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Magnesium 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:

Potassium (K) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp and Thiamine-Monophosphate, PDB code: 5dd7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5dd7

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Magnesium binding site 1 out of 8 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 Magnesium with other atoms in the Mg 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:Mg402

b:14.3
occ:1.00
 O3G B:ANP405 2.0 14.4 1.0
O3 A:TPS408 2.0 14.8 1.0
O B:HOH511 2.1 15.5 1.0
OD1 A:ASP201 2.1 14.7 1.0
O B:HOH562 2.1 16.1 1.0
OD2 A:ASP201 2.2 15.2 1.0
CG A:ASP201 2.5 16.8 1.0
PG B:ANP405 3.2 14.5 1.0
P1 A:TPS408 3.4 15.7 1.0
O2G B:ANP405 3.5 17.7 1.0
K B:K408 3.9 16.3 1.0
O1 A:TPS408 4.0 16.8 1.0
CB A:ASP201 4.0 15.0 1.0
C7 A:TPS408 4.0 18.1 1.0
N3B B:ANP405 4.0 11.7 1.0
OE2 B:GLU3 4.1 17.6 1.0
O7 A:TPS408 4.1 17.8 1.0
C6 A:TPS408 4.2 21.3 1.0
OE1 B:GLU3 4.3 21.0 1.0
OG A:SER200 4.4 15.0 1.0
O A:TYR301 4.4 20.9 1.0
O A:HOH558 4.4 19.0 1.0
O1G B:ANP405 4.5 12.9 1.0
O2A B:ANP405 4.5 16.2 1.0
O2 A:TPS408 4.5 15.9 1.0
CD B:GLU3 4.6 18.9 1.0
CZ B:PHE4 4.7 23.9 1.0
O A:HOH544 4.8 19.0 1.0
CA A:ASP201 4.8 15.1 1.0
CB A:SER200 5.0 11.5 1.0
N A:ASP201 5.0 14.5 1.0
CD1 A:TYR301 5.0 24.7 1.0

Magnesium binding site 2 out of 8 in 5dd7

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Magnesium binding site 2 out of 8 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 Magnesium with other atoms in the Mg 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:Mg403

b:16.7
occ:1.00
 OD1 B:ASP43 2.0 16.0 1.0
OD1 A:ASP118 2.1 17.9 1.0
O2A A:ANP401 2.1 16.6 1.0
O1G A:ANP401 2.1 15.8 1.0
O A:HOH528 2.2 12.2 1.0
O1B A:ANP401 2.5 15.8 1.0
CG A:ASP118 3.0 15.9 1.0
CG B:ASP43 3.1 17.9 1.0
PG A:ANP401 3.1 17.6 1.0
PA A:ANP401 3.3 16.2 1.0
PB A:ANP401 3.4 15.9 1.0
O3A A:ANP401 3.5 16.4 1.0
OD2 B:ASP43 3.5 16.9 1.0
O2G A:ANP401 3.6 17.3 1.0
N3B A:ANP401 3.6 17.6 1.0
K A:K406 3.7 18.1 1.0
MG B:MG402 3.8 16.8 1.0
CB A:ASP118 3.8 15.0 1.0
OD2 A:ASP118 3.9 19.9 1.0
K B:K404 4.1 17.7 1.0
O A:HOH572 4.1 15.7 1.0
O3 B:TPS401 4.2 19.1 1.0
O1A A:ANP401 4.2 18.7 1.0
O B:ALA42 4.3 16.1 1.0
CA A:ASP118 4.3 16.2 1.0
O B:HOH514 4.4 17.0 1.0
O5' A:ANP401 4.4 15.2 1.0
O A:GLY117 4.4 15.8 1.0
CB B:ASP43 4.4 14.8 1.0
O A:HOH522 4.5 17.5 1.0
O3G A:ANP401 4.5 19.7 1.0
CA B:ASP43 4.7 13.9 1.0
O2B A:ANP401 4.8 16.9 1.0
OD2 B:ASP71 4.9 16.8 1.0

