Atomistry » Magnesium » PDB 5lcf-5lmm » 5llb
Atomistry »
  Magnesium »
    PDB 5lcf-5lmm »
      5llb »

Magnesium in PDB 5llb: Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate

Enzymatic activity of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate

All present enzymatic activity of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate:
2.7.4.1;

Protein crystallography data

The structure of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate, PDB code: 5llb was solved by P.L.Roach, A.E.Parnell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.46 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.700, 144.910, 70.590, 90.00, 113.04, 90.00
R / Rfree (%) 17.9 / 23.1

Other elements in 5llb:

The structure of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate (pdb code 5llb). 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 Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate, PDB code: 5llb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5llb

Go back to Magnesium Binding Sites List in 5llb
Magnesium binding site 1 out of 4 in the Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:62.1
occ:1.00
 O01 A:6YZ303 2.3 61.2 1.0
O38 A:6YZ303 2.5 64.6 1.0
O16 A:6YZ303 2.5 73.6 1.0
OD1 A:ASP192 2.6 79.3 1.0
OD2 A:ASP62 2.8 63.6 1.0
O A:HOH401 3.0 64.0 1.0
HB3 A:ASP62 3.4 71.4 1.0
HH21 A:ARG118 3.4 71.2 1.0
O13 A:6YZ303 3.4 73.5 1.0
P02 A:6YZ303 3.6 68.1 1.0
P09 A:6YZ303 3.6 64.5 1.0
CG A:ASP192 3.7 82.4 1.0
CG A:ASP62 3.8 63.8 1.0
O08 A:6YZ303 3.8 77.8 1.0
HG A:SER189 3.9 87.8 1.0
P15 A:6YZ303 3.9 68.4 1.0
OD2 A:ASP192 4.0 93.2 1.0
CB A:ASP62 4.0 59.5 1.0
NH2 A:ARG118 4.1 59.3 1.0
H182 A:6YZ303 4.1 82.0 1.0
HA A:ASP62 4.2 74.7 1.0
OG A:SER189 4.2 73.2 1.0
O39 A:6YZ303 4.3 73.7 1.0
P12 A:6YZ303 4.3 71.4 1.0
HH22 A:ARG118 4.4 71.2 1.0
O14 A:6YZ303 4.4 73.9 1.0
HG22 A:ILE191 4.4 84.9 1.0
H181 A:6YZ303 4.4 82.0 1.0
HH12 A:ARG178 4.4 84.0 1.0
HB A:ILE191 4.5 88.7 1.0
C18 A:6YZ303 4.6 68.3 1.0
C11 A:6YZ303 4.6 66.6 1.0
HG21 A:ILE191 4.6 84.9 1.0
H A:ASP192 4.7 0.3 1.0
HE A:ARG118 4.7 70.5 1.0
O03 A:6YZ303 4.7 50.5 1.0
CA A:ASP62 4.7 62.2 1.0
O17 A:6YZ303 4.7 68.1 1.0
H A:ALA63 4.7 70.1 1.0
HA A:ASP192 4.8 99.7 1.0
HB2 A:ASP62 4.8 71.4 1.0
CG2 A:ILE191 4.9 70.7 1.0
O10 A:6YZ303 4.9 63.8 1.0
OD1 A:ASP62 4.9 67.9 1.0
O36 A:6YZ303 4.9 68.2 1.0
N A:ASP192 5.0 84.4 1.0
CB A:ASP192 5.0 78.5 1.0

