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Potassium in PDB 4bga: Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri

Protein crystallography data

The structure of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri, PDB code: 4bga was solved by M.Schacherl, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.568 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.570, 111.670, 87.880, 90.00, 89.55, 90.00
R / Rfree (%) 15.42 / 20.8

Other elements in 4bga:

The structure of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (pdb code 4bga). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri, PDB code: 4bga:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4bga

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Potassium binding site 1 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1351

b:49.0
occ:1.00
 O A:ASP138 2.8 27.9 1.0
O A:GLY141 2.9 34.5 1.0
O A:PRO143 3.1 19.1 1.0
OD2 A:ASP114 3.1 29.0 1.0
OD2 A:ASP144 3.2 31.0 1.0
O A:HOH2014 3.3 43.3 1.0
CG A:ASP144 3.3 33.0 1.0
OD1 A:ASP144 3.4 48.3 1.0
C A:ASP138 3.7 26.3 1.0
C A:PRO143 3.8 23.6 1.0
CA A:ASP144 3.9 20.8 1.0
CG A:ASP114 3.9 28.9 1.0
C A:GLY141 4.0 35.6 1.0
N A:ASP138 4.1 25.8 1.0
CB A:ASP144 4.1 18.9 1.0
N A:ASP144 4.1 27.4 1.0
CB A:ASP114 4.4 23.1 1.0
CA A:ASP138 4.5 23.0 1.0
N A:PRO139 4.5 29.6 1.0
CA A:PRO139 4.6 31.9 1.0
CA A:ALA142 4.7 22.5 1.0
N A:ALA142 4.7 25.2 1.0
N A:GLY141 4.8 27.7 1.0
OD1 A:ASP114 4.8 28.1 1.0
N A:GLY137 4.8 25.8 1.0
C A:GLY137 4.8 31.3 1.0
C A:PRO139 4.9 34.3 1.0
CA A:GLY137 4.9 23.7 1.0
O A:HOH2020 5.0 40.4 1.0
CA A:GLY141 5.0 27.0 1.0
CA A:PRO143 5.0 22.1 1.0

Potassium binding site 2 out of 8 in 4bga

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Potassium binding site 2 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1352

b:27.0
occ:1.00
 O A:ALA142 2.7 29.1 1.0
O A:ALA185 2.8 21.2 1.0
O A:PHE182 2.9 19.9 1.0
O A:GLY183 2.9 20.0 1.0
OD2 A:ASP138 3.0 22.8 1.0
C A:GLY183 3.5 18.4 1.0
CG A:ASP138 3.7 25.7 1.0
CB A:SER243 3.7 28.0 1.0
CB A:ASP138 3.9 16.8 1.0
CA A:GLY183 3.9 14.8 1.0
C A:ALA185 3.9 24.5 1.0
C A:ALA142 3.9 21.6 1.0
C A:PHE182 4.0 22.1 1.0
N A:ALA185 4.0 21.4 1.0
O A:HOH2018 4.0 33.4 1.0
OG A:SER243 4.2 30.9 1.0
N A:ASP184 4.3 25.7 1.0
C A:ASP184 4.3 26.6 1.0
CA A:ALA185 4.4 28.7 1.0
N A:GLY183 4.4 25.4 1.0
N A:ALA142 4.5 25.2 1.0
CD A:PRO143 4.6 16.4 1.0
CB A:ALA185 4.6 17.2 1.0
CA A:ASP184 4.7 21.8 1.0
N A:PRO143 4.8 24.8 1.0
OD1 A:ASP138 4.8 33.0 1.0
CA A:ALA142 4.8 22.5 1.0
O A:ASP184 4.9 22.5 1.0
CA A:SER243 4.9 31.9 1.0
N A:VAL186 5.0 24.9 1.0

Potassium binding site 3 out of 8 in 4bga

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Potassium binding site 3 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1351

b:33.8
occ:1.00
 O B:GLY141 2.7 31.7 1.0
O B:ASP138 2.8 27.2 1.0
OD2 B:ASP114 3.0 24.4 1.0
O B:HOH2019 3.1 30.4 1.0
O B:PRO143 3.1 19.4 1.0
OD2 B:ASP144 3.2 38.7 1.0
CG B:ASP144 3.4 31.4 1.0
OD1 B:ASP144 3.6 39.7 1.0
C B:ASP138 3.7 26.6 1.0
C B:GLY141 3.8 28.1 1.0
CG B:ASP114 3.8 31.4 1.0
C B:PRO143 3.9 31.2 1.0
CA B:ASP144 4.0 22.5 1.0
N B:ASP138 4.1 25.8 1.0
NH2 D:ARG88 4.1 42.5 1.0
CB B:ASP114 4.2 24.4 1.0
CB B:ASP144 4.2 23.2 1.0
N B:ASP144 4.2 30.1 1.0
CA B:ASP138 4.5 24.9 1.0
N B:GLY141 4.5 30.9 1.0
N B:PRO139 4.5 32.5 1.0
N B:ALA142 4.6 27.3 1.0
CA B:PRO139 4.6 21.4 1.0
CA B:ALA142 4.7 27.6 1.0
CA B:GLY141 4.7 34.8 1.0
N B:GLY137 4.8 28.6 1.0
OD1 B:ASP114 4.8 26.1 1.0
NH2 D:ARG84 4.8 48.9 1.0
C B:PRO139 4.8 27.5 1.0
C B:GLY137 4.8 28.9 1.0
CA B:GLY137 4.9 23.2 1.0

Potassium binding site 4 out of 8 in 4bga

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Potassium binding site 4 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1352

b:28.6
occ:1.00
 O B:ALA185 2.7 17.2 1.0
O B:ALA142 2.7 26.1 1.0
O B:PHE182 2.9 20.6 1.0
OD2 B:ASP138 3.0 26.8 1.0
O B:GLY183 3.1 20.8 1.0
C B:GLY183 3.5 28.1 1.0
CB B:SER243 3.7 25.5 1.0
CG B:ASP138 3.7 30.5 1.0
CB B:ASP138 3.7 23.9 1.0
C B:ALA185 3.7 17.6 1.0
CA B:GLY183 3.8 24.4 1.0
C B:ALA142 3.9 26.8 1.0
N B:ALA185 3.9 23.8 1.0
C B:PHE182 3.9 20.5 1.0
O B:HOH2034 4.0 50.6 1.0
OG B:SER243 4.2 29.7 1.0
N B:ASP184 4.2 26.0 1.0
O B:HOH2021 4.3 34.6 1.0
CA B:ALA185 4.3 17.3 1.0
C B:ASP184 4.3 20.2 1.0
N B:GLY183 4.4 25.3 1.0
N B:ALA142 4.5 27.3 1.0
CB B:ALA185 4.6 18.0 1.0
CD B:PRO143 4.7 16.9 1.0
CA B:ASP184 4.7 23.9 1.0
N B:PRO143 4.8 28.1 1.0
OD1 B:ASP138 4.8 38.6 1.0
N B:VAL186 4.8 19.7 1.0
O B:ASP184 4.8 21.6 1.0
CA B:SER243 4.9 27.9 1.0
CA B:ALA142 4.9 27.6 1.0

Potassium binding site 5 out of 8 in 4bga

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Potassium binding site 5 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1359

b:47.1
occ:1.00
 O C:GLY141 2.8 29.7 1.0
O C:ASP138 2.8 36.9 1.0
OD2 C:ASP114 3.0 23.9 1.0
OD2 C:ASP144 3.2 32.1 1.0
O C:HOH2016 3.3 43.1 1.0
O C:PRO143 3.4 23.3 1.0
CG C:ASP144 3.6 35.2 1.0
C C:ASP138 3.7 27.3 1.0
CG C:ASP114 3.8 33.8 1.0
OD1 C:ASP144 3.8 59.3 1.0
C C:GLY141 3.9 27.9 1.0
CB C:ASP114 4.0 28.1 1.0
C C:PRO143 4.2 24.5 1.0
N C:ASP138 4.2 21.4 1.0
CA C:ASP144 4.2 21.9 1.0
CB C:ASP144 4.4 28.4 1.0
N C:GLY141 4.5 35.2 1.0
CA C:PRO139 4.5 26.8 1.0
N C:PRO139 4.5 30.6 1.0
N C:ASP144 4.6 20.5 1.0
CA C:ASP138 4.6 29.9 1.0
C C:PRO139 4.7 39.8 1.0
CA C:GLY141 4.7 23.9 1.0
OD1 C:ASP114 4.8 32.2 1.0
N C:ALA142 4.8 22.9 1.0
N C:GLY137 4.9 19.2 1.0
CA C:ALA142 4.9 19.6 1.0
O C:PRO139 4.9 37.5 1.0
C C:GLY137 5.0 27.8 1.0

Potassium binding site 6 out of 8 in 4bga

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Potassium binding site 6 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1360

