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

Go back to Magnesium Binding Sites List in 5wq0
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

Go back to Magnesium Binding Sites List in 5wq0
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

Go back to Magnesium Binding Sites List in 5wq0
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

Go back to Magnesium Binding Sites List in 5wq0
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

Go back to Magnesium Binding Sites List in 5wq0
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

Go back to Magnesium Binding Sites List in 5wq0
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

Go back to Magnesium Binding Sites List in 5wq0
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 Dec 14 21:24:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy