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Zinc in PDB 7zmm: Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G2-001

Enzymatic activity of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G2-001

All present enzymatic activity of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G2-001:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G2-001, PDB code: 7zmm 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) 95.94 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.612, 183.969, 100.947, 90, 108.12, 90
R / Rfree (%) 23.6 / 28.1

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) G2-001 (pdb code 7zmm). 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) G2-001, PDB code: 7zmm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7zmm

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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) G2-001


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) G2-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:63.1
occ:1.00
 SG B:CYS427 2.1 53.3 1.0
SG B:CYS411 2.3 57.3 1.0
SG B:CYS434 2.3 76.5 1.0
SG B:CYS431 2.3 55.2 1.0
CB B:CYS434 3.0 70.3 1.0
CB B:CYS427 3.1 64.6 1.0
CB B:CYS411 3.3 49.3 1.0
CB B:CYS431 3.4 67.1 1.0
CA B:CYS411 3.6 57.0 1.0
N B:CYS431 4.0 57.6 1.0
N B:ARG412 4.1 52.2 1.0
CA B:CYS434 4.2 78.2 1.0
N B:CYS434 4.2 73.4 1.0
CA B:CYS431 4.2 60.9 1.0
C B:CYS411 4.3 50.7 1.0
CA B:CYS427 4.4 67.9 1.0
CD2 B:HIS413 4.5 41.9 1.0
C B:GLY430 4.6 67.8 1.0
N B:GLY430 4.7 73.0 1.0
C B:CYS431 4.8 65.7 1.0
N B:HIS413 4.9 59.0 1.0
N B:CYS411 4.9 53.1 1.0
O B:CYS431 4.9 63.2 1.0

Zinc binding site 2 out of 4 in 7zmm

Go back to Zinc Binding Sites List in 7zmm
Zinc binding site 2 out of 4 in the Crystal Structure of Human RECQL5 Helicase Apo Form in Complex with Engineered Nanobody (Gluebody) G2-001


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) G2-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:68.5
occ:1.00
 SG A:CYS427 2.0 65.2 1.0
SG A:CYS411 2.3 74.0 1.0
SG A:CYS434 2.4 81.0 1.0
SG A:CYS431 2.4 68.4 1.0
CB A:CYS427 3.0 74.4 1.0
CB A:CYS434 3.1 73.8 1.0
CB A:CYS411 3.3 58.5 1.0
CB A:CYS431 3.5 65.8 1.0
CA A:CYS411 3.7 57.9 1.0
N A:CYS431 4.0 54.6 1.0
N A:ARG412 4.1 67.4 1.0
CA A:CYS431 4.3 63.1 1.0
CA A:CYS434 4.3 87.0 1.0
N A:CYS434 4.3 82.5 1.0
C A:CYS411 4.4 68.8 1.0
CD2 A:HIS413 4.4 64.6 1.0
CA A:CYS427 4.4 74.0 1.0
C A:GLY430 4.5 68.1 1.0
O A:CYS427 4.6 91.4 1.0
N A:GLY430 4.7 89.9 1.0
C A:CYS427 4.8 82.0 1.0
N A:HIS413 4.8 60.3 1.0
C A:CYS431 4.9 63.5 1.0
CB A:HIS413 4.9 65.6 1.0
N A:CYS411 5.0 52.9 1.0
O A:CYS431 5.0 64.2 1.0

Zinc binding site 3 out of 4 in 7zmm

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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) G2-001


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) G2-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:69.6
occ:1.00
 SG C:CYS427 2.1 58.0 1.0
SG C:CYS431 2.2 70.8 1.0
SG C:CYS434 2.4 107.5 1.0
SG C:CYS411 2.4 72.5 1.0
CB C:CYS434 3.0 99.1 1.0
CB C:CYS427 3.2 74.9 1.0
CB C:CYS431 3.3 62.3 1.0
CB C:CYS411 3.4 54.6 1.0
CA C:CYS411 3.7 67.0 1.0
N C:CYS431 3.8 55.5 1.0
CA C:CYS431 4.0 61.4 1.0
N C:CYS434 4.1 67.3 1.0
CA C:CYS434 4.1 85.1 1.0
N C:ARG412 4.1 76.0 1.0
C C:CYS411 4.4 75.5 1.0
C C:GLY430 4.4 53.9 1.0
CD2 C:HIS413 4.5 75.4 1.0
CA C:CYS427 4.6 75.0 1.0
N C:GLY430 4.6 71.9 1.0
C C:CYS431 4.6 63.7 1.0
O C:CYS431 4.7 61.0 1.0
N C:HIS413 4.9 58.5 1.0
N C:CYS411 5.0 56.5 1.0

Zinc binding site 4 out of 4 in 7zmm

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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) G2-001


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) G2-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:166.4
occ:1.00
 SG D:CYS434 1.9 135.9 1.0
SG D:CYS427 2.2 116.1 1.0
SG D:CYS431 2.4 116.0 1.0
SG D:CYS411 2.6 167.2 1.0
CB D:CYS434 2.7 148.7 1.0
CB D:CYS427 3.1 115.2 1.0
CB D:CYS411 3.4 127.0 1.0
CB D:CYS431 3.6 127.7 1.0
CA D:CYS411 3.7 116.9 1.0
CA D:CYS434 3.8 142.8 1.0
N D:CYS434 3.9 132.7 1.0
N D:CYS431 4.1 125.3 1.0
N D:ARG412 4.3 134.6 1.0
CA D:CYS431 4.3 121.2 1.0
C D:CYS411 4.5 132.4 1.0
CA D:CYS427 4.5 146.0 1.0
N D:GLY430 4.7 173.9 1.0
C D:GLY430 4.7 135.4 1.0
O D:CYS431 4.7 120.7 1.0
C D:CYS431 4.8 115.7 1.0
N D:CYS411 4.9 108.9 1.0
CD2 D:HIS413 4.9 165.2 1.0
ND1 D:HIS433 5.0 140.2 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 17:09:37 2024

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