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Calcium in PDB 5cm7: Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)

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

All present enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp):
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), PDB code: 5cm7 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) 44.50 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.750, 117.120, 55.890, 90.00, 108.57, 90.00
R / Rfree (%) 14.2 / 16.7

Other elements in 5cm7:

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

Magnesium (Mg) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) (pdb code 5cm7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), PDB code: 5cm7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5cm7

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Calcium binding site 1 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:10.9
occ:1.00
 O1B B:TPP401 2.3 9.6 1.0
O B:HOH621 2.4 10.6 1.0
O A:HOH544 2.4 11.5 1.0
O A:HOH621 2.4 11.3 1.0
O1A B:TPP401 2.4 10.8 1.0
OD2 A:ASP118 2.4 11.2 1.0
OD1 A:ASP118 2.6 9.6 1.0
CG A:ASP118 2.9 10.8 1.0
PA B:TPP401 3.5 10.7 1.0
MG A:MG403 3.5 9.1 1.0
PB B:TPP401 3.5 9.6 1.0
O3A B:TPP401 3.6 9.3 1.0
O B:THR44 4.0 10.7 1.0
O A:HOH532 4.1 11.5 1.0
NE2 B:HIS303 4.1 16.3 1.0
NE2 B:HIS50 4.1 11.9 1.0
OG1 A:THR120 4.1 13.3 1.0
O2A B:TPP401 4.2 12.7 1.0
OD1 B:ASP43 4.2 11.1 1.0
CB A:ASP118 4.4 8.0 1.0
N B:THR44 4.4 9.3 1.0
O2B B:TPP401 4.5 10.0 1.0
O3B B:TPP401 4.6 10.6 1.0
O B:HOH628 4.6 12.0 1.0
CG B:ASP43 4.6 12.6 1.0
O2A A:ADP401 4.7 11.0 1.0
O A:THR119 4.7 10.5 1.0
O7 B:TPP401 4.8 12.7 1.0
CD2 B:HIS303 4.8 17.6 1.0
CE1 B:HIS50 4.8 10.1 1.0
O A:HOH673 4.9 10.4 1.0
CB B:ASP43 5.0 12.7 1.0
CA B:ASP43 5.0 9.0 1.0

Calcium binding site 2 out of 6 in 5cm7

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Calcium binding site 2 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:8.6
occ:1.00
 O1B A:TPP405 2.3 9.9 1.0
OD2 A:ASP43 2.3 10.7 1.0
OD2 A:ASP71 2.3 9.7 1.0
O3B B:ADP405 2.3 8.3 1.0
O A:HOH568 2.4 11.2 1.0
O A:HOH689 2.5 7.8 1.0
OD1 A:ASP43 2.8 9.9 1.0
CG A:ASP43 2.9 10.9 1.0
CG A:ASP71 3.2 9.4 1.0
OD1 A:ASP71 3.4 7.9 1.0
PB B:ADP405 3.5 10.6 1.0
PB A:TPP405 3.5 8.2 1.0
MG B:MG407 3.7 8.5 1.0
O3B A:TPP405 3.8 8.8 1.0
O1B B:ADP405 3.9 9.9 1.0
MG A:MG408 3.9 7.1 1.0
O A:HOH708 3.9 12.5 1.0
O2B B:ADP405 4.0 10.8 1.0
O A:HOH637 4.1 10.5 1.0
NA A:NA404 4.1 11.3 1.0
O B:HOH614 4.1 11.2 1.0
O2B A:TPP405 4.2 8.4 1.0
O A:VAL67 4.3 9.0 1.0
OD2 A:ASP198 4.4 10.9 1.0
CB A:ASP43 4.4 7.8 1.0
CB A:ASP71 4.6 7.7 1.0
OG A:SER200 4.6 9.8 1.0
O3A A:TPP405 4.7 8.8 1.0
CB A:SER200 4.7 8.8 1.0
O B:HOH564 4.8 8.4 1.0
O3A B:ADP405 4.8 8.6 1.0
CE1 A:TYR250 4.9 10.4 1.0
OD1 A:ASP198 4.9 8.8 1.0

