Magnesium in PDB 6dtq: Maltose Bound T. Maritima MALE3

Protein crystallography data

The structure of Maltose Bound T. Maritima MALE3, PDB code: 6dtq was solved by M.J.Cuneo, S.Shukla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.09 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.370, 124.034, 174.847, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Maltose Bound T. Maritima MALE3 (pdb code 6dtq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Maltose Bound T. Maritima MALE3, PDB code: 6dtq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6dtq

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Magnesium binding site 1 out of 4 in the Maltose Bound T. Maritima MALE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Maltose Bound T. Maritima MALE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:22.9
occ:1.00
 OD1 A:ASP78 2.0 36.8 1.0
O A:HOH668 2.3 35.0 1.0
OE2 A:GLU308 2.4 37.9 1.0
OD1 A:ASP80 2.4 30.6 1.0
O A:HOH676 2.5 35.1 1.0
OD2 A:ASP80 2.5 31.4 1.0
O A:THR77 2.6 37.3 1.0
CG A:ASP80 2.8 28.6 1.0
CD A:GLU308 3.1 35.8 1.0
CG A:ASP78 3.2 41.9 1.0
OE1 A:GLU308 3.6 38.0 1.0
C A:THR77 3.7 41.2 1.0
OD2 A:ASP78 3.8 47.5 1.0
CA A:ASP78 4.2 37.0 1.0
CG A:GLU308 4.2 36.6 1.0
OG1 A:THR23 4.3 30.2 1.0
CB A:ASP78 4.3 36.9 1.0
CB A:ASP80 4.3 28.2 1.0
N A:ASP78 4.3 41.6 1.0
OG A:SER304 4.5 35.1 1.0
OG1 A:THR77 4.5 46.6 1.0
O A:LYS21 4.6 41.5 1.0
O A:HOH675 4.7 43.3 1.0
CB A:THR77 4.7 43.9 1.0
N A:ASP80 4.7 29.6 1.0
N A:THR23 4.8 31.5 1.0
CA A:THR77 4.8 42.6 1.0
CB A:GLU308 4.8 36.4 1.0
CA A:ILE22 4.9 33.7 1.0
CA A:ASP80 4.9 30.5 1.0

Magnesium binding site 2 out of 4 in 6dtq

Go back to Magnesium Binding Sites List in 6dtq
Magnesium binding site 2 out of 4 in the Maltose Bound T. Maritima MALE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Maltose Bound T. Maritima MALE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:17.2
occ:1.00
 OD1 B:ASP78 2.1 30.0 1.0
OE2 B:GLU308 2.2 30.7 1.0
O B:HOH656 2.2 32.2 1.0
O B:HOH686 2.4 29.6 1.0
OD1 B:ASP80 2.4 28.5 1.0
O B:THR77 2.5 32.8 1.0
OD2 B:ASP80 2.5 28.3 1.0
CG B:ASP80 2.8 28.5 1.0
CG B:ASP78 3.2 29.9 1.0
CD B:GLU308 3.2 30.2 1.0
C B:THR77 3.6 31.0 1.0
OE1 B:GLU308 3.7 31.2 1.0
OD2 B:ASP78 3.8 35.4 1.0
CA B:ASP78 4.2 29.4 1.0
OG1 B:THR23 4.3 23.4 1.0
CG B:GLU308 4.3 29.0 1.0
CB B:ASP78 4.3 27.1 1.0
N B:ASP78 4.3 33.5 1.0
CB B:ASP80 4.3 23.6 1.0
OG1 B:THR77 4.3 32.4 1.0
CB B:THR77 4.5 36.0 1.0
O B:HOH658 4.5 35.1 1.0
CA B:THR77 4.7 35.5 1.0
OG B:SER304 4.7 29.0 1.0
N B:ASP80 4.7 23.9 1.0
O B:LYS21 4.7 29.3 1.0
N B:THR23 4.8 22.9 1.0
CA B:ASP80 4.9 24.3 1.0
CA B:ILE22 5.0 27.4 1.0

