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Zinc 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:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5lb5

Go back to Zinc Binding Sites List in 5lb5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:39.9
occ:1.00
 SG A:CYS427 2.4 36.5 1.0
SG A:CYS431 2.4 36.2 1.0
SG A:CYS411 2.4 36.7 1.0
SG A:CYS434 2.5 49.6 1.0
CB A:CYS427 3.1 33.8 1.0
CB A:CYS434 3.3 45.6 1.0
CB A:CYS411 3.4 32.7 1.0
CB A:CYS431 3.4 33.5 1.0
CA A:CYS411 3.7 32.4 1.0
N A:CYS431 4.0 36.1 1.0
N A:ARG412 4.1 30.4 1.0
CD2 A:HIS413 4.2 31.2 1.0
CA A:CYS431 4.2 35.7 1.0
C A:CYS411 4.3 33.6 1.0
N A:CYS434 4.4 45.0 1.0
CA A:CYS434 4.4 45.2 1.0
CA A:CYS427 4.6 35.6 1.0
C A:GLY430 4.6 39.1 1.0
N A:HIS413 4.6 28.1 1.0
N A:GLY430 4.7 38.8 1.0
O A:CYS431 4.8 44.4 1.0
C A:CYS431 4.9 44.2 1.0
CG A:HIS413 5.0 30.4 1.0
CB A:HIS413 5.0 26.8 1.0

Zinc binding site 2 out of 4 in 5lb5

Go back to Zinc Binding Sites List in 5lb5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:45.5
occ:1.00
 SG B:CYS427 2.3 51.0 1.0
SG B:CYS411 2.4 39.6 1.0
SG B:CYS431 2.5 39.9 1.0
SG B:CYS434 2.6 52.7 1.0
CB B:CYS427 3.1 47.4 1.0
CB B:CYS434 3.2 49.0 1.0
CB B:CYS431 3.3 35.8 1.0
CB B:CYS411 3.4 34.9 1.0
CA B:CYS411 3.9 34.0 1.0
N B:CYS431 4.0 38.9 1.0
CA B:CYS431 4.1 37.6 1.0
N B:ARG412 4.1 36.1 1.0
N B:CYS434 4.2 48.5 1.0
CA B:CYS434 4.3 48.6 1.0
CD2 B:HIS413 4.4 35.9 1.0
C B:CYS411 4.4 36.8 1.0
O B:CYS431 4.6 42.0 1.0
CA B:CYS427 4.6 47.8 1.0
C B:GLY430 4.6 43.9 1.0
C B:CYS431 4.7 43.0 1.0
N B:HIS413 4.7 34.5 1.0
N B:GLY430 4.8 43.7 1.0

Zinc binding site 3 out of 4 in 5lb5

Go back to Zinc Binding Sites List in 5lb5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:46.0
occ:1.00
 SG C:CYS427 2.2 46.4 1.0
SG C:CYS434 2.3 53.0 1.0
SG C:CYS431 2.5 39.6 1.0
SG C:CYS411 2.5 38.9 1.0
CB C:CYS427 3.0 44.3 1.0
CB C:CYS434 3.1 48.9 1.0
CB C:CYS411 3.4 34.6 1.0
CB C:CYS431 3.5 36.6 1.0
CA C:CYS411 3.7 35.7 1.0
N C:CYS431 4.1 39.0 1.0
N C:ARG412 4.1 40.4 1.0
CA C:CYS434 4.2 48.5 1.0
N C:CYS434 4.2 47.7 1.0
CA C:CYS431 4.3 38.1 1.0
CD2 C:HIS413 4.3 40.4 1.0
C C:CYS411 4.4 41.8 1.0
CA C:CYS427 4.5 46.9 1.0
N C:GLY430 4.6 47.6 1.0
N C:HIS413 4.7 40.2 1.0
C C:GLY430 4.7 44.9 1.0
O C:CYS427 4.7 53.1 1.0
CB C:HIS413 4.9 38.4 1.0
C C:CYS431 4.9 43.5 1.0
C C:CYS427 4.9 54.0 1.0
O C:CYS431 4.9 42.9 1.0
CG C:HIS413 5.0 40.3 1.0

Zinc binding site 4 out of 4 in 5lb5

Go back to Zinc Binding Sites List in 5lb5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:45.3
occ:1.00
 SG D:CYS427 2.2 50.6 1.0
SG D:CYS411 2.4 39.7 1.0
SG D:CYS434 2.4 50.0 1.0
SG D:CYS431 2.4 37.1 1.0
CB D:CYS434 3.1 46.0 1.0
CB D:CYS411 3.3 35.8 1.0
CB D:CYS431 3.4 33.9 1.0
CB D:CYS427 3.5 48.1 1.0
N D:CYS427 3.8 52.2 1.0
CA D:CYS411 3.8 35.6 1.0
N D:CYS431 3.9 36.9 1.0
CA D:CYS427 4.1 49.6 1.0
N D:ALA428 4.1 51.7 1.0
CA D:CYS431 4.2 36.3 1.0
N D:ARG412 4.3 37.0 1.0
CA D:CYS434 4.3 46.2 1.0
N D:CYS434 4.3 45.2 1.0
CD2 D:HIS413 4.3 39.1 1.0
C D:CYS411 4.4 41.0 1.0
C D:CYS427 4.5 54.7 1.0
C D:GLY430 4.5 42.7 1.0
N D:HIS413 4.7 37.6 1.0
N D:GLY430 4.8 44.7 1.0
C D:ALA426 4.8 60.1 1.0
C D:CYS431 4.9 43.3 1.0
O D:CYS431 4.9 44.4 1.0
CB D:ALA426 4.9 61.6 1.0
CA D:ALA426 4.9 60.7 1.0
CB D:HIS413 4.9 37.1 1.0
CA D:GLY430 5.0 42.4 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 Oct 27 20:52:51 2024

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