Potassium in PDB 8jgw: Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase

Protein crystallography data

The structure of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase, PDB code: 8jgw was solved by Y.Zhao, S.Dai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.8, 97.08, 144.11, 90, 90, 90
R / Rfree (%) 18.3 / 20.7

Other elements in 8jgw:

The structure of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase (pdb code 8jgw). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase, PDB code: 8jgw:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 8jgw

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Potassium binding site 1 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:31.9
occ:1.00
 OE1 A:GLN448 2.6 27.5 1.0
O A:ALA451 2.6 29.4 1.0
O B:HOH783 2.6 29.8 1.0
OE1 B:GLN77 2.8 31.5 1.0
O B:GLU74 2.9 30.2 1.0
OG1 A:THR453 3.0 29.1 1.0
CD B:GLN77 3.3 32.7 1.0
CG B:GLU74 3.6 30.2 1.0
NE2 B:GLN77 3.6 35.7 1.0
O A:HOH809 3.7 30.5 1.0
CD A:GLN448 3.7 30.4 1.0
C A:ALA451 3.7 29.7 1.0
C B:GLU74 3.8 29.2 1.0
N A:THR453 3.9 25.3 1.0
O A:HOH789 4.0 32.1 1.0
K A:K605 4.1 35.8 1.0
CB A:THR453 4.1 30.4 1.0
CG B:GLN77 4.2 30.0 1.0
C A:THR452 4.2 31.5 1.0
NE2 A:GLN448 4.3 25.3 1.0
CA A:THR452 4.4 29.7 1.0
CA B:GLU74 4.4 29.0 1.0
CB A:ALA451 4.5 31.2 1.0
N A:THR452 4.5 29.4 1.0
OE2 B:GLU74 4.5 32.1 1.0
CB B:GLN77 4.5 35.8 1.0
CD B:GLU74 4.6 30.6 1.0
CB B:GLU74 4.6 25.8 1.0
CA A:THR453 4.6 30.6 1.0
CA A:ALA451 4.7 29.5 1.0
CB A:GLN448 4.7 29.0 1.0
OD1 A:ASN479 4.7 28.9 1.0
N B:ARG75 4.8 28.4 1.0
CG A:GLN448 4.8 30.5 1.0
O A:THR452 4.9 31.3 1.0

Potassium binding site 2 out of 8 in 8jgw

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Potassium binding site 2 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:31.3
occ:1.00
 OE1 B:GLN448 2.6 30.8 1.0
O A:HOH743 2.7 31.0 1.0
O B:ALA451 2.7 30.4 1.0
OE1 A:GLN77 2.7 36.0 1.0
O A:GLU74 2.8 29.1 1.0
OG1 B:THR453 3.1 31.9 1.0
CD A:GLN77 3.3 35.7 1.0
CG A:GLU74 3.5 31.5 1.0
CD B:GLN448 3.7 30.7 1.0
O B:HOH792 3.7 32.6 1.0
C A:GLU74 3.8 32.1 1.0
C B:ALA451 3.8 31.6 1.0
NE2 A:GLN77 3.8 35.5 1.0
N B:THR453 4.0 28.1 1.0
O B:HOH839 4.0 37.1 1.0
K B:K603 4.1 41.8 1.0
CB B:THR453 4.1 32.5 1.0
CG A:GLN77 4.3 37.1 1.0
C B:THR452 4.3 32.2 1.0
NE2 B:GLN448 4.3 28.0 1.0
CA A:GLU74 4.4 28.1 1.0
OE2 A:GLU74 4.4 35.0 1.0
CA B:THR452 4.4 30.0 1.0
CD A:GLU74 4.5 34.7 1.0
CB B:ALA451 4.5 31.2 1.0
CB A:GLU74 4.5 28.4 1.0
CB A:GLN77 4.5 32.4 1.0
N B:THR452 4.6 27.9 1.0
CA B:THR453 4.7 32.7 1.0
CB B:GLN448 4.7 31.9 1.0
N A:ARG75 4.7 27.6 1.0
CA B:ALA451 4.7 30.4 1.0
OD1 B:ASN479 4.8 34.5 1.0
CG B:GLN448 4.8 29.8 1.0
O B:THR452 5.0 31.2 1.0
CA A:ARG75 5.0 29.2 1.0

