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Magnesium in PDB 5cb6: Structure of Adenosine-5'-Phosphosulfate Kinase

Enzymatic activity of Structure of Adenosine-5'-Phosphosulfate Kinase

All present enzymatic activity of Structure of Adenosine-5'-Phosphosulfate Kinase:
2.7.1.25;

Protein crystallography data

The structure of Structure of Adenosine-5'-Phosphosulfate Kinase, PDB code: 5cb6 was solved by J.Herrmann, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.34 / 2.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.904, 109.681, 100.807, 90.00, 90.72, 90.00
R / Rfree (%) 16.4 / 21.8

Other elements in 5cb6:

The structure of Structure of Adenosine-5'-Phosphosulfate Kinase also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Adenosine-5'-Phosphosulfate Kinase (pdb code 5cb6). 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 Adenosine-5'-Phosphosulfate Kinase, PDB code: 5cb6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5cb6

Go back to Magnesium Binding Sites List in 5cb6
Magnesium binding site 1 out of 6 in the Structure of Adenosine-5'-Phosphosulfate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Adenosine-5'-Phosphosulfate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:48.8
occ:1.00
 O2G A:ANP302 1.8 43.8 1.0
OG1 A:THR19 2.0 43.2 1.0
O A:HOH402 2.3 45.8 1.0
OD2 A:ASP42 2.9 73.3 1.0
O2B A:ANP302 3.0 37.0 1.0
CB A:THR19 3.2 34.1 1.0
PG A:ANP302 3.2 0.9 1.0
OD2 A:ASP40 3.2 60.3 1.0
O3G A:ANP302 3.5 0.5 1.0
CG2 A:THR19 3.8 34.8 1.0
CG A:ASP42 3.9 74.8 1.0
NZ A:LYS120 3.9 67.1 1.0
OD1 A:ASP40 4.1 66.3 1.0
CG A:ASP40 4.1 53.9 1.0
N3B A:ANP302 4.1 92.4 1.0
PB A:ANP302 4.2 42.0 1.0
O A:HOH419 4.2 42.7 1.0
O1A A:ANP302 4.2 38.2 1.0
O1G A:ANP302 4.3 0.6 1.0
CA A:THR19 4.4 30.8 1.0
N A:THR19 4.6 30.8 1.0
OD1 A:ASP42 4.6 81.3 1.0
CB A:ASP42 4.6 65.8 1.0
CE A:LYS120 4.9 63.0 1.0

Magnesium binding site 2 out of 6 in 5cb6

Go back to Magnesium Binding Sites List in 5cb6
Magnesium binding site 2 out of 6 in the Structure of Adenosine-5'-Phosphosulfate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Adenosine-5'-Phosphosulfate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:49.8
occ:1.00
 O2G B:ANP302 1.9 38.3 1.0
OG1 B:THR19 2.2 42.9 1.0
O B:HOH402 2.7 46.1 1.0
O2B B:ANP302 3.1 44.9 1.0
PG B:ANP302 3.2 0.7 1.0
CB B:THR19 3.2 37.7 1.0
O3G B:ANP302 3.3 0.7 1.0
NZ B:LYS120 3.3 45.2 1.0
OD1 B:ASP40 3.7 72.8 1.0
OD2 B:ASP42 3.8 0.5 1.0
CG2 B:THR19 3.8 33.8 1.0
O2A B:ANP302 4.0 32.2 1.0
CG B:ASP42 4.0 94.7 1.0
N3B B:ANP302 4.1 37.8 1.0
PB B:ANP302 4.2 42.3 1.0
CE B:LYS120 4.2 52.0 1.0
OD2 B:ASP40 4.2 83.7 1.0
OD1 B:ASP42 4.2 99.8 1.0
CG B:ASP40 4.4 75.9 1.0
O1G B:ANP302 4.4 99.4 1.0
CA B:THR19 4.5 41.6 1.0
N B:THR19 4.7 42.5 1.0
CB B:ASP42 4.9 71.8 1.0
PA B:ANP302 4.9 33.1 1.0
O B:HOH401 4.9 39.6 1.0

Magnesium binding site 3 out of 6 in 5cb6

Go back to Magnesium Binding Sites List in 5cb6
Magnesium binding site 3 out of 6 in the Structure of Adenosine-5'-Phosphosulfate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Adenosine-5'-Phosphosulfate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:70.2
occ:1.00
 O2G C:ANP302 1.8 33.8 1.0
OG1 C:THR19 2.1 59.1 1.0
O3G C:ANP302 2.8 0.2 1.0
PG C:ANP302 2.9 0.5 1.0
OD2 C:ASP40 3.0 75.6 1.0
OD2 C:ASP42 3.2 91.7 1.0
CB C:THR19 3.3 52.8 1.0
O1B C:ANP302 3.4 62.6 1.0
CG2 C:THR19 3.6 56.2 1.0
OD1 C:ASP40 3.8 69.7 1.0
CG C:ASP40 3.8 65.8 1.0
CG C:ASP42 3.9 88.6 1.0
O1G C:ANP302 4.0 0.6 1.0
N3B C:ANP302 4.1 0.1 1.0
CB C:ASP42 4.2 74.1 1.0
NZ C:LYS120 4.2 84.6 1.0
PB C:ANP302 4.4 54.0 1.0
CA C:THR19 4.5 41.6 1.0
N C:THR19 4.7 50.2 1.0
CE C:LYS120 4.8 83.6 1.0
OD1 C:ASP42 4.9 93.6 1.0
O2A C:ANP302 5.0 52.1 1.0

