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

Protein crystallography data

The structure of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri, PDB code: 4bgb 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) 45.147 / 1.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.790, 108.540, 117.350, 90.00, 90.00, 90.00
R / Rfree (%) 15.76 / 18.28

Other elements in 4bgb:

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

Magnesium (Mg) 4 atoms
Calcium (Ca) 1 atom

Potassium Binding Sites:

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

Potassium binding site 1 out of 5 in 4bgb

Go back to Potassium Binding Sites List in 4bgb
Potassium binding site 1 out of 5 in the Nucleotide-Bound Closed 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 1 of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1356

b:18.1
occ:1.00
 OD2 A:ASP138 2.7 35.4 1.0
O A:ALA142 2.8 20.1 1.0
O A:GLY183 2.9 24.7 1.0
O A:HOH2143 3.0 65.4 1.0
O A:ALA185 3.0 19.4 1.0
O A:PHE182 3.1 19.3 1.0
C A:GLY183 3.6 22.2 1.0
CG A:ASP138 3.6 21.8 1.0
CB A:SER243 3.7 18.2 1.0
CB A:ASP138 3.8 20.0 1.0
CA A:GLY183 4.0 21.7 1.0
C A:ALA142 4.0 16.8 1.0
C A:ALA185 4.0 17.7 1.0
N A:ALA185 4.0 16.7 1.0
O A:HOH2141 4.1 27.7 1.0
C A:PHE182 4.2 22.8 1.0
O A:HOH2098 4.2 38.3 1.0
CD A:PRO143 4.3 19.0 1.0
C A:ASP184 4.4 17.6 1.0
OG A:SER243 4.5 18.7 1.0
CA A:ALA185 4.5 17.0 1.0
N A:ASP184 4.5 20.1 1.0
N A:GLY183 4.6 19.9 1.0
N A:ALA142 4.7 20.4 1.0
N A:PRO143 4.7 18.0 1.0
OD1 A:ASP138 4.7 20.3 1.0
CB A:ALA185 4.8 15.8 1.0
CA A:SER243 4.8 17.5 1.0
CA A:ASP184 4.8 19.6 1.0
O A:ASP184 5.0 18.8 1.0
O A:HOH2140 5.0 43.9 1.0

Potassium binding site 2 out of 5 in 4bgb

Go back to Potassium Binding Sites List in 4bgb
Potassium binding site 2 out of 5 in the Nucleotide-Bound Closed 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 2 of Nucleotide-Bound Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1357

b:32.8
occ:0.45
 K A:K1357 0.0 32.8 0.5
O A:HOH2084 2.0 30.0 0.5
K A:K1357 2.1 15.1 0.5
O A:GLY141 2.3 30.8 1.0
OD1 A:ASP144 2.6 27.6 1.0
OD2 A:ASP144 2.6 25.9 1.0
O A:HOH2100 2.8 45.4 1.0
CG A:ASP144 2.9 23.8 1.0
O A:HOH2085 3.4 58.2 1.0
C A:GLY141 3.5 24.2 1.0
CA A:ALA142 4.3 19.7 1.0
N A:ALA142 4.3 20.4 1.0
CB A:ASP144 4.3 20.1 1.0
O A:PRO143 4.4 18.0 1.0
O A:ASP138 4.4 19.7 1.0
CA A:GLY141 4.5 21.6 1.0
C A:PRO143 4.7 17.4 1.0
CA A:ASP144 4.7 16.2 1.0
OD2 A:ASP114 4.8 18.8 1.0
N A:GLY141 4.8 20.5 1.0
N A:ASP144 4.8 17.1 1.0
O1 A:GOL1353 4.9 29.5 1.0
CB A:ALA142 5.0 19.5 1.0
OE1 A:GLU115 5.0 31.9 1.0
N A:ASP114 5.0 14.9 1.0

Potassium binding site 3 out of 5 in 4bgb

Go back to Potassium Binding Sites List in 4bgb
Potassium binding site 3 out of 5 in the Nucleotide-Bound Closed 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 Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1357

