Atomistry » Magnesium » PDB 5gg8-5gr6 » 5ggd
Atomistry »
  Magnesium »
    PDB 5gg8-5gr6 »
      5ggd »

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

Go back to Magnesium Binding Sites List in 5ggd
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

Go back to Magnesium Binding Sites List in 5ggd
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

Go back to Magnesium Binding Sites List in 5ggd
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

Go back to Magnesium Binding Sites List in 5ggd
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

Go back to Magnesium Binding Sites List in 5ggd
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

Go back to Magnesium Binding Sites List in 5ggd
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: Sun Sep 29 15:17:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy