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Magnesium in PDB 7pmq: Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3

Enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3

All present enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3:
3.6.4.13;

Protein crystallography data

The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3, PDB code: 7pmq 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) 49.42 / 3.22
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.644, 159.644, 204.682, 90, 90, 90
R / Rfree (%) 22.8 / 26.4

Other elements in 7pmq:

The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 7pmq

Go back to Magnesium Binding Sites List in 7pmq
Magnesium binding site 1 out of 4 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop 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 in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:49.4
occ:1.00
 F1 C:BEF501 1.9 61.0 1.0
O3B C:ADP500 2.8 61.4 1.0
OD2 C:ASP153 3.1 61.8 1.0
OD1 C:ASP153 3.2 61.7 1.0
BE C:BEF501 3.4 61.0 1.0
OE1 C:GLU154 3.4 61.8 1.0
OG1 C:THR54 3.5 59.8 1.0
CG C:ASP153 3.6 61.9 1.0
O1A C:ADP500 3.7 61.4 1.0
O1B C:ADP500 3.7 61.4 1.0
PB C:ADP500 3.9 61.4 1.0
F2 C:BEF501 4.0 61.0 1.0
OE2 C:GLU154 4.0 61.9 1.0
CD C:GLU154 4.1 62.1 1.0
CA C:GLY304 4.2 59.1 1.0
CE C:LYS53 4.2 60.4 1.0
F3 C:BEF501 4.3 61.0 1.0
O C:GLY304 4.6 59.0 1.0
NZ C:LYS53 4.6 60.6 1.0
O2B C:ADP500 4.8 61.4 1.0
N C:THR54 4.8 59.9 1.0
PA C:ADP500 4.8 61.4 1.0
CB C:THR54 4.9 60.1 1.0
C C:GLY304 4.9 58.6 1.0
CD1 C:LEU83 4.9 58.3 1.0
CB C:LYS53 5.0 60.5 1.0

Magnesium binding site 2 out of 4 in 7pmq

Go back to Magnesium Binding Sites List in 7pmq
Magnesium binding site 2 out of 4 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop 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 in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:46.0
occ:1.00
 F1 A:BEF501 2.0 58.5 1.0
O3B A:ADP500 2.7 57.9 1.0
F2 A:BEF501 2.8 58.5 1.0
BE A:BEF501 2.8 58.5 1.0
OD2 A:ASP153 2.9 56.3 1.0
OD1 A:ASP153 3.0 56.3 1.0
CG A:ASP153 3.3 56.1 1.0
OG1 A:THR54 3.4 55.0 1.0
OE1 A:GLU154 3.6 58.3 1.0
O1A A:ADP500 3.9 57.9 1.0
PB A:ADP500 3.9 57.9 1.0
O1B A:ADP500 3.9 57.9 1.0
F3 A:BEF501 4.1 58.5 1.0
OE2 A:GLU154 4.2 59.6 1.0
CD A:GLU154 4.3 59.1 1.0
CA A:GLY304 4.5 57.3 1.0
N A:THR54 4.7 54.7 1.0
CB A:THR54 4.7 55.0 1.0
PA A:ADP500 4.8 57.9 1.0
NZ A:LYS53 4.8 56.9 1.0
CB A:ASP153 4.8 55.9 1.0
O3A A:ADP500 4.8 57.9 1.0
CB A:LYS53 4.9 54.8 1.0
O A:GLY304 4.9 57.1 1.0
O2B A:ADP500 4.9 57.9 1.0
CA A:THR54 5.0 54.4 1.0

Magnesium binding site 3 out of 4 in 7pmq

Go back to Magnesium Binding Sites List in 7pmq
Magnesium binding site 3 out of 4 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop 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 in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:61.5
occ:1.00
 F1 B:BEF501 1.9 68.8 1.0
F2 B:BEF501 2.5 68.8 1.0
BE B:BEF501 2.6 68.8 1.0
O3B B:ADP500 2.7 70.0 1.0
OD2 B:ASP153 2.7 73.4 1.0
O2A B:ADP500 3.2 70.0 1.0
OG1 B:THR54 3.3 71.0 1.0
OD1 B:ASP153 3.4 74.0 1.0
CG B:ASP153 3.5 74.0 1.0
O2B B:ADP500 3.5 70.0 1.0
PB B:ADP500 3.7 70.0 1.0
OE1 B:GLU154 3.8 70.9 1.0
F3 B:BEF501 3.9 68.8 1.0
OE2 B:GLU154 4.2 70.8 1.0
CA B:GLY304 4.4 66.0 1.0
PA B:ADP500 4.4 70.0 1.0
CD B:GLU154 4.4 71.0 1.0
O B:GLY304 4.5 65.0 1.0
CB B:THR54 4.7 71.5 1.0
O3A B:ADP500 4.7 70.0 1.0
O1A B:ADP500 4.7 70.0 1.0
CD1 B:LEU83 4.8 68.8 1.0
N B:THR54 4.8 72.0 1.0
O1B B:ADP500 4.8 70.0 1.0
CB B:ASP153 4.9 74.8 1.0
C B:GLY304 5.0 64.6 1.0

Magnesium binding site 4 out of 4 in 7pmq

Go back to Magnesium Binding Sites List in 7pmq
Magnesium binding site 4 out of 4 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Hairpin Loop 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 in the Active Conformation Bound to A Hairpin Loop Rna and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:82.7
occ:1.00
 F1 D:BEF501 2.0 86.5 1.0
F2 D:BEF501 2.7 86.5 1.0
BE D:BEF501 2.7 86.5 1.0
OD2 D:ASP153 2.8 88.2 1.0
O3B D:ADP500 2.8 88.1 1.0
OG1 D:THR54 3.4 89.0 1.0
OD1 D:ASP153 3.4 90.2 1.0
O2A D:ADP500 3.5 88.1 1.0
CG D:ASP153 3.5 89.4 1.0
O2B D:ADP500 3.6 88.1 1.0
PB D:ADP500 3.8 88.1 1.0
OE1 D:GLU154 3.9 87.6 1.0
F3 D:BEF501 4.1 86.5 1.0
OE2 D:GLU154 4.3 88.2 1.0
CA D:GLY304 4.5 80.8 1.0
CD D:GLU154 4.5 88.1 1.0
N D:THR54 4.6 92.6 1.0
PA D:ADP500 4.6 88.1 1.0
CB D:THR54 4.7 90.2 1.0
O D:GLY304 4.7 79.9 1.0
NZ D:LYS53 4.7 89.0 1.0
CB D:LYS53 4.8 90.5 1.0
O3A D:ADP500 4.9 88.1 1.0
O1B D:ADP500 4.9 88.1 1.0
CE D:LYS53 4.9 89.8 1.0
CA D:THR54 4.9 91.9 1.0
O1A D:ADP500 4.9 88.1 1.0
CB D:ASP153 5.0 90.0 1.0

Reference:

J.P.Wurm, J.P.Wurm. N/A N/A.
Page generated: Thu Aug 14 13:15:22 2025

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