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Zinc in PDB 7zmv: Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006

Enzymatic activity of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006

All present enzymatic activity of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006, PDB code: 7zmv was solved by M.Ye, M.Makola, J.A.Newman, M.Fairhead, E.Maclean, T.Krojer, H.Aitkenhead, C.Bountra, O.Gileadi, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.69 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 232.589, 89.965, 164.126, 90, 110.06, 90
R / Rfree (%) 24.3 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006 (pdb code 7zmv). 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 Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006, PDB code: 7zmv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7zmv

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Zinc binding site 1 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006


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 Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:47.2
occ:1.00
 SG A:CYS427 2.1 48.0 1.0
SG A:CYS434 2.3 55.8 1.0
SG A:CYS431 2.4 44.2 1.0
SG A:CYS411 2.5 45.4 1.0
CB A:CYS427 3.1 53.2 1.0
CB A:CYS434 3.1 58.8 1.0
CB A:CYS411 3.4 42.7 1.0
CB A:CYS431 3.4 41.4 1.0
CA A:CYS411 3.8 44.1 1.0
N A:CYS431 3.9 46.0 1.0
N A:ARG412 4.1 51.5 1.0
CA A:CYS431 4.2 43.4 1.0
N A:CYS434 4.3 61.8 1.0
CA A:CYS434 4.3 65.8 1.0
CD2 A:HIS413 4.3 42.0 1.0
C A:CYS411 4.3 48.6 1.0
C A:GLY430 4.5 44.8 1.0
CA A:CYS427 4.5 52.0 1.0
N A:GLY430 4.6 52.0 1.0
N A:HIS413 4.6 45.9 1.0
O A:CYS431 4.8 47.4 1.0
C A:CYS431 4.8 45.0 1.0
CB A:HIS413 4.9 47.0 1.0
CA A:GLY430 5.0 46.6 1.0
CG A:HIS413 5.0 48.2 1.0

Zinc binding site 2 out of 4 in 7zmv

Go back to Zinc Binding Sites List in 7zmv
Zinc binding site 2 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006


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 Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:44.1
occ:1.00
 SG B:CYS427 2.2 39.7 1.0
SG B:CYS434 2.3 45.5 1.0
SG B:CYS431 2.4 39.6 1.0
SG B:CYS411 2.4 38.4 1.0
CB B:CYS434 3.1 50.2 1.0
CB B:CYS427 3.1 47.5 1.0
CB B:CYS411 3.3 35.8 1.0
CB B:CYS431 3.4 39.7 1.0
CA B:CYS411 3.7 38.2 1.0
N B:CYS431 4.0 40.1 1.0
N B:ARG412 4.1 38.6 1.0
N B:CYS434 4.2 48.7 1.0
CA B:CYS434 4.2 51.9 1.0
CA B:CYS431 4.2 39.5 1.0
C B:CYS411 4.3 42.0 1.0
CD2 B:HIS413 4.4 37.4 1.0
C B:GLY430 4.6 39.8 1.0
CA B:CYS427 4.6 50.6 1.0
N B:GLY430 4.6 47.7 1.0
N B:HIS413 4.7 39.3 1.0
O B:CYS431 4.8 39.4 1.0
C B:CYS431 4.8 39.1 1.0
N B:CYS411 4.9 38.6 1.0
CB B:HIS413 5.0 35.8 1.0

Zinc binding site 3 out of 4 in 7zmv

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Zinc binding site 3 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006


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 Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:42.0
occ:1.00
 SG C:CYS427 2.2 39.7 1.0
SG C:CYS434 2.3 48.2 1.0
SG C:CYS431 2.3 40.3 1.0
SG C:CYS411 2.4 36.0 1.0
CB C:CYS434 3.1 50.0 1.0
CB C:CYS427 3.1 49.9 1.0
CB C:CYS411 3.3 33.9 1.0
CB C:CYS431 3.4 37.2 1.0
CA C:CYS411 3.6 40.8 1.0
N C:CYS431 4.0 39.0 1.0
N C:ARG412 4.0 37.9 1.0
C C:CYS411 4.2 43.5 1.0
CA C:CYS431 4.2 38.9 1.0
N C:CYS434 4.3 48.2 1.0
CA C:CYS434 4.3 51.1 1.0
CD2 C:HIS413 4.3 35.4 1.0
C C:GLY430 4.6 38.6 1.0
CA C:CYS427 4.6 55.8 1.0
N C:HIS413 4.6 34.6 1.0
N C:GLY430 4.7 46.9 1.0
O C:CYS431 4.8 39.7 1.0
C C:CYS431 4.8 37.5 1.0
CB C:HIS413 4.9 37.0 1.0
N C:CYS411 4.9 39.8 1.0

Zinc binding site 4 out of 4 in 7zmv

Go back to Zinc Binding Sites List in 7zmv
Zinc binding site 4 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006


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 Apo Form in Complex with Engineered Nanobody (Gluebody) G5-006 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:44.9
occ:1.00
 SG D:CYS427 2.1 41.4 1.0
SG D:CYS431 2.3 42.8 1.0
SG D:CYS434 2.4 48.6 1.0
SG D:CYS411 2.5 40.9 1.0
CB D:CYS427 3.1 50.3 1.0
CB D:CYS434 3.2 52.0 1.0
CB D:CYS411 3.3 43.9 1.0
CB D:CYS431 3.4 39.4 1.0
CA D:CYS411 3.7 41.2 1.0
N D:CYS431 3.9 45.3 1.0
N D:ARG412 4.0 37.2 1.0
CA D:CYS431 4.2 48.0 1.0
N D:CYS434 4.3 60.9 1.0
C D:CYS411 4.3 39.0 1.0
CD2 D:HIS413 4.3 36.0 1.0
CA D:CYS434 4.3 58.6 1.0
C D:GLY430 4.5 42.4 1.0
CA D:CYS427 4.5 52.8 1.0
N D:GLY430 4.6 48.3 1.0
N D:HIS413 4.6 35.6 1.0
O D:CYS431 4.8 44.3 1.0
C D:CYS431 4.8 44.5 1.0
CB D:HIS413 4.9 31.7 1.0
CG D:HIS413 5.0 36.0 1.0
CA D:GLY430 5.0 43.4 1.0

Reference:

M.Ye, M.Makola, J.A.Newman, M.Fairhead, E.Maclean, T.Krojer, N.D.Wright, L.Koekemoer, A.Thompson, G.A.Bezerra, G.Yi, H.Li, V.L.Rangel, D.Mamalis, H.Aitkenhead, R.J.C.Gilbert, K.Duerr, B.G.Davis, C.Bountra, O.Gileadi, F.Von Delft. Gluebodies Improve Crystal Reliability and Diversity Through Transferable Nanobody Mutations That Introduce Constitutive Crystal Contacts To Be Published.
Page generated: Wed Oct 30 17:12:20 2024

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