Calcium binding site 3 out of 6 in 5cm7

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Calcium binding site 3 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:12.3
occ:1.00
 O A:HOH538 2.2 14.7 1.0
O1A A:TPP405 2.2 10.6 1.0
O B:HOH572 2.3 11.9 1.0
O B:HOH523 2.3 11.4 1.0
OD1 A:ASP201 2.3 18.8 1.0
O2B A:TPP405 2.4 8.4 1.0
OD2 A:ASP201 2.5 24.5 1.0
CG A:ASP201 2.7 16.5 1.0
PA A:TPP405 3.5 9.5 1.0
PB A:TPP405 3.5 8.2 1.0
O3A A:TPP405 3.7 8.8 1.0
O2B B:ADP405 4.1 10.8 1.0
O3B A:TPP405 4.1 8.8 1.0
CB A:ASP201 4.2 11.3 1.0
O A:HOH586 4.3 16.1 1.0
OE2 B:GLU3 4.4 15.0 1.0
O1A B:ADP405 4.4 10.6 1.0
O2A A:TPP405 4.4 9.7 1.0
OE1 B:GLU3 4.4 16.3 1.0
O2A B:ADP405 4.5 8.5 1.0
O B:HOH650 4.5 11.2 1.0
OG A:SER200 4.5 9.8 1.0
O7 A:TPP405 4.6 10.6 1.0
O A:TYR301 4.6 31.3 1.0
C7 A:TPP405 4.6 13.5 1.0
CD2 A:TYR301 4.7 30.4 1.0
O1B A:TPP405 4.8 9.9 1.0
CD B:GLU3 4.9 14.2 1.0
C6 A:TPP405 4.9 12.2 1.0
PA B:ADP405 5.0 9.1 1.0

Calcium binding site 4 out of 6 in 5cm7

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Calcium binding site 4 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:9.3
occ:1.00
 OD2 B:ASP71 2.3 9.9 1.0
O2B B:TPP401 2.3 10.0 1.0
OD2 B:ASP43 2.3 10.6 1.0
O3B A:ADP401 2.3 11.1 1.0
O B:HOH588 2.5 10.8 1.0
O B:HOH675 2.5 9.7 1.0
OD1 B:ASP43 2.9 11.1 1.0
CG B:ASP43 2.9 12.6 1.0
CG B:ASP71 3.2 9.9 1.0
OD1 B:ASP71 3.4 10.3 1.0
PB A:ADP401 3.5 14.2 1.0
PB B:TPP401 3.5 9.6 1.0
MG A:MG403 3.7 9.1 1.0
O1B A:ADP401 3.9 12.4 1.0
O1B B:TPP401 3.9 9.6 1.0
MG B:MG404 3.9 8.3 1.0
O B:HOH628 4.0 12.0 1.0
O2B A:ADP401 4.0 12.1 1.0
O B:HOH586 4.0 9.8 1.0
O A:HOH601 4.1 11.8 1.0
NA B:NA408 4.1 14.6 1.0
O3B B:TPP401 4.2 10.6 1.0
O B:VAL67 4.4 11.0 1.0
OD2 B:ASP198 4.4 12.9 1.0
CB B:ASP43 4.4 12.7 1.0
CB B:ASP71 4.5 7.0 1.0
OG B:SER200 4.6 11.7 1.0
O3A B:TPP401 4.7 9.3 1.0
CB B:SER200 4.7 12.2 1.0
O A:HOH582 4.7 10.0 1.0
O3A A:ADP401 4.8 12.0 1.0
OD1 B:ASP198 4.9 10.2 1.0
CE1 B:TYR250 4.9 11.8 1.0