Magnesium binding site 3 out of 8 in 5dd7

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Magnesium binding site 3 out of 8 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 Magnesium with other atoms in the Mg 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:Mg409

b:13.7
occ:1.00
 O1G B:ANP405 2.0 12.9 1.0
O A:HOH582 2.0 15.5 1.0
OD2 A:ASP43 2.0 16.6 1.0
OD2 A:ASP71 2.1 13.7 1.0
O B:HOH572 2.2 12.7 1.0
O2B B:ANP405 2.3 16.7 1.0
CG A:ASP43 3.1 15.3 1.0
CG A:ASP71 3.1 11.6 1.0
PG B:ANP405 3.1 14.5 1.0
PB B:ANP405 3.2 14.4 1.0
N3B B:ANP405 3.4 11.7 1.0
OD1 A:ASP71 3.4 12.7 1.0
OD1 A:ASP43 3.4 16.6 1.0
O A:HOH533 3.6 16.1 1.0
O1B B:ANP405 3.6 13.4 1.0
O2G B:ANP405 3.7 17.7 1.0
MG A:MG410 3.8 12.6 1.0
MG A:MG411 3.8 13.0 1.0
O A:HOH584 3.9 15.7 1.0
K A:K404 3.9 14.6 1.0
O A:VAL67 4.2 12.7 1.0
OD2 A:ASP198 4.3 13.2 1.0
CB A:ASP43 4.4 16.5 1.0
CB A:ASP71 4.4 13.2 1.0
O3G B:ANP405 4.4 14.4 1.0
OG A:SER200 4.5 15.0 1.0
O A:HOH549 4.6 11.9 1.0
O3A B:ANP405 4.6 13.3 1.0
CB A:SER200 4.7 11.5 1.0
O1 A:TPS408 4.8 16.8 1.0
OD1 A:ASP198 4.9 13.3 1.0
O A:HOH626 4.9 14.3 1.0

Magnesium binding site 4 out of 8 in 5dd7

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Magnesium binding site 4 out of 8 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 Magnesium with other atoms in the Mg 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
A:Mg410

b:12.6
occ:1.00
 OD1 A:ASP71 2.0 12.7 1.0
O1B B:ANP405 2.0 13.4 1.0
OD1 A:ASP198 2.1 13.3 1.0
OD1 B:ASP26 2.1 14.7 1.0
O A:HOH626 2.1 14.3 1.0
O B:HOH572 2.2 12.7 1.0
CG A:ASP198 3.1 14.0 1.0
CG A:ASP71 3.1 11.6 1.0
CG B:ASP26 3.2 16.0 1.0
PB B:ANP405 3.2 14.4 1.0
OD2 A:ASP198 3.4 13.2 1.0
OD2 A:ASP71 3.6 13.7 1.0
CB B:ASP26 3.6 12.8 1.0
NH2 A:ARG143 3.7 14.8 1.0
MG A:MG409 3.8 13.7 1.0
N3B B:ANP405 3.8 11.7 1.0
O2B B:ANP405 3.9 16.7 1.0
CA B:ASP26 4.2 12.6 1.0
O A:ASP198 4.2 14.6 1.0
OD2 B:ASP26 4.3 14.6 1.0
N A:ASP198 4.3 11.7 1.0
CB A:ASP71 4.4 13.2 1.0
CB A:ASP198 4.4 13.7 1.0
O3A B:ANP405 4.5 13.3 1.0
OG A:SER200 4.5 15.0 1.0
O A:HOH558 4.5 19.0 1.0
O1G B:ANP405 4.5 12.9 1.0
CG1 A:ILE197 4.6 13.9 1.0
CA A:ASP71 4.7 13.1 1.0
O A:HOH582 4.7 15.5 1.0
CA A:ASP198 4.7 11.4 1.0
C A:ASP198 4.8 12.5 1.0
PG B:ANP405 4.9 14.5 1.0
CZ A:ARG143 4.9 15.2 1.0
O B:ASP26 4.9 14.9 1.0
CB A:ALA74 5.0 12.2 1.0
K A:K404 5.0 14.6 1.0

