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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

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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: Tue Aug 12 14:06:00 2025

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