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Magnesium in PDB 5lb5: Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).

Enzymatic activity of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).

All present enzymatic activity of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form)., PDB code: 5lb5 was solved by J.A.Newman, H.Aitkenhead, P.Savitsky, T.Krojer, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, O.Gileadi, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.90 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.590, 84.750, 106.691, 108.82, 90.06, 96.86
R / Rfree (%) 24.4 / 28.2

Other elements in 5lb5:

The structure of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form). also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form). (pdb code 5lb5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form)., PDB code: 5lb5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5lb5

Go back to Magnesium Binding Sites List in 5lb5
Magnesium binding site 1 out of 4 in the Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:53.4
occ:1.00
 O A:HOH637 2.0 57.3 1.0
O A:HOH675 2.2 49.0 1.0
O1B A:ADP504 2.3 41.6 1.0
O A:HOH691 2.5 47.8 1.0
O A:HOH672 2.5 59.1 1.0
PB A:ADP504 3.5 41.4 1.0
O2B A:ADP504 3.7 43.6 1.0
OG A:SER59 4.0 38.3 1.0
OD2 A:ASP157 4.1 56.9 1.0
OD1 A:ASP157 4.1 47.3 1.0
O A:HOH660 4.4 43.5 1.0
CE A:LYS58 4.4 26.1 1.0
CG A:ASP157 4.5 47.4 1.0
OE2 A:GLU158 4.5 60.4 1.0
O3B A:ADP504 4.6 39.2 1.0
O3A A:ADP504 4.6 42.6 1.0
O1A A:ADP504 4.8 42.2 1.0
NE2 A:GLN86 4.8 61.4 1.0
O2A A:ADP504 4.8 46.0 1.0
NZ A:LYS58 4.9 25.9 1.0
CB A:LYS58 4.9 29.0 1.0

Magnesium binding site 2 out of 4 in 5lb5

Go back to Magnesium Binding Sites List in 5lb5
Magnesium binding site 2 out of 4 in the Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:50.8
occ:1.00
 O B:HOH684 2.1 43.1 1.0
O3B B:ADP504 2.2 37.4 1.0
O B:HOH605 2.2 47.4 1.0
O B:HOH686 2.3 43.3 1.0
O B:HOH630 2.3 37.6 1.0
PB B:ADP504 3.3 34.2 1.0
O2B B:ADP504 3.4 36.8 1.0
OG B:SER59 3.9 38.3 1.0
OE2 B:GLU158 4.1 63.9 1.0
O2A B:ADP504 4.1 34.5 1.0
O3A B:ADP504 4.3 37.0 1.0
O1B B:ADP504 4.4 31.8 1.0
OD2 B:ASP157 4.5 45.3 1.0
O B:HOH663 4.5 28.3 1.0
OD1 B:ASP157 4.6 38.2 1.0
PA B:ADP504 4.6 37.8 1.0
O1A B:ADP504 4.6 39.4 1.0
CE B:LYS58 4.6 29.6 1.0
O B:HOH613 4.8 53.0 1.0
NE2 B:GLN86 4.9 63.6 1.0
CG B:ASP157 4.9 38.7 1.0
CB B:LYS58 5.0 31.7 1.0
NZ B:LYS58 5.0 26.4 1.0

Magnesium binding site 3 out of 4 in 5lb5

Go back to Magnesium Binding Sites List in 5lb5
Magnesium binding site 3 out of 4 in the Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:71.1
occ:1.00
 O C:HOH657 2.0 52.0 1.0
O C:HOH668 2.3 52.6 1.0
O C:HOH615 2.7 54.5 1.0
O2B C:ADP503 2.9 67.5 1.0
O3B C:ADP503 3.7 62.2 1.0
OE2 C:GLU158 3.7 82.0 1.0
PB C:ADP503 3.9 64.2 1.0
OD1 C:ASP157 4.1 54.8 1.0
CD C:GLU158 4.5 85.5 1.0
OG C:SER59 4.6 60.9 1.0
OD2 C:ASP157 4.6 61.4 1.0
NZ C:LYS58 4.7 41.5 1.0
NE2 C:GLN86 4.7 0.7 1.0
CG C:ASP157 4.7 55.1 1.0
O2A C:ADP503 4.7 60.5 1.0
CE C:LYS58 4.7 47.3 1.0
O1B C:ADP503 4.9 61.2 1.0
O3A C:ADP503 4.9 62.6 1.0

Magnesium binding site 4 out of 4 in 5lb5

Go back to Magnesium Binding Sites List in 5lb5
Magnesium binding site 4 out of 4 in the Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human RECQL5 Helicase in Complex with Adp/Mg (Tricilinc Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:68.0
occ:1.00
 O D:HOH649 2.1 51.4 1.0
O D:HOH618 2.4 58.2 1.0
O D:HOH660 2.5 47.5 1.0
O1B D:ADP504 2.6 68.0 1.0
O D:HOH610 3.0 59.5 1.0
PB D:ADP504 3.8 67.0 1.0
OG D:SER59 3.9 62.9 1.0
O3B D:ADP504 3.9 65.2 1.0
OD2 D:ASP157 4.1 57.6 1.0
O1A D:ADP504 4.2 73.8 1.0
OD1 D:ASP157 4.3 52.1 1.0
NE2 D:GLN86 4.6 0.5 1.0
O2A D:ADP504 4.6 71.6 1.0
CG D:ASP157 4.6 51.5 1.0
O3A D:ADP504 4.7 69.6 1.0
PA D:ADP504 4.8 72.4 1.0
OE1 D:GLU158 4.9 71.0 1.0
O2B D:ADP504 5.0 65.7 1.0

Reference:

J.A.Newman, H.Aitkenhead, P.Savitsky, O.Gileadi. Insights Into the Recq Helicase Mechanism Revealed By the Structure of the Helicase Domain of Human RECQL5. Nucleic Acids Res. V. 45 4231 2017.
ISSN: ESSN 1362-4962
PubMed: 28100692
DOI: 10.1093/NAR/GKW1362
Page generated: Sun Sep 29 19:48:31 2024

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