Potassium binding site 3 out of 8 in 8jgw

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Potassium binding site 3 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:35.8
occ:1.00
 OE1 B:GLN77 2.7 31.5 1.0
O A:HOH915 2.7 58.4 1.0
O A:HOH940 2.9 49.0 1.0
O A:ALA451 2.9 29.4 1.0
O A:THR452 3.1 31.3 1.0
OG1 A:THR453 3.1 29.1 1.0
C A:THR452 3.6 31.5 1.0
C A:ALA451 3.7 29.7 1.0
CD B:GLN77 3.8 32.7 1.0
N A:THR453 3.9 25.3 1.0
CA A:THR453 4.0 30.6 1.0
K A:K603 4.1 31.9 1.0
CB B:GLN77 4.1 35.8 1.0
CB A:THR453 4.1 30.4 1.0
CA A:ALA451 4.4 29.5 1.0
N A:THR452 4.4 29.4 1.0
CG B:GLN77 4.6 30.0 1.0
CA A:THR452 4.6 29.7 1.0
CG2 A:THR453 4.7 28.6 1.0
NE2 B:GLN77 4.8 35.7 1.0
O A:HOH873 4.8 47.2 1.0
O A:GLN450 5.0 31.2 1.0

Potassium binding site 4 out of 8 in 8jgw

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Potassium binding site 4 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:37.6
occ:1.00
 N A:LYS288 3.2 30.3 1.0
NE1 A:TRP210 3.3 29.0 1.0
N A:GLU289 3.5 31.3 1.0
O A:GLU289 3.8 34.7 1.0
CA A:LYS288 3.9 35.0 1.0
CG2 A:ILE287 3.9 29.1 1.0
CB A:LYS288 4.0 37.0 1.0
O A:HOH732 4.0 45.4 1.0
CA A:ILE287 4.1 29.3 1.0
C A:ILE287 4.1 30.0 1.0
C A:LYS288 4.2 32.0 1.0
CE2 A:TRP210 4.2 28.9 1.0
CD1 A:TRP210 4.3 30.2 1.0
CZ2 A:TRP210 4.5 29.0 1.0
CA A:GLU289 4.5 30.1 1.0
C A:GLU289 4.5 32.8 1.0
CG A:LYS288 4.6 46.4 1.0
CB A:ILE287 4.6 30.7 1.0
CB A:ALA213 4.6 28.3 1.0
CB A:GLU289 4.9 37.0 1.0

Potassium binding site 5 out of 8 in 8jgw

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Potassium binding site 5 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K607

b:51.2
occ:1.00
 N A:ARG166 3.1 32.6 1.0
CD A:ARG165 3.6 34.1 1.0
CA A:ARG165 3.7 36.4 1.0
CB A:ARG166 3.9 37.0 1.0
C A:ARG165 3.9 32.0 1.0
NZ A:LYS197 3.9 47.4 1.0
CA A:ARG166 4.0 33.4 1.0
CB A:ARG165 4.0 34.6 1.0
CD A:LYS197 4.4 41.4 1.0
CG A:ARG165 4.5 35.0 1.0
C A:ARG166 4.6 35.3 1.0
CG A:LYS197 4.7 37.9 1.0
O A:ARG166 4.7 37.4 1.0
CE A:LYS197 4.7 41.6 1.0
NE A:ARG165 4.8 38.6 1.0
O A:SER164 4.9 34.1 1.0
CB A:LYS197 5.0 32.0 1.0

Potassium binding site 6 out of 8 in 8jgw

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Potassium binding site 6 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K608