Magnesium binding site 2 out of 4 in 5llb

Go back to Magnesium Binding Sites List in 5llb
Magnesium binding site 2 out of 4 in the Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:74.0
occ:1.00
 O01 B:6YZ303 2.0 73.8 1.0
O38 B:6YZ303 2.5 90.5 1.0
OD1 B:ASP192 2.7 90.9 1.0
O16 B:6YZ303 2.7 0.4 1.0
OD1 B:ASP62 3.1 64.4 1.0
OD2 B:ASP192 3.2 0.0 1.0
P02 B:6YZ303 3.2 84.8 1.0
HH21 B:ARG118 3.3 79.2 1.0
CG B:ASP192 3.3 97.2 1.0
HB3 B:ASP62 3.5 68.4 1.0
P09 B:6YZ303 3.5 84.3 1.0
O39 B:6YZ303 3.5 68.7 1.0
O13 B:6YZ303 3.6 0.4 1.0
HH12 B:ARG178 3.6 73.7 1.0
O08 B:6YZ303 3.7 99.1 1.0
CG B:ASP62 3.9 62.6 1.0
HG B:SER189 3.9 0.7 1.0
NH2 B:ARG118 3.9 66.0 1.0
P15 B:6YZ303 4.0 87.3 1.0
CB B:ASP62 4.1 57.0 1.0
HA B:ASP62 4.1 62.2 1.0
HH22 B:ARG118 4.2 79.2 1.0
P12 B:6YZ303 4.3 85.7 1.0
OG B:SER189 4.3 83.9 1.0
H182 B:6YZ303 4.3 78.7 1.0
O14 B:6YZ303 4.3 0.1 1.0
NH1 B:ARG178 4.3 61.5 1.0
C11 B:6YZ303 4.3 0.1 1.0
HH11 B:ARG178 4.3 73.7 1.0
O03 B:6YZ303 4.3 53.9 1.0
HG22 B:ILE191 4.4 0.4 1.0
H181 B:6YZ303 4.4 78.7 1.0
HE B:ARG118 4.5 69.1 1.0
H111 B:6YZ303 4.5 0.1 1.0
H B:ALA63 4.5 63.7 1.0
CA B:ASP62 4.7 51.9 1.0
C18 B:6YZ303 4.7 65.6 1.0
CB B:ASP192 4.8 89.5 1.0
HG21 B:ILE191 4.9 0.4 1.0
O17 B:6YZ303 4.9 68.7 1.0
CZ B:ARG118 4.9 59.2 1.0
O10 B:6YZ303 4.9 68.7 1.0
OD2 B:ASP62 4.9 67.0 1.0
H B:ASP192 4.9 0.4 1.0
HB2 B:ASP62 5.0 68.4 1.0

Magnesium binding site 3 out of 4 in 5llb

Go back to Magnesium Binding Sites List in 5llb
Magnesium binding site 3 out of 4 in the Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.0
occ:1.00
 OD1 C:ASP192 2.1 52.7 1.0
O38 C:6YZ303 2.1 51.9 1.0
OD1 C:ASP62 2.3 46.4 1.0
O01 C:6YZ303 2.3 48.1 1.0
O C:HOH410 2.4 52.1 1.0
O16 C:6YZ303 2.4 53.9 1.0
CG C:ASP192 3.1 56.1 1.0
CG C:ASP62 3.3 46.8 1.0
HB3 C:ASP62 3.3 56.1 1.0
HG C:SER189 3.4 60.0 1.0
P09 C:6YZ303 3.5 52.2 1.0
OD2 C:ASP192 3.5 52.5 1.0
P02 C:6YZ303 3.5 53.7 1.0
O13 C:6YZ303 3.5 60.4 1.0
HH21 C:ARG118 3.6 60.5 1.0
P15 C:6YZ303 3.7 52.9 1.0
HA C:ASP62 3.7 58.3 1.0
CB C:ASP62 3.7 46.8 1.0
O08 C:6YZ303 3.7 56.2 1.0
OG C:SER189 3.8 50.0 1.0
H182 C:6YZ303 3.9 59.8 1.0
HG22 C:ILE191 4.0 64.8 1.0
O14 C:6YZ303 4.1 58.9 1.0
NH2 C:ARG118 4.2 50.4 1.0
H181 C:6YZ303 4.2 59.8 1.0
P12 C:6YZ303 4.2 59.6 1.0
CA C:ASP62 4.3 48.6 1.0
OD2 C:ASP62 4.3 46.5 1.0
H C:ASP192 4.3 60.4 1.0
HH22 C:ARG118 4.4 60.5 1.0
C18 C:6YZ303 4.4 49.8 1.0
O39 C:6YZ303 4.4 56.2 1.0
HA C:ASP192 4.4 63.5 1.0
H C:ALA63 4.5 54.7 1.0
CB C:ASP192 4.5 57.9 1.0
C11 C:6YZ303 4.5 53.5 1.0
O17 C:6YZ303 4.6 46.9 1.0
O03 C:6YZ303 4.6 53.2 1.0
HB2 C:ASP62 4.6 56.1 1.0
HH12 C:ARG178 4.6 63.6 1.0
O10 C:6YZ303 4.6 52.6 1.0
N C:ASP192 4.6 50.3 1.0
HB3 C:SER189 4.7 68.5 1.0
HE C:ARG118 4.7 54.9 1.0
CA C:ASP192 4.8 52.9 1.0
HG21 C:ILE191 4.8 64.8 1.0
CG2 C:ILE191 4.8 54.0 1.0
O36 C:6YZ303 4.8 50.9 1.0
CB C:SER189 4.9 57.1 1.0
HB C:ILE191 5.0 60.4 1.0
H C:SER189 5.0 70.2 1.0