b:28.8
occ:1.00
 O C:ALA142 2.7 33.4 1.0
O C:ALA185 2.8 26.8 1.0
O C:PHE182 2.8 24.7 1.0
OD2 C:ASP138 3.0 33.3 1.0
O C:GLY183 3.0 25.4 1.0
C C:GLY183 3.5 28.5 1.0
CG C:ASP138 3.7 32.2 1.0
CB C:ASP138 3.8 28.3 1.0
C C:ALA185 3.8 21.3 1.0
CA C:GLY183 3.8 18.4 1.0
CB C:SER243 3.9 33.5 1.0
C C:ALA142 3.9 20.2 1.0
C C:PHE182 3.9 25.8 1.0
N C:ALA185 4.0 17.1 1.0
O C:HOH2020 4.1 47.4 1.0
OG C:SER243 4.2 36.4 1.0
CA C:ALA185 4.3 17.2 1.0
N C:ASP184 4.3 24.7 1.0
N C:GLY183 4.4 24.6 1.0
N C:ALA142 4.4 22.9 1.0
C C:ASP184 4.4 34.9 1.0
CB C:ALA185 4.5 23.6 1.0
CD C:PRO143 4.6 18.2 1.0
N C:PRO143 4.7 16.4 1.0
CA C:ALA142 4.8 19.6 1.0
OD1 C:ASP138 4.8 34.7 1.0
CA C:ASP184 4.8 24.0 1.0
N C:VAL186 4.8 21.2 1.0

Potassium binding site 7 out of 8 in 4bga

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Potassium binding site 7 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1351

b:29.6
occ:1.00
 O D:ALA185 2.7 23.0 1.0
O D:PHE182 2.8 28.0 1.0
O D:ALA142 2.9 30.5 1.0
OD2 D:ASP138 3.0 27.0 1.0
O D:GLY183 3.1 21.8 1.0
CB D:SER243 3.5 25.3 1.0
O D:HOH2021 3.5 32.0 1.0
C D:GLY183 3.6 24.7 1.0
CG D:ASP138 3.7 27.0 1.0
C D:ALA185 3.8 23.8 1.0
CB D:ASP138 3.8 22.3 1.0
CA D:GLY183 3.9 18.4 1.0
C D:PHE182 3.9 21.8 1.0
N D:ALA185 4.0 25.1 1.0
C D:ALA142 4.0 21.8 1.0
O D:HOH2009 4.1 28.7 1.0
O D:HOH2023 4.1 41.8 1.0
OG D:SER243 4.2 31.4 1.0
C D:ASP184 4.3 24.5 1.0
CA D:ALA185 4.3 21.3 1.0
N D:ASP184 4.4 31.0 1.0
N D:GLY183 4.4 20.8 1.0
N D:ALA142 4.5 22.7 1.0
CB D:ALA185 4.6 20.1 1.0
CA D:SER243 4.6 26.8 1.0
CD D:PRO143 4.7 16.6 1.0
O D:ASP184 4.7 21.7 1.0
CA D:ASP184 4.8 21.9 1.0
OD1 D:ASP138 4.8 33.0 1.0
N D:VAL186 4.8 24.6 1.0
N D:PRO143 4.8 21.3 1.0
CA D:ALA142 5.0 24.3 1.0

Potassium binding site 8 out of 8 in 4bga

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Potassium binding site 8 out of 8 in the Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Nucleotide-Bound Open Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1352

b:46.1
occ:1.00
 O D:GLY141 2.8 32.6 1.0
O D:PRO143 2.9 19.2 1.0
OD2 D:ASP114 2.9 24.4 1.0
O D:ASP138 3.0 28.5 1.0
OD2 D:ASP144 3.2 33.6 1.0
CG D:ASP144 3.3 37.2 1.0
OD1 D:ASP144 3.5 50.1 1.0
O B:HOH2012 3.5 37.6 1.0
CG D:ASP114 3.6 31.4 1.0
C D:PRO143 3.7 27.8 1.0
CA D:ASP144 3.7 20.6 1.0
C D:ASP138 3.8 28.4 1.0
C D:GLY141 3.9 29.6 1.0
N D:ASP144 4.0 25.3 1.0
CB D:ASP144 4.0 20.8 1.0
CB D:ASP114 4.1 29.5 1.0
N D:ASP138 4.1 26.9 1.0
NH2 B:ARG88 4.2 37.8 1.0
OD1 D:ASP114 4.5 27.0 1.0
CA D:ALA142 4.6 24.3 1.0
CA D:ASP138 4.6 34.2 1.0
NH1 B:ARG84 4.6 44.1 1.0
N D:ALA142 4.6 22.7 1.0
N D:PRO139 4.6 25.5 1.0
N D:GLY137 4.7 23.6 1.0
CA D:PRO139 4.8 32.1 1.0
CA D:PRO143 4.8 21.8 1.0
N D:GLY141 4.8 29.7 1.0
C D:GLY137 4.9 27.3 1.0
CA D:GLY137 4.9 24.7 1.0
CA D:GLY141 4.9 28.2 1.0
C D:ASP144 5.0 27.7 1.0

Reference:

M.Schacherl, S.M.Waltersperger, U.Baumann. Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase MK0840 From Methanopyrus Kandleri Acta Crystallogr.,Sect.D V. 69 2440 2013.
ISSN: ISSN 0907-4449
PubMed: 24311585
DOI: 10.1107/S0907444913022683
Page generated: Mon Aug 12 10:11:55 2024

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