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Potassium in PDB 4bg8: Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)

Protein crystallography data

The structure of Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group), PDB code: 4bg8 was solved by M.Schacherl, S.M.Waltersperger, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.629 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 73.280, 116.380, 90.00, 95.89, 90.00
R / Rfree (%) 17.64 / 20.86

Other elements in 4bg8:

The structure of Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group) (pdb code 4bg8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group), PDB code: 4bg8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4bg8

Go back to Potassium Binding Sites List in 4bg8
Potassium binding site 1 out of 6 in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)


Mono view


Stereo pair view

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

b:21.6
occ:1.00
 O A:ALA185 2.6 21.8 1.0
OG A:SER243 2.6 39.4 1.0
OD2 A:ASP138 2.6 23.7 1.0
O A:ALA142 2.6 21.3 1.0
O A:GLY183 2.9 31.9 1.0
O A:PHE182 2.9 24.0 1.0
O A:HOH2097 3.3 45.0 1.0
C A:GLY183 3.4 27.2 1.0
CG A:ASP138 3.6 29.2 1.0
C A:ALA185 3.7 25.0 1.0
CB A:ASP138 3.8 17.8 1.0
C A:ALA142 3.9 23.1 1.0
CA A:GLY183 3.9 24.1 1.0
N A:ALA185 3.9 22.1 1.0
CB A:SER243 3.9 33.2 1.0
C A:PHE182 4.0 21.3 1.0
O A:HOH2064 4.0 38.3 1.0
CA A:ALA185 4.3 22.4 1.0
N A:ASP184 4.3 27.5 1.0
C A:ASP184 4.3 28.5 1.0
N A:GLY183 4.4 26.2 1.0
CD A:PRO143 4.5 22.8 1.0
N A:ALA142 4.5 30.0 1.0
N A:PRO143 4.6 23.5 1.0
CB A:ALA185 4.7 20.1 1.0
OD1 A:ASP138 4.7 23.2 1.0
CA A:ASP184 4.7 29.6 1.0
CA A:SER243 4.7 27.4 1.0
N A:VAL186 4.8 18.3 1.0
CA A:ALA142 4.9 26.9 1.0
O A:ASP184 4.9 27.8 1.0

Potassium binding site 2 out of 6 in 4bg8

Go back to Potassium Binding Sites List in 4bg8
Potassium binding site 2 out of 6 in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)


Mono view


Stereo pair view

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

b:25.9
occ:1.00
 O A:ASP138 2.6 24.8 1.0
O A:GLY141 2.7 27.9 1.0
OD2 A:ASP114 2.7 23.8 1.0
O A:HOH2055 2.9 31.2 1.0
O A:PRO143 3.0 22.7 1.0
OD2 A:ASP144 3.2 37.3 1.0
O A:HOH2054 3.3 55.9 1.0
CG A:ASP144 3.4 40.6 1.0
OD1 A:ASP144 3.5 47.9 1.0
CG A:ASP114 3.6 24.9 1.0
C A:ASP138 3.6 22.9 1.0
C A:GLY141 3.8 26.5 1.0
C A:PRO143 3.9 24.6 1.0
CA A:ASP144 4.0 28.3 1.0
CB A:ASP114 4.1 20.1 1.0
N A:ASP138 4.1 22.0 1.0
O A:HOH2066 4.1 60.5 1.0
CB A:ASP144 4.3 29.8 1.0
N A:ASP144 4.3 23.4 1.0
NH2 B:ARG88 4.3 28.9 1.0
CA A:ASP138 4.4 19.4 1.0
CA A:ALA142 4.5 26.9 1.0
N A:PRO139 4.5 22.7 1.0
N A:ALA142 4.5 30.0 1.0
OD1 A:ASP114 4.6 19.6 1.0
N A:GLY137 4.6 25.7 1.0
N A:GLY141 4.6 21.2 1.0
CA A:PRO139 4.6 26.0 1.0
C A:PRO139 4.7 23.9 1.0
CA A:GLY141 4.8 21.2 1.0
O A:PRO139 4.8 26.7 1.0
C A:GLY137 4.8 23.1 1.0
CB A:ASP138 4.8 17.8 1.0
CA A:GLY137 4.9 22.1 1.0

Potassium binding site 3 out of 6 in 4bg8

Go back to Potassium Binding Sites List in 4bg8
Potassium binding site 3 out of 6 in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1353

b:29.7
occ:1.00
 O A:ARG66 2.6 29.2 1.0
OE2 A:GLU67 2.9 54.4 1.0
O A:HOH2021 3.2 37.5 1.0
CD A:GLU67 3.6 56.5 1.0
C A:ARG66 3.7 31.0 1.0
OE1 A:GLU67 3.8 61.7 1.0
N A:ARG66 4.5 22.9 1.0
CA A:GLU67 4.5 31.4 1.0
N A:GLU67 4.6 34.3 1.0
CA A:ARG66 4.6 27.4 1.0
CG A:GLU67 4.7 42.4 1.0
CB A:ARG66 4.9 29.1 1.0

Potassium binding site 4 out of 6 in 4bg8

Go back to Potassium Binding Sites List in 4bg8
Potassium binding site 4 out of 6 in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1351

b:24.4
occ:1.00
 O B:GLY141 2.6 24.9 1.0
O B:ASP138 2.6 20.2 1.0
OD2 B:ASP114 2.7 24.6 1.0
O A:HOH2039 2.8 29.6 1.0
O B:PRO143 3.0 22.0 1.0
OD2 B:ASP144 3.2 35.7 1.0
CG B:ASP144 3.4 36.3 1.0
OD1 B:ASP144 3.6 43.9 1.0
CG B:ASP114 3.6 23.1 1.0
C B:ASP138 3.7 19.7 1.0
C B:GLY141 3.8 26.8 1.0
C B:PRO143 3.9 21.0 1.0
CA B:ASP144 4.0 24.1 1.0
N B:ASP138 4.1 18.2 1.0
CB B:ASP114 4.1 15.6 1.0
CB B:ASP144 4.3 23.3 1.0
N B:ASP144 4.3 20.1 1.0
NH2 A:ARG88 4.4 28.9 1.0
CA B:ASP138 4.4 17.5 1.0
CA B:ALA142 4.5 19.6 1.0
OD1 B:ASP114 4.5 23.7 1.0
N B:GLY141 4.5 18.0 1.0
N B:PRO139 4.5 20.3 1.0
N B:ALA142 4.5 25.1 1.0
CA B:PRO139 4.6 22.9 1.0
N B:GLY137 4.6 21.1 1.0
CA B:GLY141 4.7 21.6 1.0
C B:PRO139 4.8 23.8 1.0
C B:GLY137 4.8 22.6 1.0
CB B:ASP138 4.8 16.0 1.0
CA B:GLY137 4.9 21.1 1.0
O B:PRO139 4.9 25.0 1.0

Potassium binding site 5 out of 6 in 4bg8

Go back to Potassium Binding Sites List in 4bg8
Potassium binding site 5 out of 6 in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1352

b:17.9
occ:1.00
 OD2 B:ASP138 2.6 19.7 1.0
O B:ALA142 2.6 20.2 1.0
O B:ALA185 2.6 18.7 1.0
OG B:SER243 2.7 29.9 0.5
O B:PHE182 2.8 20.7 1.0
O B:GLY183 2.9 29.6 1.0
O B:HOH2095 3.2 43.7 1.0
C B:GLY183 3.5 25.4 1.0
CG B:ASP138 3.5 25.5 1.0
CB B:SER243 3.5 25.4 0.5
C B:ALA185 3.7 22.0 1.0
CB B:ASP138 3.7 16.0 1.0
CB B:SER243 3.8 26.2 0.5
C B:ALA142 3.8 18.8 1.0
N B:ALA185 3.9 18.6 1.0
CA B:GLY183 3.9 23.6 1.0
C B:PHE182 4.0 20.4 1.0
O B:HOH2094 4.2 41.5 1.0
O B:HOH2062 4.3 36.0 1.0
CA B:ALA185 4.3 20.7 1.0
N B:ASP184 4.3 21.5 1.0
OG B:SER243 4.3 22.4 0.5
C B:ASP184 4.3 21.8 1.0
N B:GLY183 4.5 21.1 1.0
CD B:PRO143 4.5 20.8 1.0
N B:ALA142 4.5 25.1 1.0
N B:PRO143 4.6 17.8 1.0
CB B:ALA185 4.7 14.0 1.0
OD1 B:ASP138 4.7 25.7 1.0
CA B:SER243 4.7 24.9 0.5
CA B:ASP184 4.7 21.3 1.0
CA B:SER243 4.7 24.5 0.5
N B:VAL186 4.8 13.7 1.0
CA B:ALA142 4.8 19.6 1.0
O B:ASP184 4.9 25.7 1.0

Potassium binding site 6 out of 6 in 4bg8

Go back to Potassium Binding Sites List in 4bg8
Potassium binding site 6 out of 6 in the Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Apo Form of A Putative Sugar Kinase MK0840 From Methanopyrus Kandleri (Monoclinic Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1353

b:25.1
occ:1.00
 O B:ARG66 2.6 27.4 1.0
OE2 B:GLU67 3.0 49.0 1.0
O B:HOH2020 3.2 39.8 1.0
CD B:GLU67 3.6 51.8 1.0
C B:ARG66 3.7 27.8 1.0
OE1 B:GLU67 3.8 56.0 1.0
N B:ARG66 4.4 21.3 1.0
CA B:ARG66 4.6 27.0 1.0
CA B:GLU67 4.6 28.0 1.0
N B:GLU67 4.6 28.8 1.0
CG B:GLU67 4.7 36.8 1.0
CB B:ARG66 4.8 24.8 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 10:10:10 2024

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