Magnesium binding site 5 out of 8 in 5dd7

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Magnesium binding site 5 out of 8 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 Magnesium with other atoms in the Mg 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
A:Mg411

b:13.0
occ:1.00
 OD1 A:ASP43 2.0 16.6 1.0
O1A B:ANP405 2.0 17.0 1.0
O A:HOH549 2.1 11.9 1.0
O2G B:ANP405 2.1 17.7 1.0
OD1 B:ASP118 2.1 14.7 1.0
O2B B:ANP405 2.4 16.7 1.0
CG B:ASP118 3.1 13.7 1.0
CG A:ASP43 3.1 15.3 1.0
PG B:ANP405 3.2 14.5 1.0
PA B:ANP405 3.3 14.6 1.0
PB B:ANP405 3.3 14.4 1.0
O3A B:ANP405 3.5 13.3 1.0
OD2 A:ASP43 3.5 16.6 1.0
N3B B:ANP405 3.6 11.7 1.0
O1G B:ANP405 3.7 12.9 1.0
K B:K408 3.7 16.3 1.0
MG A:MG409 3.8 13.7 1.0
CB B:ASP118 3.8 16.3 1.0
OD2 B:ASP118 3.9 16.7 1.0
K A:K404 4.0 14.6 1.0
O B:HOH571 4.1 14.6 1.0
O2A B:ANP405 4.2 16.2 1.0
O A:ALA42 4.2 14.5 1.0
O1 A:TPS408 4.2 16.8 1.0
CA B:ASP118 4.3 13.4 1.0
O B:GLY117 4.3 15.5 1.0
O5' B:ANP405 4.3 13.3 1.0
CB A:ASP43 4.4 16.5 1.0
O A:HOH509 4.5 13.7 1.0
O3G B:ANP405 4.6 14.4 1.0
O B:HOH511 4.6 15.5 1.0
CA A:ASP43 4.6 13.5 1.0
O1B B:ANP405 4.7 13.4 1.0
OD2 A:ASP71 4.9 13.7 1.0
O A:HOH584 5.0 15.7 1.0

Magnesium binding site 6 out of 8 in 5dd7

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Magnesium binding site 6 out of 8 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 Magnesium with other atoms in the Mg 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:Mg402

b:16.8
occ:1.00
 O2G A:ANP401 2.0 17.3 1.0
OD2 B:ASP43 2.0 16.9 1.0
OD2 B:ASP71 2.1 16.8 1.0
O B:HOH577 2.1 16.7 1.0
O1B A:ANP401 2.3 15.8 1.0
O B:HOH553 2.3 15.5 1.0
CG B:ASP71 3.1 21.2 1.0
CG B:ASP43 3.1 17.9 1.0
PG A:ANP401 3.2 17.6 1.0
PB A:ANP401 3.2 15.9 1.0
N3B A:ANP401 3.4 17.6 1.0
OD1 B:ASP71 3.4 17.7 1.0
OD1 B:ASP43 3.5 16.0 1.0
O2B A:ANP401 3.5 16.9 1.0
O B:HOH539 3.6 20.1 1.0
O1G A:ANP401 3.7 15.8 1.0
MG B:MG403 3.8 14.6 1.0
MG A:MG403 3.8 16.7 1.0
K B:K404 3.9 17.7 1.0
O B:HOH620 4.0 16.6 1.0
O B:VAL67 4.2 15.9 1.0
OD2 B:ASP198 4.3 18.9 1.0
CB B:ASP71 4.4 16.7 1.0
CB B:ASP43 4.4 14.8 1.0
OG B:SER200 4.5 20.1 1.0
O3G A:ANP401 4.5 19.7 1.0
O3A A:ANP401 4.6 16.4 1.0
O A:HOH528 4.7 12.2 1.0
CB B:SER200 4.7 18.6 1.0
O3 B:TPS401 4.9 19.1 1.0
O B:HOH607 4.9 16.5 1.0
OD1 B:ASP198 4.9 15.7 1.0

