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Chlorine 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:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Polyphosphate Kinase 2 From Francisella Tularensis with AMPPCH2PPP and Polyphosphate, PDB code: 5llb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5llb

Go back to Chlorine Binding Sites List in 5llb
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:57.2
occ:1.00
 HE A:ARG61 2.4 60.8 1.0
HG A:SER165 2.4 63.4 1.0
HE1 A:TRP163 2.5 55.9 1.0
HH11 A:ARG61 2.8 56.1 1.0
HZ3 A:LYS206 3.0 72.0 1.0
NE A:ARG61 3.2 50.7 1.0
HA A:SER165 3.2 61.6 1.0
OG A:SER165 3.2 52.9 1.0
NE1 A:TRP163 3.3 46.6 1.0
HD3 A:LYS206 3.4 62.6 1.0
NH1 A:ARG61 3.6 46.8 1.0
HB2 A:SER165 3.6 57.1 1.0
HZ2 A:TRP163 3.7 55.3 1.0
NZ A:LYS206 3.7 60.0 1.0
HZ2 A:LYS206 3.8 72.0 1.0
O A:HOH438 3.8 51.5 1.0
CB A:SER165 3.8 47.6 1.0
CZ A:ARG61 3.8 52.0 1.0
CA A:SER165 3.9 51.3 1.0
H A:VAL166 3.9 54.5 1.0
HD2 A:LYS206 4.0 62.6 1.0
CD A:LYS206 4.1 52.2 1.0
HD2 A:ARG61 4.1 58.6 1.0
CE2 A:TRP163 4.2 48.6 1.0
CD A:ARG61 4.2 48.9 1.0
O A:VAL166 4.3 49.6 1.0
HG3 A:ARG61 4.3 62.4 1.0
CZ2 A:TRP163 4.3 46.1 1.0
HH12 A:ARG61 4.3 56.1 1.0
HZ1 A:LYS206 4.4 72.0 1.0
CD1 A:TRP163 4.4 44.5 1.0
N A:VAL166 4.4 45.4 1.0
CE A:LYS206 4.5 53.9 1.0
HD1 A:TRP163 4.5 53.4 1.0
C A:SER165 4.6 46.9 1.0
HB3 A:SER165 4.7 57.1 1.0
HE2 A:LYS206 4.7 64.6 1.0
HH2 A:TRP199 4.8 62.4 1.0
CG A:ARG61 4.8 52.0 1.0
HZ2 A:TRP199 4.9 62.4 1.0

Chlorine binding site 2 out of 4 in 5llb

Go back to Chlorine Binding Sites List in 5llb
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:62.8
occ:1.00
 HE B:ARG61 2.3 59.0 1.0
HG B:SER165 2.5 67.1 1.0
HE1 B:TRP163 2.5 55.2 1.0
HH11 B:ARG61 2.8 54.3 1.0
HZ3 B:LYS206 2.9 0.8 1.0
NE B:ARG61 3.1 49.1 1.0
OG B:SER165 3.2 55.9 1.0
HB2 B:SER165 3.3 61.1 1.0
NE1 B:TRP163 3.4 46.0 1.0
HD3 B:LYS206 3.4 73.3 1.0
HZ2 B:LYS206 3.4 0.8 1.0
HA B:SER165 3.5 58.8 1.0
NH1 B:ARG61 3.5 45.3 1.0
NZ B:LYS206 3.6 97.4 1.0
HG3 B:ARG61 3.6 69.1 1.0
CB B:SER165 3.7 50.9 1.0
CZ B:ARG61 3.8 50.5 1.0
HD2 B:LYS206 3.8 73.3 1.0
HZ2 B:TRP163 3.9 58.6 1.0
HG2 B:ARG61 3.9 69.1 1.0
CD B:LYS206 4.0 61.1 1.0
H B:VAL166 4.1 56.3 1.0
CG B:ARG61 4.1 57.6 1.0
CA B:SER165 4.1 49.0 1.0
CD B:ARG61 4.2 55.5 1.0
HZ1 B:LYS206 4.2 0.8 1.0
HH12 B:ARG61 4.3 54.3 1.0
CE2 B:TRP163 4.3 50.0 1.0
CE B:LYS206 4.3 77.1 1.0
CD1 B:TRP163 4.4 46.3 1.0
O B:VAL166 4.4 48.3 1.0
HD1 B:TRP163 4.4 55.6 1.0
CZ2 B:TRP163 4.5 48.8 1.0
HB3 B:SER165 4.6 61.1 1.0
HD2 B:ARG61 4.6 66.6 1.0
N B:VAL166 4.6 46.9 1.0
HH2 B:TRP199 4.7 56.6 1.0
HE2 B:LYS206 4.8 92.5 1.0
HZ2 B:TRP199 4.8 59.5 1.0
HD3 B:ARG61 4.9 66.6 1.0
C B:SER165 4.9 48.5 1.0

Chlorine binding site 3 out of 4 in 5llb

Go back to Chlorine Binding Sites List in 5llb
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:50.2
occ:1.00
 HE C:ARG61 2.3 56.0 1.0
HE1 C:TRP163 2.4 52.3 1.0
HZ2 C:LYS206 2.4 66.7 1.0
HA C:SER165 2.8 52.2 1.0
HB2 C:SER165 3.0 57.2 1.0
O C:HOH451 3.2 40.2 1.0
NE C:ARG61 3.2 46.6 1.0
NE1 C:TRP163 3.2 43.6 1.0
NZ C:LYS206 3.3 55.6 1.0
HB3 C:SER165 3.3 57.2 1.0
H C:VAL166 3.3 56.5 1.0
CB C:SER165 3.4 47.7 1.0
O C:HOH491 3.4 52.6 1.0
HZ1 C:LYS206 3.5 66.7 1.0
HH11 C:ARG61 3.5 54.8 1.0
O C:HOH501 3.5 58.2 1.0
CA C:SER165 3.5 43.5 1.0
HZ2 C:TRP163 3.6 51.3 1.0
HE3 C:LYS206 3.6 69.2 1.0
HD2 C:LYS206 3.6 57.9 1.0
HD2 C:ARG61 3.6 53.0 1.0
HG3 C:ARG61 3.7 57.3 1.0
O C:VAL166 3.9 47.1 1.0
CE C:LYS206 3.9 57.7 1.0
CD C:ARG61 3.9 44.1 1.0
HZ3 C:LYS206 3.9 66.7 1.0
N C:VAL166 3.9 47.0 1.0
CE2 C:TRP163 4.0 44.1 1.0
NH1 C:ARG61 4.1 45.7 1.0
CZ C:ARG61 4.1 42.5 1.0
CZ2 C:TRP163 4.2 42.8 1.0
C C:SER165 4.2 42.0 1.0
CD1 C:TRP163 4.3 45.2 1.0
CD C:LYS206 4.3 48.3 1.0
CG C:ARG61 4.3 47.8 1.0
HD1 C:TRP163 4.4 54.3 1.0
N C:SER165 4.7 40.4 1.0
O C:PHE164 4.7 39.8 1.0
HH2 C:TRP199 4.7 56.8 1.0
OG C:SER165 4.8 53.4 1.0
HD3 C:ARG61 4.8 53.0 1.0
HE2 C:LYS206 4.8 69.2 1.0
C C:VAL166 4.8 51.0 1.0
H C:ARG61 4.8 52.6 1.0
HG22 C:VAL166 4.8 54.9 1.0
HG23 C:VAL166 4.9 54.9 1.0
HG3 C:LYS206 4.9 58.2 1.0
HH12 C:ARG61 4.9 54.8 1.0
HD3 C:LYS206 4.9 57.9 1.0
HG2 C:ARG61 4.9 57.3 1.0
O C:HOH494 5.0 55.2 1.0
CA C:VAL166 5.0 52.0 1.0
HG C:SER165 5.0 64.1 1.0

Chlorine binding site 4 out of 4 in 5llb

Go back to Chlorine Binding Sites List in 5llb
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:72.7
occ:1.00
 HE1 D:TRP163 2.4 59.4 1.0
HE D:ARG61 2.4 83.6 1.0
HG D:SER165 2.7 79.0 1.0
HD3 D:LYS206 3.0 76.4 1.0
HE2 D:LYS206 3.0 88.9 1.0
HA D:SER165 3.1 66.2 1.0
NE1 D:TRP163 3.2 49.5 1.0
HH11 D:ARG61 3.2 71.3 1.0
NE D:ARG61 3.3 69.7 1.0
OG D:SER165 3.5 65.8 1.0
H D:VAL166 3.5 66.7 1.0
HD2 D:LYS206 3.5 76.4 1.0
HZ2 D:TRP163 3.5 63.1 1.0
CD D:LYS206 3.6 63.6 1.0
HG3 D:ARG61 3.7 98.2 1.0
CE D:LYS206 3.7 74.1 1.0
CA D:SER165 3.9 55.1 1.0
NH1 D:ARG61 3.9 59.5 1.0
CE2 D:TRP163 4.0 47.6 1.0
HB2 D:SER165 4.0 66.4 1.0
CB D:SER165 4.1 55.3 1.0
CZ D:ARG61 4.1 60.6 1.0
O D:VAL166 4.1 65.2 1.0
CZ2 D:TRP163 4.1 52.5 1.0
HD2 D:ARG61 4.1 97.2 1.0
CD D:ARG61 4.2 81.0 1.0
N D:VAL166 4.2 55.6 1.0
CD1 D:TRP163 4.2 52.3 1.0
HE3 D:LYS206 4.4 88.9 1.0
HD1 D:TRP163 4.4 62.8 1.0
CG D:ARG61 4.4 81.9 1.0
HZ3 D:LYS206 4.5 87.6 1.0
C D:SER165 4.6 49.9 1.0
HH2 D:TRP199 4.6 70.7 1.0
HH12 D:ARG61 4.7 71.3 1.0
NZ D:LYS206 4.7 73.0 1.0
HG2 D:ARG61 4.9 98.2 1.0
O D:PHE164 4.9 46.6 1.0
HG12 D:VAL166 4.9 75.5 1.0
HZ2 D:TRP199 4.9 67.7 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: Fri Jul 26 11:44:01 2024

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