:ARG299 3.9 40.9 1.0
OD1 F:ASP238 4.1 55.6 1.0
O3B F:ATP400 4.2 38.4 1.0
CG F:ASP238 4.2 51.3 1.0
O G:HOH57 4.3 42.0 1.0
N F:GLU174 4.3 39.4 1.0
CD F:GLU174 4.4 58.1 1.0
O3G F:ATP400 4.5 46.2 1.0
CA F:GLU174 4.5 35.9 1.0
CG F:GLU174 4.6 42.4 1.0
NH1 G:ARG253 4.8 53.0 1.0
O F:HOH426 4.8 55.1 1.0
PA F:ATP400 4.8 34.6 1.0
O3A F:ATP400 4.9 41.2 1.0
O2B F:ATP400 4.9 35.4 1.0

Magnesium binding site 7 out of 7 in 3m0e

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Magnesium binding site 7 out of 7 in the Crystal Structure of the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain


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 the Atp-Bound State of Walker B Mutant of NTRC1 Atpase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:50.6
occ:1.00
 O2G G:ATP400 2.6 26.4 1.0
O G:HOH422 2.7 54.6 1.0
O1B G:ATP400 2.7 30.3 1.0
O G:HOH7 2.7 26.4 1.0
OE1 G:GLU174 3.2 64.2 1.0
OD2 G:ASP238 3.5 57.4 1.0
O A:HOH395 3.6 39.4 1.0
CB G:GLU174 3.6 34.7 1.0
O G:HOH388 3.8 44.3 1.0
NH2 A:ARG299 3.9 41.9 1.0
OD1 G:ASP238 4.0 51.3 1.0
PB G:ATP400 4.0 30.4 1.0
PG G:ATP400 4.0 34.8 1.0
CG G:ASP238 4.1 49.6 1.0
CD G:GLU174 4.3 57.1 1.0
O3B G:ATP400 4.3 35.9 1.0
N G:GLU174 4.4 34.2 1.0
CA G:GLU174 4.5 30.7 1.0
CG G:GLU174 4.5 49.3 1.0
NH1 A:ARG253 4.6 50.5 1.0
O1A G:ATP400 4.6 48.4 1.0
O1G G:ATP400 4.7 29.6 1.0
O A:HOH36 4.8 44.1 1.0
O G:HOH48 4.8 40.4 1.0
O3A G:ATP400 4.9 36.9 1.0

Reference:

B.Chen, T.A.Sysoeva, S.Chowdhury, L.Guo, S.De Carlo, J.A.Hanson, H.Yang, B.T.Nixon. Engagement of Arginine Finger to Atp Triggers Large Conformational Changes in NTRC1 Aaa+ Atpase For Remodeling Bacterial Rna Polymerase. Structure V. 18 1420 2010.
ISSN: ISSN 0969-2126
PubMed: 21070941
DOI: 10.1016/J.STR.2010.08.018
Page generated: Mon Dec 14 08:25:16 2020

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