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Magnesium in PDB 7pli: Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3

Enzymatic activity of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3

All present enzymatic activity of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3:
3.6.4.13;

Protein crystallography data

The structure of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3, PDB code: 7pli was solved by J.P.Wurm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.88 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.643, 121.599, 122.417, 97.16, 92.43, 103.44
R / Rfree (%) 21.3 / 24.7

Other elements in 7pli:

The structure of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 (pdb code 7pli). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3, PDB code: 7pli:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7pli

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Magnesium binding site 1 out of 6 in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:40.0
occ:1.00
 O A:HOH604 2.0 37.7 1.0
O1B A:ADP500 2.0 36.5 1.0
F2 A:BEF501 2.1 37.1 1.0
O A:HOH603 2.1 38.2 1.0
O A:HOH601 2.3 40.2 1.0
O A:HOH602 2.5 41.4 1.0
PB A:ADP500 3.3 38.6 1.0
BE A:BEF501 3.4 41.2 1.0
O2A A:ADP500 3.5 48.2 1.0
OG1 A:THR54 3.5 43.8 1.0
OD2 A:ASP153 3.6 46.9 1.0
O2B A:ADP500 3.7 42.6 1.0
OE2 A:GLU154 3.9 45.7 1.0
OD1 A:ASP153 4.0 46.3 1.0
F3 A:BEF501 4.2 41.2 1.0
PA A:ADP500 4.2 36.9 1.0
CG A:ASP153 4.3 45.6 1.0
O3A A:ADP500 4.3 40.2 1.0
CA A:GLY304 4.3 39.6 1.0
O3B A:ADP500 4.3 41.8 1.0
F1 A:BEF501 4.5 40.6 1.0
O1A A:ADP500 4.6 39.2 1.0
O A:GLY304 4.6 39.7 1.0
N A:THR54 4.7 43.6 1.0
CE A:LYS53 4.7 42.6 1.0
CB A:LYS53 4.8 42.1 1.0
CB A:THR54 4.8 46.0 1.0

Magnesium binding site 2 out of 6 in 7pli

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Magnesium binding site 2 out of 6 in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:34.6
occ:1.00
 F2 B:BEF501 2.0 31.6 1.0
O B:HOH602 2.0 36.6 1.0
O B:HOH603 2.1 34.5 1.0
O3B B:ADP500 2.1 34.7 1.0
O B:HOH601 2.1 29.6 1.0
O B:HOH604 2.2 34.7 1.0
PB B:ADP500 3.3 28.0 1.0
BE B:BEF501 3.4 35.8 1.0
OD2 B:ASP153 3.6 41.1 1.0
O1B B:ADP500 3.6 34.6 1.0
O1A B:ADP500 3.6 40.8 1.0
OG1 B:THR54 3.7 38.9 1.0
OD1 B:ASP153 3.9 40.1 1.0
OE2 B:GLU154 3.9 37.3 1.0
F3 B:BEF501 4.0 36.2 1.0
CG B:ASP153 4.1 41.5 1.0
CA B:GLY304 4.2 35.5 1.0
O3A B:ADP500 4.3 35.0 1.0
O2B B:ADP500 4.3 36.0 1.0
PA B:ADP500 4.3 33.6 1.0
F1 B:BEF501 4.5 35.1 1.0
CB B:LYS53 4.6 35.8 1.0
O B:GLY304 4.6 36.8 1.0
NZ B:LYS53 4.6 35.1 1.0
O2A B:ADP500 4.7 33.2 1.0
N B:THR54 4.8 34.8 1.0
C B:GLY304 5.0 36.3 1.0
CD B:GLU154 5.0 39.0 1.0

Magnesium binding site 3 out of 6 in 7pli

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Magnesium binding site 3 out of 6 in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:47.4
occ:1.00
 F2 E:BEF501 2.0 47.4 1.0
O E:HOH601 2.0 46.2 1.0
O3B E:ADP500 2.0 45.9 1.0
O E:HOH603 2.0 45.8 1.0
O E:HOH604 2.3 52.6 1.0
O E:HOH602 2.4 51.0 1.0
PB E:ADP500 3.2 45.3 1.0
BE E:BEF501 3.4 47.0 1.0
O1B E:ADP500 3.4 45.1 1.0
O1A E:ADP500 3.5 49.1 1.0
OG1 E:THR54 3.5 47.3 1.0
OD2 E:ASP153 3.8 50.4 1.0
OD1 E:ASP153 3.9 51.8 1.0
OE2 E:GLU154 4.0 54.5 1.0
F3 E:BEF501 4.2 50.8 1.0
O3A E:ADP500 4.2 47.9 1.0
PA E:ADP500 4.2 44.3 1.0
CG E:ASP153 4.3 53.5 1.0
O2B E:ADP500 4.3 46.6 1.0
CB E:LYS53 4.4 47.3 1.0
CA E:GLY304 4.4 43.7 1.0
F1 E:BEF501 4.4 44.9 1.0
N E:THR54 4.5 47.4 1.0
O E:GLY304 4.6 44.8 1.0
O2A E:ADP500 4.7 46.4 1.0
NZ E:LYS53 4.8 46.8 1.0
CB E:THR54 4.8 49.9 1.0
CD E:LYS53 5.0 49.1 1.0

Magnesium binding site 4 out of 6 in 7pli

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Magnesium binding site 4 out of 6 in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg502

b:51.3
occ:1.00
 O J:HOH602 2.1 53.8 1.0
O J:HOH601 2.1 51.2 1.0
F2 J:BEF501 2.1 47.3 1.0
O J:HOH604 2.1 56.5 1.0
O3B J:ADP500 2.2 53.4 1.0
O J:HOH603 2.3 56.5 1.0
BE J:BEF501 3.4 49.8 1.0
PB J:ADP500 3.4 46.8 1.0
OD2 J:ASP153 3.5 72.6 1.0
O2A J:ADP500 3.7 54.3 1.0
O2B J:ADP500 3.7 49.0 1.0
OG1 J:THR54 3.7 56.3 1.0
OE2 J:GLU154 3.9 58.0 1.0
OD1 J:ASP153 3.9 70.2 1.0
CG J:ASP153 4.1 71.1 1.0
CA J:GLY304 4.2 48.9 1.0
F3 J:BEF501 4.3 48.8 1.0
F1 J:BEF501 4.5 51.0 1.0
O3A J:ADP500 4.5 49.6 1.0
O1B J:ADP500 4.5 52.7 1.0
PA J:ADP500 4.5 48.8 1.0
O J:GLY304 4.5 47.9 1.0
CB J:LYS53 4.7 56.4 1.0
NZ J:LYS53 4.7 53.0 1.0
O1A J:ADP500 4.9 54.2 1.0
N J:THR54 4.9 56.3 1.0
C J:GLY304 4.9 48.5 1.0
CD J:GLU154 4.9 60.1 1.0

Magnesium binding site 5 out of 6 in 7pli

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Magnesium binding site 5 out of 6 in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg502

b:49.6
occ:1.00
 O I:HOH604 2.0 50.5 1.0
O I:HOH602 2.0 44.5 1.0
O I:HOH603 2.0 45.6 1.0
F2 I:BEF501 2.2 47.4 1.0
O I:HOH601 2.3 50.4 1.0
O1B I:ADP500 2.3 46.0 1.0
OD2 I:ASP153 3.3 59.2 1.0
PB I:ADP500 3.4 42.7 1.0
OD1 I:ASP153 3.5 56.6 1.0
BE I:BEF501 3.5 50.5 1.0
OE2 I:GLU154 3.6 55.5 1.0
O2B I:ADP500 3.6 52.0 1.0
OG1 I:THR54 3.8 50.4 1.0
CG I:ASP153 3.8 56.6 1.0
O1A I:ADP500 3.9 57.8 1.0
F3 I:BEF501 4.1 49.0 1.0
O3B I:ADP500 4.4 51.2 1.0
CB I:LYS53 4.4 46.0 1.0
CA I:GLY304 4.5 57.6 1.0
NZ I:LYS53 4.5 50.2 1.0
O3A I:ADP500 4.6 46.0 1.0
CD I:GLU154 4.7 56.2 1.0
PA I:ADP500 4.7 52.9 1.0
N I:THR54 4.7 44.7 1.0
F1 I:BEF501 4.7 53.8 1.0
CD I:LYS53 4.8 49.2 1.0
O I:GLY304 4.9 54.8 1.0
O2A I:ADP500 5.0 53.3 1.0

Magnesium binding site 6 out of 6 in 7pli

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Magnesium binding site 6 out of 6 in the Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dead-Box Helicase Dbpa Bound to Single Stranded Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:53.8
occ:1.00
 O F:HOH601 2.0 58.2 1.0
O F:HOH604 2.0 57.8 1.0
O F:HOH602 2.1 55.1 1.0
O F:HOH603 2.1 57.9 1.0
F2 F:BEF501 2.2 55.9 1.0
O3B F:ADP500 2.5 53.1 1.0
OD2 F:ASP153 3.2 64.1 1.0
BE F:BEF501 3.5 56.7 1.0
PB F:ADP500 3.6 58.1 1.0
OD1 F:ASP153 3.6 60.4 1.0
OE2 F:GLU154 3.7 58.8 1.0
O2B F:ADP500 3.7 56.6 1.0
O2A F:ADP500 3.7 63.5 1.0
OG1 F:THR54 3.8 55.6 1.0
CG F:ASP153 3.8 62.8 1.0
CA F:GLY304 4.2 59.4 1.0
F3 F:BEF501 4.3 57.5 1.0
PA F:ADP500 4.6 58.8 1.0
O3A F:ADP500 4.6 57.9 1.0
F1 F:BEF501 4.7 58.7 1.0
O1B F:ADP500 4.7 55.9 1.0
CD F:GLU154 4.7 59.8 1.0
O F:GLY304 4.7 60.6 1.0
CB F:LYS53 4.7 57.8 1.0
NZ F:LYS53 4.9 55.1 1.0
N F:THR54 4.9 59.0 1.0

Reference:

J.P.Wurm, J.P.Wurm. N/A N/A.
Page generated: Thu Oct 3 04:11:26 2024

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