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Magnesium 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:

Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp, PDB code: 5cc8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5cc8

Go back to Magnesium Binding Sites List in 5cc8
Magnesium binding site 1 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:13.9
occ:1.00
 O1A A:ANP413 2.0 14.6 1.0
OD1 B:ASP118 2.1 12.6 1.0
O2G A:ANP413 2.1 15.4 1.0
OD1 A:ASP43 2.1 15.5 1.0
O A:HOH532 2.2 11.0 1.0
O2B A:ANP413 2.5 16.4 1.0
CG B:ASP118 3.0 16.5 1.0
PG A:ANP413 3.2 15.0 1.0
CG A:ASP43 3.2 15.8 1.0
PA A:ANP413 3.2 14.8 1.0
PB A:ANP413 3.3 14.4 1.0
O3A A:ANP413 3.5 13.5 1.0
N3B A:ANP413 3.6 11.9 1.0
OD2 A:ASP43 3.7 15.4 1.0
O1G A:ANP413 3.7 12.5 1.0
O B:HOH629 3.8 25.2 1.0
CB B:ASP118 3.8 13.5 1.0
OD2 B:ASP118 3.8 20.6 1.0
O B:HOH636 3.9 23.2 1.0
MG A:MG404 3.9 13.2 1.0
O A:HOH582 4.0 14.6 1.0
K A:K408 4.1 20.7 1.0
O A:ALA42 4.2 13.1 1.0
O2A A:ANP413 4.3 15.7 1.0
O5' A:ANP413 4.3 14.6 1.0
CA B:ASP118 4.3 10.5 1.0
O B:GLY117 4.4 13.9 1.0
CB A:ASP43 4.5 10.9 1.0
O A:HOH704 4.5 20.8 0.6
O3G A:ANP413 4.6 17.1 1.0
CA A:ASP43 4.7 10.2 1.0
O1B A:ANP413 4.8 13.2 1.0

Magnesium binding site 2 out of 6 in 5cc8

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Magnesium binding site 2 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:13.2
occ:1.00
 OD2 A:ASP71 2.0 12.8 1.0
OD2 A:ASP43 2.1 15.4 1.0
O1G A:ANP413 2.1 12.5 1.0
O A:HOH557 2.1 13.3 1.0
O A:HOH563 2.3 10.8 1.0
O2B A:ANP413 2.3 16.4 1.0
CG A:ASP71 3.0 12.7 1.0
CG A:ASP43 3.1 15.8 1.0
PB A:ANP413 3.1 14.4 1.0
PG A:ANP413 3.2 15.0 1.0
N3B A:ANP413 3.4 11.9 1.0
OD1 A:ASP71 3.4 11.7 1.0
OD1 A:ASP43 3.5 15.5 1.0
O1B A:ANP413 3.5 13.2 1.0
O A:HOH536 3.6 18.0 1.0
MG A:MG405 3.7 10.1 1.0
O2G A:ANP413 3.8 15.4 1.0
MG A:MG402 3.9 13.9 1.0
K A:K408 3.9 20.7 1.0
O A:HOH616 4.0 14.6 1.0
O A:VAL67 4.2 11.2 1.0
OD2 A:ASP198 4.2 12.1 1.0
OG A:SER200 4.3 14.7 1.0
CB A:ASP71 4.4 9.8 1.0
CB A:ASP43 4.4 10.9 1.0
O3G A:ANP413 4.5 17.1 1.0
O3A A:ANP413 4.6 13.5 1.0
CB A:SER200 4.6 14.9 1.0
O A:HOH532 4.7 11.0 1.0
OD1 A:ASP198 4.8 12.7 1.0
O A:HOH569 4.9 11.4 1.0
CG A:ASP198 5.0 11.4 1.0

Magnesium binding site 3 out of 6 in 5cc8

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Magnesium binding site 3 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:10.1
occ:1.00
 O1B A:ANP413 2.0 13.2 1.0
OD1 A:ASP71 2.0 11.7 1.0
OD1 B:ASP26 2.1 12.1 1.0
OD1 A:ASP198 2.1 12.7 1.0
O A:HOH569 2.1 11.4 1.0
O A:HOH563 2.2 10.8 1.0
CG A:ASP198 3.1 11.4 1.0
CG A:ASP71 3.1 12.7 1.0
CG B:ASP26 3.2 12.2 1.0
PB A:ANP413 3.3 14.4 1.0
OD2 A:ASP198 3.4 12.1 1.0
OD2 A:ASP71 3.6 12.8 1.0
CB B:ASP26 3.7 10.5 1.0
NH2 A:ARG143 3.7 12.4 1.0
MG A:MG404 3.7 13.2 1.0
O2B A:ANP413 3.8 16.4 1.0
N3B A:ANP413 3.9 11.9 1.0
O A:ASP198 4.2 12.5 1.0
CA B:ASP26 4.2 10.4 1.0
OD2 B:ASP26 4.3 14.4 1.0
OG A:SER200 4.3 14.7 1.0
N A:ASP198 4.3 10.6 1.0
CB A:ASP71 4.4 9.8 1.0
CB A:ASP198 4.4 11.7 1.0
O3A A:ANP413 4.4 13.5 1.0
O A:HOH589 4.4 19.1 1.0
CG1 A:ILE197 4.6 8.2 1.0
O1G A:ANP413 4.7 12.5 1.0
CA A:ASP71 4.7 10.0 1.0
O A:HOH557 4.7 13.3 1.0
CA A:ASP198 4.8 9.7 1.0
C A:ASP198 4.8 9.4 1.0
CZ A:ARG143 4.9 10.3 1.0
O B:ASP26 4.9 11.6 1.0
K A:K408 5.0 20.7 1.0
PG A:ANP413 5.0 15.0 1.0

Magnesium binding site 4 out of 6 in 5cc8

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Magnesium binding site 4 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:17.1
occ:1.00
 O2A A:ANP401 2.0 15.2 1.0
OD1 B:ASP43 2.1 14.3 1.0
OD1 A:ASP118 2.1 16.1 1.0
O B:HOH532 2.1 11.7 1.0
O1G A:ANP401 2.2 16.1 1.0
O2B A:ANP401 2.6 16.4 1.0
CG A:ASP118 3.1 17.7 1.0
PG A:ANP401 3.2 15.5 1.0
CG B:ASP43 3.2 16.2 1.0
PA A:ANP401 3.2 17.1 1.0
PB A:ANP401 3.3 15.4 1.0
O3A A:ANP401 3.4 15.8 1.0
N3B A:ANP401 3.5 14.2 1.0
O2G A:ANP401 3.6 14.9 1.0
OD2 B:ASP43 3.7 16.0 1.0
O A:HOH641 3.7 25.8 1.0
MG B:MG401 3.8 14.1 1.0
CB A:ASP118 3.9 12.9 1.0
OD2 A:ASP118 3.9 17.4 1.0
O A:HOH685 4.0 13.3 0.4
O A:HOH601 4.1 13.1 1.0
K A:K412 4.1 26.6 1.0
O B:ALA42 4.2 13.6 1.0
O1A A:ANP401 4.2 19.2 1.0
O5' A:ANP401 4.3 16.5 1.0
CA A:ASP118 4.4 11.1 1.0
O A:HOH685 4.4 17.7 0.6
O A:GLY117 4.4 13.5 1.0
CB B:ASP43 4.5 11.6 1.0
O3G A:ANP401 4.5 17.7 1.0
CA B:ASP43 4.7 10.8 1.0
O1B A:ANP401 4.8 15.2 1.0
OD2 B:ASP71 5.0 12.9 1.0

Magnesium binding site 5 out of 6 in 5cc8

Go back to Magnesium Binding Sites List in 5cc8
Magnesium binding site 5 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:13.8
occ:1.00
 O1B A:ANP401 2.0 15.2 1.0
OD1 B:ASP71 2.0 14.2 1.0
OD1 B:ASP198 2.0 17.1 1.0
OD1 A:ASP26 2.1 14.5 1.0
O B:HOH559 2.1 14.3 1.0
O B:HOH571 2.2 14.7 1.0
CG B:ASP198 3.1 18.4 1.0
CG B:ASP71 3.1 13.4 1.0
CG A:ASP26 3.2 14.6 1.0
PB A:ANP401 3.3 15.4 1.0
OD2 B:ASP198 3.4 14.8 1.0
OD2 B:ASP71 3.6 12.9 1.0
CB A:ASP26 3.7 13.3 1.0
NH2 B:ARG143 3.7 14.4 1.0
MG B:MG401 3.8 14.1 1.0
O2B A:ANP401 3.8 16.4 1.0
N3B A:ANP401 3.9 14.2 1.0
O B:ASP198 4.1 14.8 1.0
CA A:ASP26 4.2 12.9 1.0
OD2 A:ASP26 4.2 18.7 1.0
OG B:SER200 4.3 15.9 1.0
N B:ASP198 4.3 15.2 1.0
CB B:ASP71 4.4 11.5 1.0
CB B:ASP198 4.4 17.7 1.0
O B:HOH563 4.4 16.3 1.0
O3A A:ANP401 4.5 15.8 1.0
CG1 B:ILE197 4.6 13.7 1.0
CA B:ASP71 4.6 11.2 1.0
O2G A:ANP401 4.7 14.9 1.0
CA B:ASP198 4.7 13.3 1.0
O B:HOH519 4.8 12.8 1.0
C B:ASP198 4.8 13.5 1.0
CZ B:ARG143 4.9 13.8 1.0
O A:ASP26 5.0 14.5 1.0
K A:K412 5.0 26.6 1.0

Magnesium binding site 6 out of 6 in 5cc8

Go back to Magnesium Binding Sites List in 5cc8
Magnesium binding site 6 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Amppnp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:14.1
occ:1.00
 O2G A:ANP401 2.0 14.9 1.0
OD2 B:ASP43 2.1 16.0 1.0
OD2 B:ASP71 2.1 12.9 1.0
O B:HOH519 2.1 12.8 1.0
O B:HOH571 2.3 14.7 1.0
O2B A:ANP401 2.3 16.4 1.0
CG B:ASP43 3.1 16.2 1.0
CG B:ASP71 3.1 13.4 1.0
PB A:ANP401 3.1 15.4 1.0
PG A:ANP401 3.1 15.5 1.0
N3B A:ANP401 3.4 14.2 1.0
OD1 B:ASP43 3.5 14.3 1.0
OD1 B:ASP71 3.5 14.2 1.0
O A:HOH543 3.6 18.5 1.0
O1B A:ANP401 3.6 15.2 1.0
O1G A:ANP401 3.8 16.1 1.0
MG A:MG410 3.8 13.8 1.0
MG A:MG406 3.8 17.1 1.0
K A:K412 4.0 26.6 1.0
O B:HOH603 4.0 12.6 1.0
O B:VAL67 4.1 11.7 1.0
OG B:SER200 4.3 15.9 1.0
OD2 B:ASP198 4.3 14.8 1.0
CB B:ASP43 4.4 11.6 1.0
CB B:ASP71 4.4 11.5 1.0
O3G A:ANP401 4.5 17.7 1.0
CB B:SER200 4.6 16.4 1.0
O3A A:ANP401 4.6 15.8 1.0
O B:HOH532 4.6 11.7 1.0
OD1 B:ASP198 4.8 17.1 1.0
O B:HOH559 4.9 14.3 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 02:03:27 2024

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