Magnesium binding site 7 out of 8 in 5dd7

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Magnesium binding site 7 out of 8 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 Magnesium with other atoms in the Mg binding site number 7 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:Mg403

b:14.6
occ:1.00
 O2B A:ANP401 2.0 16.9 1.0
OD1 B:ASP71 2.0 17.7 1.0
OD1 B:ASP198 2.0 15.7 1.0
O B:HOH607 2.1 16.5 1.0
OD1 A:ASP26 2.1 18.7 1.0
O B:HOH553 2.1 15.5 1.0
CG B:ASP198 3.0 18.9 1.0
CG B:ASP71 3.1 21.2 1.0
CG A:ASP26 3.2 20.4 1.0
PB A:ANP401 3.2 15.9 1.0
OD2 B:ASP198 3.4 18.9 1.0
OD2 B:ASP71 3.6 16.8 1.0
CB A:ASP26 3.7 15.7 1.0
NH2 B:ARG143 3.7 17.4 1.0
MG B:MG402 3.8 16.8 1.0
N3B A:ANP401 3.8 17.6 1.0
O1B A:ANP401 3.8 15.8 1.0
O B:ASP198 4.1 16.7 1.0
CA A:ASP26 4.2 15.0 1.0
N B:ASP198 4.3 15.4 1.0
OD2 A:ASP26 4.3 19.5 1.0
CB B:ASP198 4.4 15.6 1.0
CB B:ASP71 4.4 16.7 1.0
OG B:SER200 4.4 20.1 1.0
O3A A:ANP401 4.5 16.4 1.0
CG1 B:ILE197 4.5 19.1 1.0
O2G A:ANP401 4.6 17.3 1.0
O B:HOH541 4.6 19.2 1.0
CA B:ASP71 4.7 16.6 1.0
CA B:ASP198 4.7 14.1 1.0
O B:HOH577 4.7 16.7 1.0
C B:ASP198 4.8 16.2 1.0
PG A:ANP401 4.9 17.6 1.0
CZ B:ARG143 4.9 18.8 1.0
O A:ASP26 4.9 16.2 1.0
CB B:ALA74 4.9 18.0 1.0
K B:K404 5.0 17.7 1.0

Magnesium binding site 8 out of 8 in 5dd7

Go back to Magnesium Binding Sites List in 5dd7
Magnesium binding site 8 out of 8 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 Magnesium with other atoms in the Mg binding site number 8 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:Mg406

b:16.9
occ:1.00
 O1 B:TPS401 2.0 18.7 1.0
O3G A:ANP401 2.0 19.7 1.0
O A:HOH522 2.1 17.5 1.0
O A:HOH592 2.1 16.2 1.0
OD1 B:ASP201 2.1 15.9 1.0
OD2 B:ASP201 2.2 18.5 1.0
CG B:ASP201 2.5 18.0 1.0
PG A:ANP401 3.2 17.6 1.0
P1 B:TPS401 3.4 19.6 1.0
O1G A:ANP401 3.4 15.8 1.0
K A:K406 3.9 18.1 1.0
O3 B:TPS401 3.9 19.1 1.0
CB B:ASP201 4.0 17.1 1.0
C7 B:TPS401 4.0 20.9 1.0
N3B A:ANP401 4.0 17.6 1.0
OE2 A:GLU3 4.0 19.7 1.0
O7 B:TPS401 4.1 20.5 1.0
O B:HOH541 4.3 19.2 1.0
C6 B:TPS401 4.3 20.9 1.0
OE1 A:GLU3 4.4 22.5 1.0
O B:TYR301 4.4 25.3 1.0
OG B:SER200 4.4 20.1 1.0
O2G A:ANP401 4.4 17.3 1.0
O2 B:TPS401 4.5 19.4 1.0
O1A A:ANP401 4.5 18.7 1.0
CD A:GLU3 4.6 20.9 1.0
CZ A:PHE4 4.8 25.5 1.0
O B:HOH536 4.8 19.8 1.0
CA B:ASP201 4.8 19.0 1.0
N B:ASP201 4.9 16.0 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 Sep 29 02:41:23 2024

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