b:15.1
occ:0.53
 K A:K1357 0.0 15.1 0.5
K A:K1357 2.1 32.8 0.5
O A:ASP138 2.8 19.7 1.0
O A:GLY141 2.8 30.8 1.0
O A:HOH2085 3.0 58.2 1.0
OD2 A:ASP144 3.1 25.9 1.0
OD2 A:ASP114 3.2 18.8 1.0
O A:HOH2084 3.4 30.0 0.5
CG A:ASP144 3.4 23.8 1.0
O A:PRO143 3.4 18.0 1.0
OD1 A:ASP144 3.5 27.6 1.0
C A:ASP138 3.7 20.2 1.0
CG A:ASP114 3.8 16.9 1.0
C A:GLY141 3.8 24.2 1.0
CB A:ASP114 4.1 16.2 1.0
CA A:ASP144 4.1 16.2 1.0
C A:PRO143 4.2 17.4 1.0
N A:ASP138 4.2 16.6 1.0
CB A:ASP144 4.3 20.1 1.0
CA A:PRO139 4.4 20.3 1.0
N A:GLY141 4.5 20.5 1.0
N A:ASP144 4.5 17.1 1.0
CA A:ASP138 4.5 16.6 1.0
N A:PRO139 4.6 18.0 1.0
C A:PRO139 4.6 19.9 1.0
N A:ALA142 4.6 20.4 1.0
CA A:ALA142 4.6 19.7 1.0
OD1 A:ASP114 4.7 16.0 1.0
CA A:GLY141 4.7 21.6 1.0
O A:HOH2100 4.7 45.4 1.0
O A:PRO139 4.8 22.6 1.0
N A:GLY137 4.8 14.6 1.0
C A:GLY137 4.9 16.3 1.0
CB A:ASP138 4.9 20.0 1.0

Potassium binding site 4 out of 5 in 4bgb

Go back to Potassium Binding Sites List in 4bgb
Potassium binding site 4 out of 5 in the Nucleotide-Bound Closed 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 Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1357

b:26.0
occ:0.68
 O B:ASP138 2.6 23.2 1.0
O B:HOH2117 2.8 26.3 1.0
O B:HOH2095 2.8 28.2 1.0
OD2 B:ASP114 2.9 21.1 1.0
O B:GLY141 3.0 25.9 1.0
OD2 B:ASP144 3.1 22.3 1.0
CG B:ASP144 3.4 17.3 1.0
O B:PRO143 3.4 21.0 1.0
OD1 B:ASP144 3.5 17.4 1.0
C B:ASP138 3.5 17.4 1.0
CG B:ASP114 3.7 16.7 1.0
C B:GLY141 3.9 21.5 1.0
CB B:ASP114 4.0 13.6 1.0
N B:ASP138 4.2 14.5 1.0
CA B:PRO139 4.2 19.8 1.0
C B:PRO143 4.2 16.6 1.0
CA B:ASP144 4.3 12.3 1.0
N B:PRO139 4.3 17.7 1.0
CB B:ASP144 4.3 14.4 1.0
CA B:ASP138 4.4 14.6 1.0
CA B:ALA142 4.5 15.5 1.0
N B:ALA142 4.6 17.5 1.0
N B:ASP144 4.6 13.2 1.0
C B:PRO139 4.6 19.1 1.0
N B:GLY141 4.7 18.8 1.0
OD1 B:ASP114 4.8 14.1 1.0
C B:GLY137 4.8 14.9 1.0
N B:GLY137 4.9 12.1 1.0
O B:PRO139 4.9 21.8 1.0
N B:ASP114 4.9 12.3 1.0
CA B:GLY141 4.9 21.0 1.0
CB B:ASP138 5.0 15.2 1.0

Potassium binding site 5 out of 5 in 4bgb

Go back to Potassium Binding Sites List in 4bgb
Potassium binding site 5 out of 5 in the Nucleotide-Bound Closed 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 Closed Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1358

b:16.1
occ:1.00
 O B:ALA142 2.7 16.7 1.0
O B:GLY183 2.9 22.0 1.0
OG B:SER243 2.9 34.7 1.0
O B:ALA185 3.0 15.6 1.0
OD2 B:ASP138 3.1 18.9 1.0
O B:PHE182 3.2 15.7 1.0
C B:GLY183 3.5 17.8 1.0
C B:ALA142 3.8 14.3 1.0
CB B:SER243 3.9 27.1 1.0
CG B:ASP138 3.9 16.4 1.0
N B:ALA185 3.9 13.1 1.0
O B:HOH2145 4.0 54.4 1.0
C B:ALA185 4.0 14.2 1.0
CA B:GLY183 4.0 17.3 1.0
O B:HOH2112 4.1 33.3 1.0
CB B:ASP138 4.1 15.2 1.0
C B:PHE182 4.2 16.8 1.0
N B:ASP184 4.3 17.1 1.0
N B:ALA142 4.3 17.5 1.0
C B:ASP184 4.4 16.0 1.0
CA B:ALA185 4.4 13.4 1.0
O B:HOH2144 4.5 38.7 1.0
CD B:PRO143 4.5 13.8 1.0
N B:PRO143 4.6 12.8 1.0
N B:GLY183 4.6 16.1 1.0
CA B:ASP184 4.6 18.2 1.0
CB B:ALA185 4.7 12.9 1.0
CA B:SER243 4.8 20.1 1.0
CA B:ALA142 4.8 15.5 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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