Atomistry » Zinc » PDB 7zdp-7zn7 » 7zmm
Atomistry »
  Zinc »
    PDB 7zdp-7zn7 »
      7zmm »

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

Go back to Zinc Binding Sites List in 7zmm
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

Go back to Zinc Binding Sites List in 7zmm
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

Go back to Zinc Binding Sites List in 7zmm
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy