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Magnesium in PDB 5ggd: Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II), PDB code: 5ggd was solved by S.M.Arif, A.G.Patil, U.Varshney, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.57 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.950, 87.600, 90.530, 90.00, 100.06, 90.00
R / Rfree (%) 21.6 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) (pdb code 5ggd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II), PDB code: 5ggd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5ggd

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Magnesium binding site 1 out of 6 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)


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 Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:28.2
occ:1.00
 O1 A:PO4401 1.9 31.9 1.0
O A:HOH591 1.9 33.7 1.0
OE2 A:GLU85 2.0 23.9 1.0
O A:LYS65 2.1 22.7 1.0
OE2 A:GLU127 2.2 28.5 1.0
O A:HOH547 2.2 26.0 1.0
MG A:MG403 2.9 29.9 1.0
CD A:GLU85 3.0 24.1 1.0
CD A:GLU127 3.0 37.1 1.0
OE1 A:GLU127 3.2 31.0 1.0
C A:LYS65 3.3 24.5 1.0
P A:PO4401 3.4 34.4 1.0
OE1 A:GLU85 3.4 26.3 1.0
OE1 A:GLU81 3.8 29.4 1.0
CA A:GLY66 3.9 24.1 1.0
O3 A:PO4401 4.0 33.2 1.0
O A:HOH548 4.0 44.9 1.0
N A:GLY66 4.1 23.5 1.0
O2 A:PO4401 4.1 30.2 1.0
CG A:GLU85 4.3 21.4 1.0
N A:LYS65 4.3 21.4 1.0
O4 A:PO4401 4.4 26.8 1.0
CA A:LYS65 4.4 24.7 1.0
CG A:GLU127 4.4 38.3 1.0
CG A:LYS65 4.6 25.6 1.0
NH2 A:ARG55 4.6 36.4 1.0
O A:HOH724 4.7 20.1 1.0
CD A:GLU81 4.7 27.9 1.0
O A:HOH572 4.7 26.2 1.0
O A:HOH584 4.8 30.4 1.0

Magnesium binding site 2 out of 6 in 5ggd

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Magnesium binding site 2 out of 6 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)


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 Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:29.9
occ:1.00
 O2 A:PO4401 2.0 30.2 1.0
OE1 A:GLU127 2.0 31.0 1.0
O A:HOH584 2.0 30.4 1.0
OE1 A:GLU81 2.1 29.4 1.0
O1 A:PO4401 2.2 31.9 1.0
OE2 A:GLU85 2.3 23.9 1.0
P A:PO4401 2.6 34.4 1.0
MG A:MG402 2.9 28.2 1.0
CD A:GLU127 3.0 37.1 1.0
CD A:GLU81 3.1 27.9 1.0
CD A:GLU85 3.3 24.1 1.0
OE2 A:GLU127 3.4 28.5 1.0
OE2 A:GLU81 3.4 25.8 1.0
CG A:GLU85 3.6 21.4 1.0
MG A:MG404 3.6 36.9 1.0
O3 A:PO4401 3.7 33.2 1.0
O4 A:PO4401 3.7 26.8 1.0
OE2 A:GLU84 4.1 32.3 1.0
O A:LYS65 4.1 22.7 1.0
O A:HOH502 4.2 35.5 1.0
O A:HOH654 4.4 35.3 1.0
CG A:GLU127 4.4 38.3 1.0
CG A:GLU81 4.4 25.5 1.0
OE1 A:GLU85 4.4 26.3 1.0
O A:HOH591 4.5 33.7 1.0
CA A:GLY66 4.6 24.1 1.0
O A:HOH547 4.8 26.0 1.0
CB A:GLU81 4.8 27.4 1.0
CB A:GLU127 4.8 35.9 1.0
C A:LYS65 4.9 24.5 1.0

Magnesium binding site 3 out of 6 in 5ggd

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Magnesium binding site 3 out of 6 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)


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 Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:36.9
occ:1.00
 O A:HOH601 1.9 27.1 1.0
OE2 A:GLU81 2.0 25.8 1.0
O2 A:PO4401 2.2 30.2 1.0
O4 A:PO4401 2.2 26.8 1.0
O A:HOH699 2.3 27.5 1.0
O A:HOH502 2.4 35.5 1.0
P A:PO4401 2.6 34.4 1.0
CD A:GLU81 3.1 27.9 1.0
OE1 A:GLU81 3.5 29.4 1.0
MG A:MG403 3.6 29.9 1.0
O3 A:PO4401 3.7 33.2 1.0
O1 A:PO4401 3.8 31.9 1.0
NH1 A:ARG80 3.9 29.2 1.0
N A:LYS67 4.1 25.3 1.0
OE2 A:GLU84 4.1 32.3 1.0
O A:LYS67 4.2 28.2 1.0
O A:HOH584 4.4 30.4 1.0
CG A:GLU81 4.4 25.5 1.0
NZ A:LYS67 4.5 37.4 1.0
CA A:GLY66 4.6 24.1 1.0
NH2 A:ARG80 4.6 28.6 1.0
CZ A:ARG80 4.7 27.4 1.0
CB A:LYS67 4.8 32.0 1.0
CA A:LYS67 4.8 31.3 1.0
C A:GLY66 4.8 29.1 1.0
OD1 A:ASP69 4.9 49.7 1.0
C A:LYS67 4.9 26.9 1.0

Magnesium binding site 4 out of 6 in 5ggd

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Magnesium binding site 4 out of 6 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)


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 Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:28.0
occ:1.00
 O B:HOH548 1.8 32.5 1.0
O1 B:PO4401 1.9 26.9 1.0
OE2 B:GLU127 2.1 34.3 1.0
OE2 B:GLU85 2.1 21.4 1.0
O B:LYS65 2.1 22.8 1.0
O B:HOH510 2.3 26.3 1.0
MG B:MG403 3.0 32.6 1.0
CD B:GLU127 3.0 42.7 1.0
CD B:GLU85 3.2 24.7 1.0
C B:LYS65 3.3 23.9 1.0
P B:PO4401 3.3 34.9 1.0
OE1 B:GLU127 3.3 33.1 1.0
OE1 B:GLU85 3.5 26.0 1.0
O3 B:PO4401 3.8 29.7 1.0
CA B:GLY66 4.0 27.7 1.0
N B:GLY66 4.1 23.3 1.0
O2 B:PO4401 4.1 27.0 1.0
OE1 B:GLU81 4.2 20.2 1.0
N B:LYS65 4.2 21.7 1.0
O4 B:PO4401 4.3 27.5 1.0
NH2 B:ARG55 4.4 33.4 1.0
CA B:LYS65 4.4 24.8 1.0
CG B:GLU85 4.5 22.7 1.0
CG B:GLU127 4.5 42.3 1.0
CG B:LYS65 4.5 29.5 1.0
O B:HOH711 4.5 18.8 1.0
O B:HOH571 4.6 24.4 1.0
CD B:ARG55 4.8 30.6 1.0
CD B:GLU81 4.9 24.3 1.0

Magnesium binding site 5 out of 6 in 5ggd

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Magnesium binding site 5 out of 6 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)


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 Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:32.6
occ:1.00
 O2 B:PO4401 1.9 27.0 1.0
O1 B:PO4401 1.9 26.9 1.0
OE1 B:GLU81 2.1 20.2 1.0
O B:HOH535 2.1 25.7 1.0
OE1 B:GLU127 2.1 33.1 1.0
OE2 B:GLU85 2.2 21.4 1.0
P B:PO4401 2.5 34.9 1.0
MG B:MG402 3.0 28.0 1.0
CD B:GLU81 3.1 24.3 1.0
CD B:GLU127 3.1 42.7 1.0
CD B:GLU85 3.1 24.7 1.0
OE2 B:GLU127 3.4 34.3 1.0
CG B:GLU85 3.4 22.7 1.0
OE2 B:GLU81 3.5 25.9 1.0
O4 B:PO4401 3.6 27.5 1.0
MG B:MG404 3.6 33.8 1.0
O3 B:PO4401 3.6 29.7 1.0
OE2 B:GLU84 4.0 29.0 1.0
O B:LYS65 4.1 22.8 1.0
OE1 B:GLU85 4.2 26.0 1.0
CG B:GLU81 4.3 24.9 1.0
CG B:GLU127 4.4 42.3 1.0
O B:HOH587 4.6 25.7 1.0
O B:HOH510 4.6 26.3 1.0
CA B:GLY66 4.6 27.7 1.0
CB B:GLU81 4.7 22.7 1.0
O B:HOH548 4.7 32.5 1.0
C B:LYS65 4.8 23.9 1.0
CB B:GLU127 4.8 38.6 1.0
CB B:GLU85 4.9 21.9 1.0

Magnesium binding site 6 out of 6 in 5ggd

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Magnesium binding site 6 out of 6 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II)


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 Mycobacterium Smegmatis MUTT1 in Complex with Phosphate and Magnesium Ions (Excess Magnesium, II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:33.8
occ:1.00
 O B:HOH587 2.0 25.7 1.0
OE2 B:GLU81 2.0 25.9 1.0
O B:HOH546 2.1 27.0 1.0
O2 B:PO4401 2.2 27.0 1.0
O4 B:PO4401 2.2 27.5 1.0
O B:HOH699 2.3 25.8 1.0
P B:PO4401 2.7 34.9 1.0
CD B:GLU81 3.1 24.3 1.0
OE1 B:GLU81 3.5 20.2 1.0
MG B:MG403 3.6 32.6 1.0
OE2 B:GLU84 3.7 29.0 1.0
O3 B:PO4401 3.7 29.7 1.0
O1 B:PO4401 3.7 26.9 1.0
NH1 B:ARG80 4.0 26.9 1.0
NZ B:LYS67 4.1 44.7 1.0
O B:HOH535 4.1 25.7 1.0
O B:LYS67 4.3 29.8 1.0
N B:LYS67 4.3 30.5 1.0
O B:HOH664 4.4 40.0 1.0
CG B:GLU81 4.4 24.9 1.0
NH2 B:ARG80 4.8 27.5 1.0
OD1 B:ASP69 4.8 44.8 1.0
CA B:GLY66 4.8 27.7 1.0
CD B:GLU84 4.8 26.5 1.0
CZ B:ARG80 4.9 25.7 1.0
OE1 B:GLU127 4.9 33.1 1.0
OD2 B:ASP69 4.9 45.1 1.0
C B:GLY66 5.0 28.5 1.0

Reference:

S.M.Arif, A.G.Patil, U.Varshney, M.Vijayan. Biochemical and Structural Studies of Mycobacterium Smegmatis MUTT1, A Sanitization Enzyme with Unusual Modes of Association Acta Crystallogr D Struct V. 73 349 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28375146
DOI: 10.1107/S2059798317002534
Page generated: Mon Dec 14 20:23:19 2020

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