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Potassium in PDB 5cc8: Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp

Enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp

All present enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp:
2.7.4.16;

Protein crystallography data

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp, PDB code: 5cc8 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.140, 93.760, 72.490, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.4

Other elements in 5cc8:

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp (pdb code 5cc8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp, PDB code: 5cc8:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5cc8

Go back to Potassium Binding Sites List in 5cc8
Potassium binding site 1 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:14.4
occ:1.00
 O A:MET196 2.7 12.4 1.0
OD1 B:ASP25 2.7 15.7 1.0
O A:ALA74 2.8 12.7 1.0
OD2 B:ASP26 2.9 14.4 1.0
O A:VAL141 2.9 12.6 1.0
SD A:MET75 3.4 12.4 1.0
C A:ALA74 3.7 13.2 1.0
C A:MET196 3.7 8.9 1.0
C A:LEU142 3.7 12.1 1.0
CG B:ASP25 3.8 13.9 1.0
N A:ARG143 3.8 12.4 1.0
C A:VAL141 3.9 12.3 1.0
CG B:ASP26 3.9 12.2 1.0
CA A:LEU142 4.0 12.4 1.0
CG A:ARG143 4.0 12.7 1.0
O A:LEU142 4.1 14.6 1.0
CE A:MET75 4.2 15.0 1.0
OD2 B:ASP25 4.2 15.4 1.0
N A:MET75 4.3 9.8 1.0
CA A:MET75 4.3 10.8 1.0
CB B:ASP26 4.3 10.5 1.0
N A:LEU142 4.4 12.9 1.0
CB A:ALA74 4.4 12.7 1.0
N A:ILE197 4.5 10.6 1.0
CA A:MET196 4.5 9.2 1.0
CA A:ILE197 4.5 9.7 1.0
N B:ASP26 4.5 12.2 1.0
CA A:ARG143 4.6 12.0 1.0
CB A:MET196 4.6 10.3 1.0
CA A:ALA74 4.6 9.3 1.0
N A:MET196 4.7 10.5 1.0
CG A:MET75 4.7 11.3 1.0
CB A:ARG143 4.9 11.7 1.0
NE A:ARG143 5.0 10.2 1.0

Potassium binding site 2 out of 4 in 5cc8

Go back to Potassium Binding Sites List in 5cc8
Potassium binding site 2 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:20.7
occ:1.00
 O2B A:ANP413 2.8 16.4 1.0
O B:ASP26 2.8 11.6 1.0
O A:HOH532 2.8 11.0 1.0
O A:HOH693 2.9 12.7 1.0
O A:HOH616 2.9 14.6 1.0
OD2 A:ASP71 3.0 12.8 1.0
CG A:ASP71 3.4 12.7 1.0
CB A:CYS41 3.7 10.5 1.0
PB A:ANP413 3.8 14.4 1.0
O A:ALA42 3.9 13.1 1.0
MG A:MG404 3.9 13.2 1.0
CB A:ASP71 3.9 9.8 1.0
OD2 A:ASP43 4.0 15.4 1.0
C B:ASP26 4.0 11.1 1.0
OD1 A:ASP71 4.0 11.7 1.0
O1B A:ANP413 4.0 13.2 1.0
MG A:MG402 4.1 13.9 1.0
O3A A:ANP413 4.1 13.5 1.0
OD1 A:ASP43 4.3 15.5 1.0
CG A:ASP43 4.3 15.8 1.0
N A:ALA42 4.4 10.5 1.0
CA B:ASP26 4.6 10.4 1.0
C A:ALA42 4.6 10.1 1.0
O B:GLY117 4.6 13.9 1.0
CA A:CYS41 4.6 8.5 1.0
O A:HOH653 4.7 15.3 1.0
SG A:CYS41 4.8 14.0 1.0
O2' A:ANP413 4.8 14.1 1.0
O1A A:ANP413 4.8 14.6 1.0
C A:CYS41 4.9 11.1 1.0
C2' A:ANP413 4.9 14.2 1.0
MG A:MG405 5.0 10.1 1.0

