Atomistry » Magnesium » PDB 5dar-5djg » 5dd7
Atomistry »
  Magnesium »
    PDB 5dar-5djg »
      5dd7 »

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

Go back to Magnesium Binding Sites List in 5dd7
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

Go back to Magnesium Binding Sites List in 5dd7
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

Go back to Magnesium Binding Sites List in 5dd7
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

Go back to Magnesium Binding Sites List in 5dd7
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

Go back to Magnesium Binding Sites List in 5dd7
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

Go back to Magnesium Binding Sites List in 5dd7
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

Go back to Magnesium Binding Sites List in 5dd7
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: Mon Dec 14 20:11:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy