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Sodium in PDB 6mfm: Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form

Enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form

All present enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form:
2.7.4.16;

Protein crystallography data

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form, PDB code: 6mfm 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) 41.34 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.150, 93.920, 73.700, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.2

Other elements in 6mfm:

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form (pdb code 6mfm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form, PDB code: 6mfm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6mfm

Go back to Sodium Binding Sites List in 6mfm
Sodium binding site 1 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:26.2
occ:1.00
 O2A B:TPP404 2.4 22.8 1.0
O1B B:TPP404 2.4 23.4 1.0
O A:HOH613 2.5 27.3 1.0
O B:HOH610 2.6 35.7 1.0
OD2 A:ASP118 2.6 28.5 1.0
OD1 A:ASP118 2.8 24.9 1.0
O3A B:TPP404 3.0 23.9 1.0
CG A:ASP118 3.1 23.6 1.0
PA B:TPP404 3.2 25.1 1.0
PB B:TPP404 3.4 25.7 1.0
MG A:MG408 3.4 24.4 1.0
CG2 A:THR120 3.6 30.1 1.0
OD1 B:ASP43 3.7 25.3 1.0
O A:HOH507 3.9 27.1 1.0
O B:THR44 4.0 22.1 1.0
NE2 B:HIS50 4.0 19.6 1.0
O1A B:TPP404 4.1 29.2 1.0
CG B:ASP43 4.1 30.1 1.0
NE2 B:HIS303 4.3 50.6 1.0
O2B B:TPP404 4.3 19.9 1.0
N B:THR44 4.4 22.5 1.0
O2A A:ADP406 4.5 31.7 1.0
O7 B:TPP404 4.5 24.9 1.0
CB B:ASP43 4.5 20.8 1.0
O3B B:TPP404 4.5 24.1 1.0
O B:HOH560 4.6 27.8 1.0
CB A:ASP118 4.6 15.3 1.0
OD2 B:ASP43 4.7 27.2 1.0
CA B:ASP43 4.7 16.4 1.0
CD2 B:HIS50 4.8 22.1 1.0
O A:THR119 4.8 25.3 1.0
CE1 B:HIS50 4.9 19.2 1.0
MG B:MG406 4.9 33.5 1.0
O A:HOH567 5.0 19.2 1.0
C B:THR44 5.0 24.7 1.0

Sodium binding site 2 out of 4 in 6mfm

Go back to Sodium Binding Sites List in 6mfm
Sodium binding site 2 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:28.8
occ:1.00
 O B:HOH569 2.3 22.1 1.0
O B:HOH571 2.3 16.8 1.0
O A:HOH588 2.4 14.4 1.0
O A:ALA42 2.6 15.5 1.0
O B:HOH636 2.6 13.8 1.0
OD1 A:ASP43 2.8 21.4 1.0
C A:ALA42 3.2 13.5 1.0
CG A:ASP43 3.3 19.6 1.0
N A:ALA42 3.5 11.9 1.0
O1B B:ADP401 3.5 16.4 1.0
MG A:MG405 3.5 20.5 1.0
OD2 A:ASP71 3.6 14.4 1.0
OD2 A:ASP43 3.7 18.0 1.0
O B:GLY117 3.9 20.5 1.0
N A:ASP43 3.9 16.6 1.0
CB A:CYS41 3.9 13.0 1.0
CA A:ALA42 4.0 14.0 1.0
CB A:ASP43 4.2 17.5 1.0
CA A:ASP43 4.2 14.7 1.0
MG A:MG402 4.3 16.4 1.0
O B:ASP26 4.3 17.1 1.0
C A:CYS41 4.4 16.6 1.0
CG A:ASP71 4.4 15.2 1.0
CA A:CYS41 4.5 13.6 1.0
OD2 B:ASP118 4.5 16.6 1.0
PB B:ADP401 4.6 30.5 1.0
OD1 A:ASN68 4.7 13.7 1.0
O3A B:ADP401 4.7 27.5 1.0
C B:GLY117 4.8 18.0 1.0
CG B:ASP118 4.9 21.7 1.0
CB B:ASP118 4.9 16.2 1.0
CB A:ASP71 4.9 13.6 1.0
SG A:CYS41 4.9 15.8 1.0
O2B B:ADP401 4.9 17.5 1.0
O1A B:ADP401 4.9 22.1 1.0
O2' B:ADP401 4.9 17.2 1.0

