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Zinc in PDB 5py5: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65), PDB code: 5py5 was solved by N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N.Wright, E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A.Dias, J.Ng, P.E.Brennan, O.Cox, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Vondelft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.33 / 1.44
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.560, 45.269, 83.133, 90.00, 102.56, 90.00
R / Rfree (%) 17.4 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65) (pdb code 5py5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65), PDB code: 5py5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5py5

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Zinc binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:21.2
occ:1.00
ND1 A:HIS725 2.1 20.5 1.0
SG A:CYS708 2.3 21.7 1.0
SG A:CYS728 2.4 21.0 1.0
SG A:CYS705 2.4 20.0 1.0
CE1 A:HIS725 3.0 26.2 1.0
CB A:CYS705 3.0 19.9 1.0
CG A:HIS725 3.2 23.9 1.0
CB A:CYS728 3.3 18.5 1.0
CB A:CYS708 3.4 21.3 1.0
CB A:HIS725 3.6 23.7 1.0
N A:CYS708 3.8 20.4 1.0
N A:HIS725 4.1 21.6 1.0
CA A:CYS708 4.2 21.7 1.0
NE2 A:HIS725 4.2 25.2 1.0
CD2 A:HIS725 4.3 26.4 1.0
CA A:HIS725 4.4 21.2 1.0
CA A:CYS705 4.5 19.6 1.0
CA A:CYS728 4.7 19.3 1.0
CB A:VAL707 4.7 17.5 1.0
O A:HOH1240 4.7 38.9 1.0
C A:CYS708 4.9 22.9 1.0
C A:VAL707 4.9 20.7 1.0

Zinc binding site 2 out of 5 in 5py5

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Zinc binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:27.4
occ:1.00
SG A:CYS742 2.3 21.6 1.0
SG A:CYS745 2.4 29.2 1.0
SG A:CYS720 2.4 30.5 1.0
SG A:CYS717 2.4 27.5 1.0
CB A:CYS717 3.2 27.0 1.0
CB A:CYS742 3.3 17.8 1.0
CB A:CYS720 3.3 32.5 1.0
CB A:CYS745 3.5 25.8 1.0
N A:CYS720 3.8 34.1 1.0
N A:CYS742 3.8 24.3 1.0
N A:CYS745 4.0 25.5 1.0
CA A:CYS720 4.0 35.2 1.0
CA A:CYS742 4.1 22.3 1.0
OG1 A:THR719 4.1 31.9 1.0
CA A:CYS745 4.3 26.1 1.0
O A:CYS742 4.4 21.5 1.0
C A:THR719 4.5 32.0 1.0
C A:CYS720 4.6 29.7 1.0
O A:CYS720 4.6 33.0 1.0
C A:CYS742 4.6 23.5 1.0
O A:HOH1146 4.6 44.2 1.0
CA A:CYS717 4.6 29.8 1.0
NH1 A:ARG722 4.6 28.9 1.0
CB A:PHE744 4.9 22.1 1.0
N A:THR719 4.9 33.8 1.0
C A:SER741 4.9 23.7 1.0
CB A:ARG722 4.9 23.3 1.0

Zinc binding site 3 out of 5 in 5py5

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Zinc binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:97.6
occ:0.43
OE1 A:GLU756 3.2 43.0 1.0
O A:ARG753 3.5 50.6 1.0
OE2 A:GLU756 3.5 61.9 1.0
CD A:GLU756 3.8 50.1 1.0
SG A:CYS754 3.9 50.4 0.6
CA A:CYS754 4.1 35.2 0.6
CA A:CYS754 4.1 31.3 0.5
CD A:PRO755 4.3 30.4 1.0
CB A:CYS754 4.5 38.4 0.6
C A:ARG753 4.5 43.6 1.0
CB A:CYS754 4.7 30.5 0.5
SG A:CYS754 4.8 28.7 0.5
N A:CYS754 4.8 34.5 1.0
N A:PRO755 5.0 30.8 1.0
C A:CYS754 5.0 32.8 1.0

Zinc binding site 4 out of 5 in 5py5

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Zinc binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:18.5
occ:1.00
ND1 B:HIS725 2.2 18.7 1.0
SG B:CYS728 2.3 18.4 1.0
SG B:CYS708 2.3 20.4 1.0
SG B:CYS705 2.4 18.1 1.0
CB B:CYS705 3.1 16.9 1.0
CE1 B:HIS725 3.1 21.8 1.0
CG B:HIS725 3.2 19.0 1.0
CB B:CYS728 3.2 17.0 1.0
CB B:CYS708 3.3 19.7 1.0
CB B:HIS725 3.6 19.3 1.0
N B:CYS708 3.8 19.5 1.0
CA B:CYS708 4.1 21.8 1.0
N B:HIS725 4.1 17.4 1.0
NE2 B:HIS725 4.2 21.1 1.0
CD2 B:HIS725 4.3 20.9 1.0
CA B:HIS725 4.4 16.6 1.0
CA B:CYS705 4.5 18.7 1.0
CA B:CYS728 4.7 16.2 1.0
O B:HOH1206 4.7 28.7 1.0
CB B:VAL707 4.7 17.8 1.0
C B:CYS708 4.8 23.7 1.0
C B:VAL707 4.9 20.8 1.0

Zinc binding site 5 out of 5 in 5py5

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Zinc binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 65) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:21.7
occ:1.00
SG B:CYS720 2.3 22.3 1.0
SG B:CYS742 2.3 18.8 1.0
SG B:CYS717 2.3 23.1 1.0
SG B:CYS745 2.4 23.5 1.0
CB B:CYS717 3.2 20.7 1.0
CB B:CYS720 3.3 23.2 1.0
CB B:CYS742 3.4 18.0 1.0
CB B:CYS745 3.5 19.5 1.0
N B:CYS742 3.8 19.0 1.0
N B:CYS720 3.8 25.2 1.0
N B:CYS745 4.0 18.9 1.0
CA B:CYS720 4.0 24.8 1.0
CA B:CYS742 4.1 17.9 1.0
OG1 B:THR719 4.1 26.3 1.0
CA B:CYS745 4.3 20.9 1.0
C B:THR719 4.4 25.8 1.0
O B:HOH1199 4.5 36.0 1.0
O B:CYS742 4.5 18.7 1.0
NH1 B:ARG722 4.6 24.7 1.0
C B:CYS720 4.6 23.3 1.0
C B:CYS742 4.6 16.9 1.0
CA B:CYS717 4.7 22.5 1.0
O B:CYS720 4.7 26.3 1.0
CB B:PHE744 4.9 17.9 1.0
N B:THR719 4.9 26.0 1.0
C B:SER741 4.9 22.3 1.0
CB B:ARG722 4.9 20.7 1.0
O B:THR719 5.0 27.6 1.0
CA B:THR719 5.0 23.7 1.0

Reference:

N.M.Pearce, T.Krojer, A.R.Bradley, P.Collins, R.P.Nowak, R.Talon, B.D.Marsden, S.Kelm, J.Shi, C.M.Deane, F.Von Delft. A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density. Nat Commun V. 8 15123 2017.
ISSN: ESSN 2041-1723
PubMed: 28436492
DOI: 10.1038/NCOMMS15123
Page generated: Thu Aug 21 06:48:02 2025

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