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Magnesium in PDB 3nhz: Structure of N-Terminal Domain of Mtra

Protein crystallography data

The structure of Structure of N-Terminal Domain of Mtra, PDB code: 3nhz was solved by C.M.Barbieri, T.R.Mack, V.L.Robinson, M.T.Miller, A.M.Stock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.34 / 2.50
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 56.600, 56.600, 181.800, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of N-Terminal Domain of Mtra (pdb code 3nhz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of N-Terminal Domain of Mtra, PDB code: 3nhz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3nhz

Go back to Magnesium Binding Sites List in 3nhz
Magnesium binding site 1 out of 4 in the Structure of N-Terminal Domain of Mtra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of N-Terminal Domain of Mtra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg126

b:61.6
occ:1.00
O A:HOH147 2.7 39.1 1.0
O A:MET58 2.8 58.0 1.0
OD1 A:ASP13 2.9 47.8 1.0
OD2 A:ASP56 2.9 43.7 1.0
OD2 A:ASP13 3.0 58.7 1.0
CG A:ASP13 3.3 50.8 1.0
C A:MET58 3.9 48.5 1.0
CG A:ASP56 3.9 38.2 1.0
CB A:MET58 4.1 50.9 1.0
OD1 A:ASP56 4.2 40.8 1.0
O A:HOH144 4.5 46.6 1.0
CA A:MET58 4.6 49.0 1.0
OD1 A:ASP12 4.6 40.5 1.0
CB A:ASP13 4.8 41.1 1.0
CG A:MET58 4.8 53.8 1.0
NZ A:LYS105 4.9 40.7 1.0
N A:MET58 4.9 46.3 1.0
N A:LEU59 4.9 50.5 1.0

Magnesium binding site 2 out of 4 in 3nhz

Go back to Magnesium Binding Sites List in 3nhz
Magnesium binding site 2 out of 4 in the Structure of N-Terminal Domain of Mtra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of N-Terminal Domain of Mtra within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg126

b:62.0
occ:1.00
OD2 B:ASP56 2.6 40.7 1.0
O B:MET58 2.7 59.9 1.0
O B:HOH134 2.8 40.6 1.0
OD1 B:ASP13 3.3 51.0 1.0
CG B:ASP56 3.5 37.1 1.0
OD1 B:ASP56 3.6 42.1 1.0
C B:MET58 3.7 49.0 1.0
CB B:MET58 3.7 53.5 1.0
OD2 B:ASP13 3.9 62.5 1.0
O B:HOH136 4.0 46.5 1.0
CG B:ASP13 4.0 52.2 1.0
CA B:MET58 4.2 49.8 1.0
CG B:MET58 4.4 56.6 1.0
N B:MET58 4.5 47.8 1.0
OD1 B:ASP12 4.7 40.0 1.0
N B:LEU59 4.9 48.5 1.0
CB B:ASP56 4.9 32.7 1.0
NZ B:LYS105 5.0 42.8 1.0

Magnesium binding site 3 out of 4 in 3nhz

Go back to Magnesium Binding Sites List in 3nhz
Magnesium binding site 3 out of 4 in the Structure of N-Terminal Domain of Mtra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of N-Terminal Domain of Mtra within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg126

b:50.1
occ:1.00
O C:MET58 2.7 55.4 1.0
O C:HOH160 2.7 39.0 1.0
OD2 C:ASP56 2.8 37.2 1.0
OD1 C:ASP13 3.0 43.0 1.0
OD2 C:ASP13 3.4 51.4 1.0
CG C:ASP13 3.6 41.7 1.0
C C:MET58 3.7 45.3 1.0
CG C:ASP56 3.8 37.4 1.0
CB C:MET58 4.0 45.8 1.0
OD1 C:ASP56 4.1 43.2 1.0
CA C:MET58 4.4 46.8 1.0
OD1 C:ASP12 4.7 38.1 1.0
N C:LEU59 4.7 51.3 1.0
N C:MET58 4.7 46.1 1.0
CG C:MET58 4.8 49.0 1.0
CA C:LEU59 5.0 50.0 1.0

Magnesium binding site 4 out of 4 in 3nhz

Go back to Magnesium Binding Sites List in 3nhz
Magnesium binding site 4 out of 4 in the Structure of N-Terminal Domain of Mtra


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of N-Terminal Domain of Mtra within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg126

b:56.7
occ:1.00
OD2 D:ASP56 2.5 41.0 1.0
OD1 D:ASP13 2.8 45.4 1.0
O D:MET58 2.9 55.7 1.0
CG D:ASP56 3.5 39.0 1.0
CG D:ASP13 3.6 48.6 1.0
OD2 D:ASP13 3.6 54.4 1.0
OD1 D:ASP56 3.7 43.9 1.0
C D:MET58 4.0 48.0 1.0
CB D:MET58 4.2 52.2 1.0
OD1 D:ASP12 4.2 42.7 1.0
O D:HOH148 4.6 43.2 1.0
CA D:MET58 4.6 47.1 1.0
NZ D:LYS105 4.7 47.1 1.0
CB D:ASP56 4.8 34.6 1.0
N D:MET58 4.9 48.1 1.0
CB D:ASP13 5.0 42.3 1.0
N D:ASP13 5.0 33.9 1.0

Reference:

C.M.Barbieri, T.R.Mack, V.L.Robinson, M.T.Miller, A.M.Stock. Regulation of Response Regulator Autophosphorylation Through Interdomain Contacts. J.Biol.Chem. V. 285 32325 2010.
ISSN: ISSN 0021-9258
PubMed: 20702407
DOI: 10.1074/JBC.M110.157164
Page generated: Mon Dec 14 08:28:31 2020

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