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Potassium in PDB 5dd7: Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate

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

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

Protein crystallography data

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate, PDB code: 5dd7 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) 39.41 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.960, 93.290, 73.480, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.7

Other elements in 5dd7:

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

Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate (pdb code 5dd7). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate, PDB code: 5dd7:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5dd7

Go back to Potassium Binding Sites List in 5dd7
Potassium binding site 1 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate


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 and Thiamine-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:14.6
occ:1.00
 O2B B:ANP405 2.7 16.7 1.0
O B:ASP26 2.7 14.9 1.0
O A:HOH584 2.8 15.7 1.0
O A:HOH678 2.8 14.1 1.0
O A:HOH549 2.8 11.9 1.0
OD2 A:ASP71 2.9 13.7 1.0
CG A:ASP71 3.3 11.6 1.0
PB B:ANP405 3.7 14.4 1.0
CB A:CYS41 3.7 10.4 1.0
C B:ASP26 3.9 14.4 1.0
MG A:MG409 3.9 13.7 1.0
O1B B:ANP405 3.9 13.4 1.0
OD2 A:ASP43 3.9 16.6 1.0
CB A:ASP71 3.9 13.2 1.0
O3A B:ANP405 4.0 13.3 1.0
OD1 A:ASP71 4.0 12.7 1.0
O A:ALA42 4.0 14.5 1.0
MG A:MG411 4.0 13.0 1.0
OD1 A:ASP43 4.3 16.6 1.0
CG A:ASP43 4.3 15.3 1.0
N A:ALA42 4.4 11.1 1.0
CA B:ASP26 4.5 12.6 1.0
O B:GLY117 4.6 15.5 1.0
CA A:CYS41 4.6 11.4 1.0
C A:ALA42 4.7 13.1 1.0
O1A B:ANP405 4.8 17.0 1.0
SG A:CYS41 4.8 15.8 1.0
O2' B:ANP405 4.8 14.1 1.0
O A:HOH653 4.8 15.4 1.0
N B:SER27 4.9 14.7 1.0
C A:CYS41 5.0 12.7 1.0
MG A:MG410 5.0 12.6 1.0
PA B:ANP405 5.0 14.6 1.0

Potassium binding site 2 out of 6 in 5dd7

Go back to Potassium Binding Sites List in 5dd7
Potassium binding site 2 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate


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 and Thiamine-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:15.4
occ:1.00
 O A:MET196 2.6 15.4 1.0
OD1 B:ASP25 2.7 21.1 1.0
O A:ALA74 2.7 17.6 1.0
OD2 B:ASP26 2.9 14.6 1.0
O A:VAL141 2.9 18.0 1.0
SD A:MET75 3.3 16.1 1.0
C A:ALA74 3.6 16.3 1.0
C A:MET196 3.7 14.3 1.0
CG B:ASP25 3.8 20.7 1.0
C A:LEU142 3.9 18.5 1.0
CG B:ASP26 3.9 16.0 1.0
C A:VAL141 3.9 15.8 1.0
N A:ARG143 4.0 18.1 1.0
CA A:LEU142 4.0 15.4 1.0
CE A:MET75 4.1 19.0 1.0
CG A:ARG143 4.1 14.8 1.0
O A:LEU142 4.2 20.5 1.0
CA A:MET75 4.2 14.8 1.0
N A:MET75 4.3 13.5 1.0
CB B:ASP26 4.3 12.8 1.0
OD2 B:ASP25 4.3 20.6 1.0
CB A:ALA74 4.3 12.2 1.0
N A:LEU142 4.4 16.4 1.0
N A:ILE197 4.5 13.3 1.0
CA A:MET196 4.5 14.3 1.0
N B:ASP26 4.5 14.3 1.0
CB A:MET196 4.5 14.2 1.0
CA A:ILE197 4.5 13.3 1.0
CA A:ALA74 4.6 15.3 1.0
N A:MET196 4.7 16.6 1.0
CG A:MET75 4.7 15.8 1.0
CA A:ARG143 4.7 16.1 1.0
CB A:MET75 5.0 13.2 1.0
NE A:ARG143 5.0 12.3 1.0