Calcium binding site 5 out of 6 in 5cm7

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Calcium binding site 5 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:15.0
occ:1.00
 O2A B:TPP401 2.2 12.7 1.0
O A:HOH591 2.2 14.6 1.0
O3B B:TPP401 2.3 10.6 1.0
O A:HOH532 2.3 11.5 1.0
OD1 B:ASP201 2.3 26.2 1.0
O B:HOH517 2.4 14.8 0.9
OD2 B:ASP201 2.4 38.6 1.0
CG B:ASP201 2.7 27.3 1.0
PB B:TPP401 3.4 9.6 1.0
PA B:TPP401 3.4 10.7 1.0
O3A B:TPP401 3.6 9.3 1.0
O1B B:TPP401 3.9 9.6 1.0
O2B A:ADP401 4.0 12.1 1.0
CB B:ASP201 4.2 13.0 1.0
O B:HOH503 4.3 18.9 1.0
O1A B:TPP401 4.4 10.8 1.0
OE1 A:GLU3 4.4 14.0 1.0
OE2 A:GLU3 4.4 15.1 1.0
O1A A:ADP401 4.4 13.2 1.0
OG B:SER200 4.4 11.7 1.0
O B:TYR301 4.5 24.3 1.0
O2A A:ADP401 4.5 11.0 1.0
O7 B:TPP401 4.6 12.7 1.0
O A:HOH621 4.6 11.3 1.0
C7 B:TPP401 4.6 15.1 1.0
O2B B:TPP401 4.7 10.0 1.0
CD2 B:TYR301 4.8 18.9 1.0
CD A:GLU3 4.8 12.0 1.0
C6 B:TPP401 4.9 12.7 1.0
O B:HOH615 5.0 11.8 1.0
CA B:ASP201 5.0 11.9 1.0
PA A:ADP401 5.0 9.9 1.0

Calcium binding site 6 out of 6 in 5cm7

Go back to Calcium Binding Sites List in 5cm7
Calcium binding site 6 out of 6 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:10.8
occ:1.00
 O3B A:TPP405 2.3 8.8 1.0
O B:HOH650 2.3 11.2 1.0
O B:HOH515 2.3 11.9 1.0
O A:HOH683 2.4 9.6 1.0
O2A A:TPP405 2.4 9.7 1.0
OD2 B:ASP118 2.5 13.5 1.0
OD1 B:ASP118 2.5 11.1 1.0
CG B:ASP118 2.9 12.9 1.0
PA A:TPP405 3.5 9.5 1.0
PB A:TPP405 3.5 8.2 1.0
MG B:MG407 3.5 8.5 1.0
O3A A:TPP405 3.6 8.8 1.0
O A:THR44 4.1 10.0 1.0
NE2 A:HIS50 4.1 9.7 1.0
OG1 B:THR120 4.1 20.1 1.0
O B:HOH523 4.1 11.4 1.0
NE2 A:HIS303 4.2 21.3 1.0
O1A A:TPP405 4.2 10.6 1.0
OD1 A:ASP43 4.3 9.9 1.0
CB B:ASP118 4.4 10.0 1.0
N A:THR44 4.4 7.9 1.0
O1B A:TPP405 4.5 9.9 1.0
O2B A:TPP405 4.5 8.4 1.0
O A:HOH708 4.5 12.5 1.0
CG A:ASP43 4.6 10.9 1.0
O B:THR119 4.7 10.8 1.0
O2A B:ADP405 4.7 8.5 1.0
O7 A:TPP405 4.8 10.6 1.0
CE1 A:HIS50 4.8 8.7 1.0
O B:HOH660 4.9 10.5 1.0
CD2 A:HIS303 4.9 21.5 1.0
CE1 A:HIS303 5.0 22.4 1.0
CB A:ASP43 5.0 7.8 1.0
CA A:ASP43 5.0 6.2 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 Jul 14 17:11:32 2024

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