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Magnesium in PDB 5wq0: Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14

Protein crystallography data

The structure of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14, PDB code: 5wq0 was solved by J.H.Lee, C.W.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.57 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.969, 72.233, 189.650, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 (pdb code 5wq0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14, PDB code: 5wq0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5wq0

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Magnesium binding site 1 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:37.6
occ:1.00
 OD2 B:ASP56 2.2 38.2 1.0
O B:HOH311 2.6 37.1 1.0
O B:ILE58 2.6 26.3 1.0
O B:HOH307 2.6 37.1 1.0
OD1 B:ASP11 2.9 39.4 1.0
O B:HOH303 3.0 37.1 1.0
CG B:ASP56 3.1 33.3 1.0
OD1 B:ASP56 3.3 36.8 1.0
C B:ILE58 3.7 24.4 1.0
CB B:ILE58 3.9 22.9 1.0
CG B:ASP11 4.0 34.0 1.0
NZ B:LYS108 4.2 28.4 1.0
CG2 B:ILE58 4.2 22.8 1.0
CA B:ILE58 4.2 23.7 1.0
OD2 B:ASP11 4.3 35.4 1.0
OD1 B:ASP10 4.5 41.6 1.0
CB B:ASP56 4.5 28.2 1.0
N B:ILE58 4.5 24.4 1.0
N B:MET59 4.8 23.6 1.0

Magnesium binding site 2 out of 7 in 5wq0

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Magnesium binding site 2 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:43.4
occ:1.00
 OD2 A:ASP56 2.2 39.8 1.0
O A:ILE58 2.4 29.9 1.0
O A:HOH304 2.5 37.1 1.0
OD1 A:ASP11 2.8 39.5 1.0
CG A:ASP56 3.0 38.9 1.0
OD1 A:ASP56 3.0 42.3 1.0
C A:ILE58 3.5 27.0 1.0
CB A:ILE58 3.7 29.7 1.0
CG A:ASP11 3.9 35.7 1.0
CA A:ILE58 4.0 28.9 1.0
CG2 A:ILE58 4.0 30.1 1.0
N A:ILE58 4.2 30.0 1.0
OD2 A:ASP11 4.2 39.0 1.0
NZ A:LYS108 4.3 27.0 1.0
CB A:ASP56 4.4 31.9 1.0
N A:MET59 4.6 25.5 1.0
OD1 A:ASP10 4.9 41.4 1.0
CG1 A:ILE58 5.0 30.8 1.0

Magnesium binding site 3 out of 7 in 5wq0

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Magnesium binding site 3 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:42.1
occ:1.00
 O C:HOH302 2.0 37.1 1.0
OD2 C:ASP56 2.3 31.8 1.0
O C:ILE58 2.5 30.8 1.0
OD1 C:ASP11 3.1 33.5 1.0
CG C:ASP56 3.2 29.9 1.0
OD1 C:ASP56 3.4 32.1 1.0
C C:ILE58 3.5 29.8 1.0
CB C:ILE58 3.8 31.2 1.0
CA C:ILE58 4.0 30.6 1.0
CG2 C:ILE58 4.1 32.7 1.0
OD1 C:ASP10 4.1 40.3 1.0
CG C:ASP11 4.1 31.1 1.0
NZ C:LYS108 4.3 31.6 1.0
N C:ILE58 4.3 32.3 1.0
OD2 C:ASP11 4.3 39.3 1.0
CB C:ASP56 4.7 26.6 1.0
N C:MET59 4.7 28.1 1.0

Magnesium binding site 4 out of 7 in 5wq0

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Magnesium binding site 4 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:41.1
occ:1.00
 O D:HOH301 2.3 37.1 1.0
OD2 D:ASP56 2.3 41.3 1.0
O D:ILE58 2.5 30.2 1.0
OD1 D:ASP11 2.6 39.7 1.0
CG D:ASP56 3.3 35.4 1.0
OD1 D:ASP56 3.5 40.9 1.0
C D:ILE58 3.6 29.3 1.0
CG D:ASP11 3.6 36.6 1.0
CB D:ILE58 3.9 30.8 1.0
OD2 D:ASP11 4.0 36.2 1.0
CG2 D:ILE58 4.1 34.7 1.0
CA D:ILE58 4.2 29.8 1.0
OD1 D:ASP10 4.4 45.8 1.0
N D:ILE58 4.5 31.3 1.0
NZ D:LYS108 4.6 37.3 1.0
CB D:ASP56 4.7 33.6 1.0
N D:MET59 4.7 29.6 1.0
CB D:ASP11 4.9 35.4 1.0

Magnesium binding site 5 out of 7 in 5wq0

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Magnesium binding site 5 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:38.6
occ:1.00
 O E:HOH306 2.2 37.1 1.0
OD2 E:ASP56 2.3 28.6 1.0
O E:ILE58 2.4 30.6 1.0
OD1 E:ASP11 2.7 36.4 1.0
CG E:ASP56 3.2 27.8 1.0
OD1 E:ASP56 3.3 29.6 1.0
C E:ILE58 3.6 26.7 1.0
CG E:ASP11 3.6 31.2 1.0
OD2 E:ASP11 3.8 33.1 1.0
CB E:ILE58 4.1 27.6 1.0
NZ E:LYS108 4.1 34.3 1.0
CA E:ILE58 4.2 27.1 1.0
CG2 E:ILE58 4.3 29.5 1.0
O E:HOH311 4.4 37.1 1.0
CE F:MET94 4.5 50.4 1.0
OD1 E:ASP10 4.5 44.5 1.0
N E:ILE58 4.5 28.1 1.0
CB E:ASP56 4.6 26.5 1.0
N E:MET59 4.7 27.1 1.0
OD2 E:ASP10 4.9 40.8 1.0
N E:ASP11 4.9 28.9 1.0
CG E:ASP10 5.0 38.2 1.0

Magnesium binding site 6 out of 7 in 5wq0

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Magnesium binding site 6 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:39.9
occ:1.00
 OD1 F:ASP11 2.3 32.3 1.0
O F:ILE58 2.5 28.3 1.0
OD2 F:ASP56 2.5 36.1 1.0
CG F:ASP11 3.0 30.6 1.0
OD2 F:ASP11 3.0 31.9 1.0
CG F:ASP56 3.5 35.4 1.0
C F:ILE58 3.7 26.8 1.0
OD1 F:ASP56 3.9 41.1 1.0
OD1 F:ASP10 4.1 34.0 1.0
NZ F:LYS108 4.3 31.6 1.0
CB F:ILE58 4.4 24.9 1.0
CB F:ASP11 4.5 30.2 1.0
CA F:ILE58 4.5 26.1 1.0
N F:ASP11 4.5 27.4 1.0
N F:MET59 4.7 27.1 1.0
CB F:ASP56 4.8 32.0 1.0
CG F:ASP10 4.8 30.4 1.0
N F:ILE58 4.8 27.1 1.0
CG2 F:ILE58 4.9 25.5 1.0
CA F:ASP11 4.9 29.0 1.0
CA F:MET59 4.9 26.4 1.0
N F:ASN12 5.0 27.9 1.0

Magnesium binding site 7 out of 7 in 5wq0

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Magnesium binding site 7 out of 7 in the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:39.3
occ:1.00
 OD2 G:ASP56 2.0 34.6 1.0
O G:ILE58 2.2 30.5 1.0
OD1 G:ASP11 2.3 36.8 1.0
O G:HOH309 2.4 37.1 1.0
CG G:ASP56 3.1 33.9 1.0
CG G:ASP11 3.3 36.5 1.0
C G:ILE58 3.4 33.7 1.0
OD2 G:ASP11 3.5 40.2 1.0
OD1 G:ASP56 3.6 34.2 1.0
O G:HOH303 3.7 37.1 1.0
CB G:ILE58 4.0 34.3 1.0
CA G:ILE58 4.1 33.4 1.0
OD1 G:ASP10 4.1 44.2 1.0
N G:ILE58 4.3 32.2 1.0
CB G:ASP56 4.3 31.0 1.0
N G:MET59 4.4 32.2 1.0
N G:ASP11 4.5 33.3 1.0
NZ G:LYS108 4.6 28.8 1.0
CB G:ASP11 4.6 34.7 1.0
CG G:MET59 4.7 27.8 1.0
CA G:MET59 4.7 30.6 1.0
CG G:ASP10 4.8 41.6 1.0
CG2 G:ILE58 4.9 36.5 1.0

Reference:

C.W.Lee, S.H.Park, S.G.Lee, S.C.Shin, S.J.Han, H.W.Kim, H.H.Park, S.Kim, H.J.Kim, H.Park, H.Park, J.H.Lee. Crystal Structure of the Inactive State of the Receiver Domain of SPO0A From Paenisporosarcina Sp. Tg-14, A Psychrophilic Bacterium Isolated From An Antarctic Glacier J. Microbiol. V. 55 464 2017.
ISSN: ISSN 1976-3794
PubMed: 28281198
DOI: 10.1007/S12275-017-6599-9
Page generated: Mon Sep 30 06:43:22 2024

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