Magnesium binding site 4 out of 4 in 5llb

Go back to Magnesium Binding Sites List in 5llb
Magnesium binding site 4 out of 4 in the Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:58.4
occ:1.00
 OD1 D:ASP192 2.1 75.5 1.0
O01 D:6YZ303 2.2 68.7 1.0
OD1 D:ASP62 2.3 66.6 1.0
O16 D:6YZ303 2.3 66.5 1.0
O38 D:6YZ303 2.4 65.6 1.0
O D:HOH405 3.0 68.9 1.0
CG D:ASP192 3.0 80.3 1.0
HB3 D:ASP62 3.1 83.3 1.0
CG D:ASP62 3.2 74.2 1.0
O13 D:6YZ303 3.3 68.3 1.0
HG D:SER189 3.3 89.5 1.0
HH21 D:ARG118 3.3 77.4 1.0
OD2 D:ASP192 3.3 75.5 1.0
P02 D:6YZ303 3.5 62.4 1.0
P09 D:6YZ303 3.6 63.0 1.0
CB D:ASP62 3.6 69.5 1.0
OG D:SER189 3.7 74.6 1.0
P15 D:6YZ303 3.8 66.9 1.0
O08 D:6YZ303 3.8 69.0 1.0
HA D:ASP62 3.9 83.6 1.0
HG22 D:ILE191 3.9 79.9 1.0
NH2 D:ARG118 4.0 64.5 1.0
H182 D:6YZ303 4.0 75.2 1.0
HH12 D:ARG178 4.1 81.7 1.0
HH22 D:ARG118 4.1 77.4 1.0
H D:ASP192 4.1 97.8 1.0
HA D:ASP192 4.2 98.7 1.0
P12 D:6YZ303 4.3 71.5 1.0
OD2 D:ASP62 4.3 67.6 1.0
CB D:ASP192 4.3 83.9 1.0
H181 D:6YZ303 4.3 75.2 1.0
CA D:ASP62 4.3 69.7 1.0
O14 D:6YZ303 4.3 71.2 1.0
O39 D:6YZ303 4.4 67.8 1.0
HB2 D:ASP62 4.4 83.3 1.0
N D:ASP192 4.5 81.5 1.0
C18 D:6YZ303 4.5 62.7 1.0
O03 D:6YZ303 4.6 59.6 1.0
CA D:ASP192 4.6 82.2 1.0
C11 D:6YZ303 4.6 59.5 1.0
O17 D:6YZ303 4.7 60.2 1.0
HG21 D:ILE191 4.7 79.9 1.0
O36 D:6YZ303 4.7 58.5 1.0
CG2 D:ILE191 4.7 66.6 1.0
O10 D:6YZ303 4.7 67.0 1.0
H D:ALA63 4.8 73.2 1.0
HB2 D:ASP192 4.8 0.7 1.0
HB D:ILE191 4.8 79.3 1.0
HE D:ARG118 4.8 64.2 1.0
NH1 D:ARG178 4.9 68.1 1.0
HB3 D:ASP192 4.9 0.7 1.0
HB3 D:SER189 4.9 90.1 1.0
CB D:SER189 4.9 75.1 1.0
HH11 D:ARG178 5.0 81.7 1.0

Reference:

A.E.Parnell, S.Mordhorst, F.Kemper, M.Giurrandino, J.P.Prince, N.J.Schwarzer, A.Hofer, D.Wohlwend, H.J.Jessen, S.Gerhardt, O.Einsle, P.C.F.Oyston, J.N.Andexer, P.L.Roach. Substrate Recognition and Mechanism Revealed By Ligand-Bound Polyphosphate Kinase 2 Structures. Proc. Natl. Acad. Sci. V. 115 3350 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29531036
DOI: 10.1073/PNAS.1710741115
Page generated: Sun Sep 29 20:15:58 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