Sodium binding site 3 out of 4 in 6mfm

Go back to Sodium Binding Sites List in 6mfm
Sodium binding site 3 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:24.2
occ:1.00
 O1A A:TPP401 2.3 17.9 1.0
O B:HOH587 2.4 18.7 1.0
O A:HOH554 2.5 31.3 1.0
O3B A:TPP401 2.5 19.2 1.0
OD1 B:ASP118 2.5 20.9 1.0
OD2 B:ASP118 2.9 16.6 1.0
O3A A:TPP401 3.0 21.6 1.0
CG B:ASP118 3.1 21.7 1.0
PA A:TPP401 3.1 18.4 1.0
PB A:TPP401 3.4 17.9 1.0
MG A:MG405 3.5 20.5 1.0
CG2 B:THR120 3.6 25.1 1.0
OD1 A:ASP43 3.6 21.4 1.0
O2A A:TPP401 3.9 18.0 1.0
NE2 A:HIS50 3.9 16.1 1.0
O A:THR44 4.0 16.3 1.0
CG A:ASP43 4.1 19.6 1.0
O B:HOH509 4.1 24.6 1.0
NE2 A:HIS303 4.2 28.3 1.0
O1B A:TPP401 4.3 17.2 1.0
N A:THR44 4.4 15.2 1.0
O7 A:TPP401 4.4 15.9 1.0
O2B A:TPP401 4.5 17.3 1.0
CB A:ASP43 4.5 17.5 1.0
O1A B:ADP401 4.5 22.1 1.0
CB B:ASP118 4.6 16.2 1.0
O A:HOH527 4.7 18.0 1.0
OD2 A:ASP43 4.7 18.0 1.0
CD2 A:HIS50 4.7 17.3 1.0
CA A:ASP43 4.8 14.7 1.0
CE1 A:HIS50 4.8 17.9 1.0
O B:THR119 4.9 20.4 1.0
CD2 A:HIS303 4.9 28.7 1.0
MG A:MG403 4.9 19.6 1.0
O B:HOH561 4.9 17.3 1.0
C A:THR44 5.0 22.1 1.0

Sodium binding site 4 out of 4 in 6mfm

Go back to Sodium Binding Sites List in 6mfm
Sodium binding site 4 out of 4 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:25.1
occ:1.00
 O A:HOH626 2.3 20.5 1.0
O B:HOH581 2.3 17.0 1.0
O A:HOH519 2.4 23.4 1.0
O B:ALA42 2.5 14.1 1.0
O B:HOH629 2.5 17.2 1.0
OD1 B:ASP43 2.6 25.3 1.0
CG B:ASP43 3.2 30.1 1.0
C B:ALA42 3.2 19.8 1.0
MG A:MG408 3.4 24.4 1.0
O3B A:ADP406 3.5 30.5 1.0
N B:ALA42 3.5 17.4 1.0
OD2 B:ASP43 3.6 27.2 1.0
OD2 B:ASP71 3.7 17.0 1.0
O A:GLY117 3.9 22.5 1.0
N B:ASP43 3.9 18.0 1.0
CA B:ALA42 4.0 17.4 1.0
CB B:CYS41 4.1 17.1 1.0
CB B:ASP43 4.1 20.8 1.0
CA B:ASP43 4.1 16.4 1.0
MG B:MG405 4.3 23.8 1.0
O A:ASP26 4.4 30.7 1.0
C B:CYS41 4.5 16.0 1.0
CG B:ASP71 4.5 23.3 1.0
OD1 A:ASP118 4.5 24.9 1.0
CA B:CYS41 4.6 12.4 1.0
OD1 B:ASN68 4.6 23.9 1.0
PB A:ADP406 4.6 34.4 1.0
CB A:ASP118 4.7 15.3 1.0
O3A A:ADP406 4.7 36.9 1.0
CG A:ASP118 4.8 23.6 1.0
C A:GLY117 4.8 22.8 1.0
O2A A:ADP406 4.9 31.7 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: Tue Oct 8 11:56:04 2024

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