b:56.5
occ:1.00
 OE1 A:GLU150 2.4 42.0 1.0
OD1 A:ASP143 2.9 41.1 1.0
O A:SER148 3.1 30.9 1.0
O A:HOH731 3.2 46.4 1.0
CE1 A:HIS90 3.3 44.8 1.0
CD A:GLU150 3.3 44.3 1.0
OE2 A:GLU121 3.4 43.4 1.0
N A:GLY145 3.5 30.3 1.0
CA A:GLY145 3.6 30.7 1.0
OE2 A:GLU150 3.6 42.8 1.0
O A:ASP143 3.6 33.7 1.0
CG A:ASP143 3.8 39.8 1.0
ND1 A:HIS90 3.8 41.5 1.0
C A:SER148 3.9 31.1 1.0
NE2 A:HIS90 4.1 39.0 1.0
O A:HOH835 4.2 45.8 1.0
C A:ASP143 4.2 33.6 1.0
C A:ILE144 4.3 31.0 1.0
CD A:GLU121 4.3 41.6 1.0
CB A:ASP143 4.3 28.7 1.0
CA A:THR149 4.5 31.3 1.0
N A:THR149 4.5 28.3 1.0
CB A:SER148 4.6 42.4 1.0
OD2 A:ASP143 4.6 40.2 1.0
N A:GLU150 4.6 31.0 1.0
CG A:GLU150 4.7 35.8 1.0
CA A:SER148 4.7 35.0 1.0
CA A:ILE144 4.8 31.9 1.0
N A:ILE144 4.8 32.1 1.0
C A:GLY145 4.8 34.8 1.0
CD1 A:ILE125 4.8 29.2 1.0
CG A:HIS90 4.9 46.9 1.0
C A:THR149 4.9 33.1 1.0
OE1 A:GLU121 4.9 43.3 1.0
CA A:ASP143 5.0 30.7 1.0
O A:ILE144 5.0 31.4 1.0

Potassium binding site 7 out of 8 in 8jgw

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Potassium binding site 7 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:38.6
occ:1.00
 NE1 B:TRP210 3.2 30.0 1.0
N B:LYS288 3.2 34.8 1.0
CB B:LYS288 4.0 32.3 1.0
CA B:ILE287 4.0 29.5 1.0
N B:GLU289 4.0 32.7 1.0
CA B:LYS288 4.0 33.4 1.0
C B:ILE287 4.1 30.4 1.0
CD1 B:TRP210 4.1 26.6 1.0
CE2 B:TRP210 4.1 28.9 1.0
CG2 B:ILE287 4.2 29.0 1.0
CG B:LYS288 4.3 36.9 1.0
CZ2 B:TRP210 4.4 28.4 1.0
O B:GLU289 4.4 34.1 1.0
O B:HOH756 4.5 36.5 1.0
O B:ALA286 4.5 35.5 1.0
C B:LYS288 4.5 32.9 1.0
CB B:ILE287 4.6 29.1 1.0

Potassium binding site 8 out of 8 in 8jgw

Go back to Potassium Binding Sites List in 8jgw
Potassium binding site 8 out of 8 in the Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Klebsiella Pneumoniae Exopolyphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:41.8
occ:1.00
 OE1 A:GLN77 2.6 36.0 1.0
O B:ALA451 2.8 30.4 1.0
O B:HOH925 2.9 51.4 1.0
O B:THR452 3.1 31.2 1.0
OG1 B:THR453 3.2 31.9 1.0
C B:ALA451 3.6 31.6 1.0
C B:THR452 3.6 32.2 1.0
CD A:GLN77 3.8 35.7 1.0
CB A:GLN77 4.0 32.4 1.0
N B:THR453 4.0 28.1 1.0
CA B:THR453 4.0 32.7 1.0
K A:K604 4.1 31.3 1.0
CB B:THR453 4.2 32.5 1.0
CA B:ALA451 4.3 30.4 1.0
N B:THR452 4.3 27.9 1.0
CG A:GLN77 4.5 37.1 1.0
CA B:THR452 4.6 30.0 1.0
NE2 A:GLN77 4.7 35.5 1.0
CG2 B:THR453 4.8 33.0 1.0
O B:GLN450 4.9 31.4 1.0
O B:HOH793 4.9 46.9 1.0

Reference:

S.Dai, B.Wang, R.Ye, D.Zhang, Z.Xie, N.Yu, C.Cai, C.Huang, J.Zhao, F.Zhang, Y.Hua, Y.Zhao, R.Zhou, B.Tian. Structural Evolution of Bacterial Polyphosphate Degradation Enzyme For Phosphorus Cycling. Adv Sci 09602 2024.
ISSN: ESSN 2198-3844
PubMed: 38682481
DOI: 10.1002/ADVS.202309602
Page generated: Tue Aug 13 00:05:34 2024

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