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Zinc in PDB 7zml: Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G1-001

Enzymatic activity of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G1-001

All present enzymatic activity of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G1-001:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G1-001, PDB code: 7zml 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) 96.35 / 2.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.74, 185.53, 101.01, 90, 107.47, 90
R / Rfree (%) 22.4 / 26.1

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) G1-001 (pdb code 7zml). 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) G1-001, PDB code: 7zml:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7zml

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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) G1-001


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) G1-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:101.4
occ:1.00
 SG A:CYS431 2.1 112.8 1.0
SG A:CYS427 2.3 68.5 1.0
SG A:CYS411 2.3 92.4 1.0
SG A:CYS434 2.4 122.7 1.0
CB A:CYS434 3.0 116.8 1.0
CB A:CYS411 3.1 70.4 1.0
CB A:CYS431 3.1 105.5 1.0
CA A:CYS411 3.2 73.7 1.0
CB A:CYS427 3.5 94.8 1.0
N A:ARG412 3.8 95.8 1.0
C A:CYS411 3.9 76.2 1.0
N A:CYS434 3.9 97.2 1.0
N A:CYS431 3.9 81.4 1.0
CA A:CYS431 4.0 87.5 1.0
CA A:CYS434 4.0 110.2 1.0
N A:CYS411 4.5 75.2 1.0
C A:CYS431 4.6 76.5 1.0
CD2 A:HIS413 4.6 102.1 1.0
O A:CYS431 4.6 72.9 1.0
N A:HIS413 4.7 74.0 1.0
C A:GLY430 4.7 76.8 1.0
CA A:CYS427 4.9 106.5 1.0
ND1 A:HIS433 4.9 111.2 1.0
O A:CYS411 5.0 97.1 1.0
N A:GLY430 5.0 99.8 1.0

Zinc binding site 2 out of 4 in 7zml

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Zinc binding site 2 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G1-001


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) G1-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:99.3
occ:1.00
 SG B:CYS427 2.1 82.8 1.0
SG B:CYS434 2.2 109.8 1.0
SG B:CYS431 2.3 101.8 1.0
SG B:CYS411 2.4 80.0 1.0
CB B:CYS434 3.0 123.7 1.0
CB B:CYS411 3.2 74.2 1.0
CB B:CYS427 3.2 120.8 1.0
CB B:CYS431 3.2 104.6 1.0
CA B:CYS411 3.4 74.5 1.0
N B:CYS431 3.9 95.6 1.0
N B:ARG412 4.0 86.7 1.0
N B:CYS434 4.1 115.5 1.0
CA B:CYS431 4.1 96.7 1.0
CA B:CYS434 4.1 126.8 1.0
C B:CYS411 4.1 80.7 1.0
CD2 B:HIS413 4.5 84.5 1.0
CA B:CYS427 4.6 114.6 1.0
N B:CYS411 4.6 78.7 1.0
C B:GLY430 4.6 104.6 1.0
O B:CYS431 4.7 69.6 1.0
C B:CYS431 4.7 81.8 1.0
N B:GLY430 4.8 132.3 1.0
N B:HIS413 4.9 71.8 1.0
ND1 B:HIS433 4.9 115.5 1.0

Zinc binding site 3 out of 4 in 7zml

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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) G1-001


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) G1-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:102.1
occ:1.00
 SG C:CYS427 2.0 100.9 1.0
SG C:CYS434 2.1 114.9 1.0
SG C:CYS411 2.3 95.5 1.0
SG C:CYS431 2.5 120.9 1.0
CB C:CYS434 3.0 105.5 1.0
CB C:CYS427 3.1 114.7 1.0
CB C:CYS411 3.2 93.0 1.0
CB C:CYS431 3.4 103.4 1.0
CA C:CYS411 3.4 92.4 1.0
N C:CYS431 4.0 94.2 1.0
N C:ARG412 4.1 94.7 1.0
C C:CYS411 4.1 91.6 1.0
CA C:CYS434 4.2 113.5 1.0
N C:CYS434 4.2 113.7 1.0
CA C:CYS431 4.2 96.3 1.0
CD2 C:HIS413 4.5 94.8 1.0
CA C:CYS427 4.5 111.3 1.0
C C:GLY430 4.7 96.8 1.0
N C:CYS411 4.7 103.2 1.0
N C:GLY430 4.8 105.1 1.0
O C:CYS431 4.8 91.6 1.0
C C:CYS431 4.8 80.6 1.0
N C:HIS413 4.8 82.5 1.0

Zinc binding site 4 out of 4 in 7zml

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Zinc binding site 4 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G1-001


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) G1-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:146.6
occ:1.00
 SG D:CYS431 2.2 160.3 1.0
SG D:CYS434 2.2 168.4 1.0
SG D:CYS427 2.2 104.4 1.0
SG D:CYS411 2.6 150.1 1.0
CB D:CYS434 3.0 164.1 1.0
CB D:CYS431 3.1 149.5 1.0
CB D:CYS411 3.3 123.5 1.0
CA D:CYS411 3.4 109.5 1.0
CB D:CYS427 3.4 111.7 1.0
N D:CYS431 3.8 111.3 1.0
N D:ARG412 3.9 143.4 1.0
CA D:CYS431 3.9 116.3 1.0
N D:CYS434 3.9 186.1 1.0
CA D:CYS434 4.0 178.1 1.0
C D:CYS411 4.1 136.8 1.0
O D:CYS431 4.5 126.9 1.0
C D:CYS431 4.5 106.2 1.0
C D:GLY430 4.5 126.0 1.0
CD2 D:HIS413 4.6 163.9 1.0
N D:CYS411 4.6 102.5 1.0
N D:GLY430 4.7 171.5 1.0
CA D:CYS427 4.8 135.1 1.0
N D:HIS413 4.9 100.2 1.0
ND1 D:HIS433 4.9 188.1 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: Fri Aug 22 07:53:47 2025

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