Magnesium binding site 3 out of 4 in 6dtq

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Magnesium binding site 3 out of 4 in the Maltose Bound T. Maritima MALE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Maltose Bound T. Maritima MALE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:24.5
occ:1.00
 OD1 C:ASP78 2.0 39.0 1.0
O C:HOH619 2.3 32.9 1.0
OD1 C:ASP80 2.4 32.6 1.0
OE2 C:GLU308 2.4 41.2 1.0
O C:HOH644 2.4 29.3 1.0
OD2 C:ASP80 2.5 28.8 1.0
O C:THR77 2.6 35.6 1.0
CG C:ASP80 2.8 28.4 1.0
CD C:GLU308 3.1 34.9 1.0
CG C:ASP78 3.1 36.9 1.0
OE1 C:GLU308 3.5 39.0 1.0
C C:THR77 3.7 36.8 1.0
OD2 C:ASP78 3.8 40.8 1.0
O C:HOH680 4.1 45.9 1.0
CG C:GLU308 4.2 32.4 1.0
CA C:ASP78 4.2 34.3 1.0
CB C:ASP78 4.3 34.8 1.0
CB C:ASP80 4.3 28.2 1.0
N C:ASP78 4.3 34.7 1.0
O C:HOH612 4.3 39.5 1.0
OG1 C:THR23 4.3 28.2 1.0
OG1 C:THR77 4.5 35.0 1.0
OG C:SER304 4.5 36.6 1.0
O C:LYS21 4.5 38.2 1.0
CB C:THR77 4.6 36.4 1.0
N C:ASP80 4.8 24.9 1.0
CB C:GLU308 4.8 32.4 1.0
CA C:THR77 4.8 39.6 1.0
N C:THR23 4.9 26.7 1.0
CA C:ILE22 4.9 31.1 1.0
CA C:ASP80 5.0 27.6 1.0

Magnesium binding site 4 out of 4 in 6dtq

Go back to Magnesium Binding Sites List in 6dtq
Magnesium binding site 4 out of 4 in the Maltose Bound T. Maritima MALE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Maltose Bound T. Maritima MALE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:20.5
occ:1.00
 OD1 D:ASP78 2.1 35.2 1.0
OE2 D:GLU308 2.1 33.7 1.0
O D:HOH670 2.3 31.8 1.0
O D:HOH631 2.4 32.4 1.0
OD1 D:ASP80 2.5 34.6 1.0
OD2 D:ASP80 2.6 30.6 1.0
O D:THR77 2.6 36.1 1.0
CG D:ASP80 2.8 31.5 1.0
CG D:ASP78 3.1 36.0 1.0
CD D:GLU308 3.1 34.5 1.0
C D:THR77 3.7 37.8 1.0
OD2 D:ASP78 3.7 39.2 1.0
OE1 D:GLU308 3.7 34.4 1.0
CG D:GLU308 4.2 33.0 1.0
CA D:ASP78 4.2 34.5 1.0
CB D:ASP78 4.2 33.3 1.0
OG1 D:THR77 4.3 35.9 1.0
N D:ASP78 4.3 37.7 1.0
CB D:ASP80 4.3 28.6 1.0
OG1 D:THR23 4.4 29.5 1.0
O D:HOH650 4.4 34.8 1.0
CB D:THR77 4.5 37.1 1.0
OG D:SER304 4.6 33.5 1.0
CA D:THR77 4.7 39.4 1.0
N D:ASP80 4.7 27.6 1.0
O D:LYS21 4.7 30.0 1.0
N D:THR23 4.9 25.9 1.0
CA D:ILE22 4.9 30.9 1.0
CA D:ASP80 5.0 25.4 1.0
CB D:GLU308 5.0 32.6 1.0

Reference:

S.Shukla, K.Bafna, C.Gullett, D.A.A.Myles, P.K.Agarwal, M.J.Cuneo. Differential Substrate Recognition By Maltose Binding Proteins Influenced By Structure and Dynamics. Biochemistry V. 57 5864 2018.
ISSN: ISSN 1520-4995
PubMed: 30204415
DOI: 10.1021/ACS.BIOCHEM.8B00783
Page generated: Mon Dec 14 22:36:58 2020

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