Magnesium binding site 4 out of 6 in 5cb6

Go back to Magnesium Binding Sites List in 5cb6
Magnesium binding site 4 out of 6 in the Structure of Adenosine-5'-Phosphosulfate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Adenosine-5'-Phosphosulfate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:94.9
occ:1.00
 OG1 D:THR19 1.9 55.4 1.0
O2G D:ANP302 1.9 58.2 1.0
OD2 D:ASP42 2.2 83.0 1.0
PG D:ANP302 2.5 0.7 1.0
O1G D:ANP302 2.5 0.6 1.0
CB D:THR19 2.9 49.8 1.0
N3B D:ANP302 3.0 0.5 1.0
CG2 D:THR19 3.2 48.8 1.0
CG D:ASP42 3.4 83.8 1.0
OD2 D:ASP40 3.5 76.1 1.0
OD1 D:ASP42 3.9 92.2 1.0
O3G D:ANP302 4.0 70.2 1.0
O2B D:ANP302 4.2 46.7 1.0
OD1 D:ASP40 4.2 77.7 1.0
CA D:THR19 4.2 48.4 1.0
O1A D:ANP302 4.2 52.5 1.0
PB D:ANP302 4.2 44.5 1.0
CG D:ASP40 4.3 70.4 1.0
N D:THR19 4.5 44.1 1.0
CB D:ASP42 4.5 67.9 1.0
O D:HOH402 4.7 60.5 1.0
CE D:LYS120 4.8 77.6 1.0
NZ D:LYS120 4.9 79.7 1.0

Magnesium binding site 5 out of 6 in 5cb6

Go back to Magnesium Binding Sites List in 5cb6
Magnesium binding site 5 out of 6 in the Structure of Adenosine-5'-Phosphosulfate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Adenosine-5'-Phosphosulfate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:47.2
occ:1.00
 OG1 E:THR19 1.8 42.5 1.0
O2G E:ANP302 1.9 53.7 1.0
O E:HOH402 2.4 32.1 1.0
OD2 E:ASP42 2.5 78.0 1.0
CB E:THR19 3.1 41.3 1.0
O2B E:ANP302 3.2 39.2 1.0
OD2 E:ASP40 3.3 74.8 1.0
PG E:ANP302 3.4 0.8 1.0
OD1 E:ASP40 3.4 84.9 1.0
CG E:ASP42 3.5 72.3 1.0
CG2 E:THR19 3.5 43.3 1.0
CG E:ASP40 3.8 71.4 1.0
O3G E:ANP302 4.0 0.1 1.0
CB E:ASP42 4.0 56.6 1.0
CA E:THR19 4.2 42.1 1.0
O1G E:ANP302 4.2 0.3 1.0
N E:THR19 4.4 41.5 1.0
OD1 E:ASP42 4.4 77.3 1.0
N3B E:ANP302 4.4 81.0 1.0
PB E:ANP302 4.4 41.0 1.0
OG E:SER83 4.5 48.3 1.0
NZ E:LYS120 4.7 88.7 1.0
N E:ASP42 4.9 45.5 1.0

Magnesium binding site 6 out of 6 in 5cb6

Go back to Magnesium Binding Sites List in 5cb6
Magnesium binding site 6 out of 6 in the Structure of Adenosine-5'-Phosphosulfate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Adenosine-5'-Phosphosulfate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:51.3
occ:1.00
 O2G F:ANP302 1.9 0.7 1.0
OG1 F:THR19 1.9 56.7 1.0
O F:HOH406 2.2 46.0 1.0
OD2 F:ASP42 2.3 90.7 1.0
O1B F:ANP302 2.9 55.4 1.0
CB F:THR19 3.2 46.3 1.0
PG F:ANP302 3.2 1.0 1.0
CG F:ASP42 3.6 83.8 1.0
O1G F:ANP302 3.6 0.5 1.0
OD2 F:ASP40 3.6 86.0 1.0
OD1 F:ASP40 3.7 93.3 1.0
CG2 F:THR19 3.8 45.1 1.0
N3B F:ANP302 4.0 0.5 1.0
CG F:ASP40 4.1 84.8 1.0
PB F:ANP302 4.1 49.5 1.0
OD1 F:ASP42 4.2 83.5 1.0
CA F:THR19 4.3 48.4 1.0
NZ F:LYS120 4.3 70.6 1.0
O3G F:ANP302 4.4 53.2 1.0
N F:THR19 4.5 46.1 1.0
OG F:SER83 4.5 55.0 1.0
CB F:ASP42 4.6 72.3 1.0
O3' F:ADX301 4.7 62.0 1.0
CE F:LYS120 4.8 79.0 1.0
O1A F:ANP302 4.9 42.9 1.0
O2A F:ANP302 5.0 65.6 1.0

Reference:

J.Herrmann, D.Nathin, S.G.Lee, T.Sun, J.M.Jez. Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase From Cyanobacteria to Plants. J.Biol.Chem. V. 290 24705 2015.
ISSN: ESSN 1083-351X
PubMed: 26294763
DOI: 10.1074/JBC.M115.679514
Page generated: Mon Dec 14 20:06:20 2020

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