Potassium binding site 3 out of 6 in 5dd7

Go back to Potassium Binding Sites List in 5dd7
Potassium binding site 3 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate


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 and Thiamine-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:18.1
occ:1.00
 OD1 A:ASP118 2.7 17.9 1.0
O A:THR119 2.8 19.2 1.0
OE2 A:GLU3 2.9 19.7 1.0
O1 B:TPS401 3.0 18.7 1.0
O A:HOH572 3.0 15.7 1.0
O2 B:TPS401 3.0 19.4 1.0
O1G A:ANP401 3.0 15.8 1.0
O A:HOH522 3.2 17.5 1.0
P1 B:TPS401 3.3 19.6 1.0
CG A:ASP118 3.6 15.9 1.0
O3 B:TPS401 3.6 19.1 1.0
MG A:MG403 3.7 16.7 1.0
O2A A:ANP401 3.7 16.6 1.0
CD A:GLU3 3.7 20.9 1.0
OD2 A:ASP118 3.8 19.9 1.0
C A:THR119 3.8 22.0 1.0
CD2 B:HIS303 3.9 24.2 1.0
MG B:MG406 3.9 16.9 1.0
N A:THR119 4.0 14.5 1.0
CG2 A:THR120 4.0 17.2 1.0
O B:HOH514 4.1 17.0 1.0
NE2 B:HIS303 4.1 23.4 1.0
OE1 A:GLU3 4.2 22.5 1.0
PG A:ANP401 4.3 17.6 1.0
O A:HOH592 4.4 16.2 1.0
O3G A:ANP401 4.5 19.7 1.0
CA A:THR119 4.5 17.9 1.0
O1A A:ANP401 4.7 18.7 1.0
OD1 B:ASP43 4.7 16.0 1.0
N A:THR120 4.8 16.7 1.0
CG A:GLU3 4.8 20.5 1.0
PA A:ANP401 4.8 16.2 1.0
O7 B:TPS401 4.9 20.5 1.0
CB A:ASP118 4.9 15.0 1.0
C A:ASP118 4.9 14.8 1.0
CA A:THR120 5.0 16.7 1.0
CA A:ASP118 5.0 16.2 1.0

Potassium binding site 4 out of 6 in 5dd7

Go back to Potassium Binding Sites List in 5dd7
Potassium binding site 4 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate


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 and Thiamine-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:17.7
occ:1.00
 O1B A:ANP401 2.7 15.8 1.0
O A:ASP26 2.7 16.2 1.0
O B:HOH657 2.7 14.3 1.0
O A:HOH528 2.8 12.2 1.0
O B:HOH620 2.9 16.6 1.0
OD2 B:ASP71 2.9 16.8 1.0
CG B:ASP71 3.3 21.2 1.0
PB A:ANP401 3.7 15.9 1.0
CB B:CYS41 3.7 12.8 1.0
C A:ASP26 3.9 16.3 1.0
MG B:MG402 3.9 16.8 1.0
O2B A:ANP401 3.9 16.9 1.0
OD1 B:ASP71 3.9 17.7 1.0
CB B:ASP71 3.9 16.7 1.0
O3A A:ANP401 4.0 16.4 1.0
OD2 B:ASP43 4.0 16.9 1.0
O B:ALA42 4.0 16.1 1.0
MG A:MG403 4.1 16.7 1.0
CG B:ASP43 4.3 17.9 1.0
OD1 B:ASP43 4.3 16.0 1.0
N B:ALA42 4.4 12.7 1.0
CA A:ASP26 4.5 15.0 1.0
O A:GLY117 4.6 15.8 1.0
CA B:CYS41 4.6 15.4 1.0
C B:ALA42 4.7 12.9 1.0
O2A A:ANP401 4.7 16.6 1.0
SG B:CYS41 4.8 17.5 1.0
O2' A:ANP401 4.8 14.8 1.0
O B:HOH647 4.9 16.8 1.0
N A:SER27 5.0 15.7 1.0
C B:CYS41 5.0 17.6 1.0
PA A:ANP401 5.0 16.2 1.0
C2' A:ANP401 5.0 15.0 1.0
MG B:MG403 5.0 14.6 1.0

Potassium binding site 5 out of 6 in 5dd7

Go back to Potassium Binding Sites List in 5dd7
Potassium binding site 5 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K407

b:17.8
occ:1.00
 O B:MET196 2.6 16.8 1.0
O B:ALA74 2.7 17.3 1.0
OD1 A:ASP25 2.7 21.3 1.0
OD2 A:ASP26 2.8 19.5 1.0
O B:VAL141 2.9 23.9 1.0
SD B:MET75 3.3 18.3 1.0
C B:ALA74 3.6 19.1 1.0
C B:MET196 3.6 15.7 1.0
CG A:ASP25 3.8 25.3 1.0
CG A:ASP26 3.9 20.4 1.0
C B:VAL141 4.0 23.2 1.0
N B:ARG143 4.0 22.0 1.0
C B:LEU142 4.1 26.3 1.0
CG B:ARG143 4.1 18.3 1.0
CE B:MET75 4.2 18.8 1.0
CA B:LEU142 4.2 20.6 1.0
OD2 A:ASP25 4.2 24.9 1.0
N B:MET75 4.2 18.6 1.0
CA B:MET75 4.3 18.9 1.0
CB A:ASP26 4.3 15.7 1.0
CB B:ALA74 4.3 18.0 1.0
CA B:MET196 4.4 18.9 1.0
CB B:MET196 4.5 16.7 1.0
N B:ILE197 4.5 19.1 1.0
N B:LEU142 4.5 20.3 1.0
CA B:ALA74 4.5 18.7 1.0
N A:ASP26 4.5 16.0 1.0
CA B:ILE197 4.5 20.8 1.0
N B:MET196 4.6 19.1 1.0
O B:LEU142 4.6 30.4 1.0
CG B:MET75 4.7 16.9 1.0
CA B:ARG143 4.7 21.4 1.0
NE B:ARG143 4.9 17.2 1.0
OD1 A:ASP26 5.0 18.7 1.0
CB B:MET75 5.0 17.4 1.0

Potassium binding site 6 out of 6 in 5dd7

Go back to Potassium Binding Sites List in 5dd7
Potassium binding site 6 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K408

b:16.3
occ:1.00
 OD1 B:ASP118 2.7 14.7 1.0
OE2 B:GLU3 2.8 17.6 1.0
O B:THR119 2.8 17.4 1.0
O3 A:TPS408 2.9 14.8 1.0
O B:HOH571 3.0 14.6 1.0
O2G B:ANP405 3.0 17.7 1.0
O2 A:TPS408 3.1 15.9 1.0
O B:HOH511 3.2 15.5 1.0
P1 A:TPS408 3.3 15.7 1.0
O1 A:TPS408 3.5 16.8 1.0
CG B:ASP118 3.6 13.7 1.0
O1A B:ANP405 3.7 17.0 1.0
MG A:MG411 3.7 13.0 1.0
CD B:GLU3 3.8 18.9 1.0
OD2 B:ASP118 3.8 16.7 1.0
MG A:MG402 3.9 14.3 1.0
C B:THR119 3.9 18.2 1.0
CD2 A:HIS303 3.9 19.4 1.0
N B:THR119 4.0 13.1 1.0
O A:HOH509 4.1 13.7 1.0
NE2 A:HIS303 4.1 18.6 1.0
CG2 B:THR120 4.1 19.8 1.0
PG B:ANP405 4.3 14.5 1.0
OE1 B:GLU3 4.3 21.0 1.0
O B:HOH562 4.4 16.1 1.0
O3G B:ANP405 4.5 14.4 1.0
CA B:THR119 4.6 18.2 1.0
OD1 A:ASP43 4.7 16.6 1.0
O2A B:ANP405 4.7 16.2 1.0
PA B:ANP405 4.8 14.6 1.0
N B:THR120 4.8 15.3 1.0
O7 A:TPS408 4.9 17.8 1.0
CG B:GLU3 4.9 20.0 1.0
CB B:ASP118 4.9 16.3 1.0
C B:ASP118 5.0 16.2 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: Sun Dec 13 23:55:51 2020

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