Potassium binding site 3 out of 4 in 5cc8

Go back to Potassium Binding Sites List in 5cc8
Potassium binding site 3 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K411

b:18.6
occ:1.00
 O B:MET196 2.7 14.8 1.0
OD1 A:ASP25 2.7 17.6 1.0
O B:ALA74 2.7 15.3 1.0
OD2 A:ASP26 2.9 18.7 1.0
O B:VAL141 2.9 17.9 1.0
SD B:MET75 3.4 15.7 1.0
C B:ALA74 3.6 16.4 1.0
C B:MET196 3.7 16.7 1.0
CG A:ASP25 3.8 23.0 1.0
C B:LEU142 3.9 23.5 1.0
CG A:ASP26 3.9 14.6 1.0
C B:VAL141 4.0 21.0 1.0
N B:ARG143 4.0 18.4 1.0
CG B:ARG143 4.0 17.2 1.0
CA B:LEU142 4.1 16.8 1.0
CE B:MET75 4.2 16.9 1.0
OD2 A:ASP25 4.3 22.6 1.0
CA B:MET75 4.3 13.1 1.0
O B:LEU142 4.3 25.1 1.0
N B:MET75 4.3 13.7 1.0
CB A:ASP26 4.3 13.3 1.0
CB B:ALA74 4.4 15.1 1.0
N B:LEU142 4.5 16.9 1.0
CA B:MET196 4.5 12.5 1.0
N B:ILE197 4.5 13.5 1.0
CB B:MET196 4.5 13.1 1.0
CA B:ILE197 4.6 14.9 1.0
N A:ASP26 4.6 13.4 1.0
CA B:ALA74 4.6 14.9 1.0
CA B:ARG143 4.7 16.1 1.0
N B:MET196 4.7 16.8 1.0
CG B:MET75 4.7 13.3 1.0
NE B:ARG143 4.9 14.9 1.0
CB B:ARG143 5.0 15.8 1.0

Potassium binding site 4 out of 4 in 5cc8

Go back to Potassium Binding Sites List in 5cc8
Potassium binding site 4 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K412

b:26.6
occ:1.00
 O2B A:ANP401 2.7 16.4 1.0
O A:ASP26 2.8 14.5 1.0
O B:HOH648 2.9 11.2 1.0
O B:HOH532 2.9 11.7 1.0
O B:HOH603 3.0 12.6 1.0
OD2 B:ASP71 3.0 12.9 1.0
CG B:ASP71 3.4 13.4 1.0
CB B:CYS41 3.7 13.1 1.0
PB A:ANP401 3.8 15.4 1.0
O B:ALA42 3.9 13.6 1.0
C A:ASP26 3.9 14.3 1.0
CB B:ASP71 3.9 11.5 1.0
OD1 B:ASP71 4.0 14.2 1.0
MG B:MG401 4.0 14.1 1.0
OD2 B:ASP43 4.0 16.0 1.0
O1B A:ANP401 4.0 15.2 1.0
O3A A:ANP401 4.1 15.8 1.0
MG A:MG406 4.1 17.1 1.0
OD1 B:ASP43 4.3 14.3 1.0
CG B:ASP43 4.3 16.2 1.0
N B:ALA42 4.4 9.0 1.0
CA A:ASP26 4.5 12.9 1.0
CA B:CYS41 4.6 10.0 1.0
C B:ALA42 4.7 12.6 1.0
O A:GLY117 4.7 13.5 1.0
O2' A:ANP401 4.8 13.2 1.0
O2A A:ANP401 4.8 15.2 1.0
SG B:CYS41 4.8 14.9 1.0
O B:HOH646 4.9 12.2 1.0
C2' A:ANP401 5.0 15.4 1.0
C B:CYS41 5.0 12.6 1.0
MG A:MG410 5.0 13.8 1.0
N A:SER27 5.0 12.5 1.0

Reference:

A.H.Sullivan, D.M.Dranow, P.S.Horanyi, D.D.Lorimer, T.E.Edwards, J.Abendroth. Crystal Structures of Thiamine Monophosphate Kinase From Acinetobacter Baumannii in Complex with Substrates and Products. Sci Rep V. 9 4392 2019.
ISSN: ESSN 2045-2322
PubMed: 30867460
DOI: 10.1038/S41598-019-40558-X
Page generated: Mon Aug 12 13:07:03 2024

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