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:
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
|