Zinc in PDB 5pyl: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 81)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 81), PDB code: 5pyl 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) 42.72 / 1.53
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.560, 45.460, 83.360, 90.00, 101.85, 90.00
R / Rfree (%) 17.8 / 20.9

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 81) (pdb code 5pyl). 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 81), PDB code: 5pyl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5pyl

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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 81)


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 81) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:23.8
occ:1.00
ND1 A:HIS725 2.1 21.3 1.0
SG A:CYS708 2.3 24.2 1.0
SG A:CYS705 2.3 23.0 1.0
SG A:CYS728 2.4 23.9 1.0
CE1 A:HIS725 3.0 29.1 1.0
CB A:CYS705 3.0 21.4 1.0
CG A:HIS725 3.2 28.5 1.0
CB A:CYS728 3.3 21.3 1.0
CB A:CYS708 3.4 22.6 1.0
CB A:HIS725 3.6 25.9 1.0
N A:CYS708 3.8 22.2 1.0
O A:HOH1276 4.0 55.0 1.0
N A:HIS725 4.1 25.3 1.0
CA A:CYS708 4.1 21.3 1.0
NE2 A:HIS725 4.1 28.2 1.0
CD2 A:HIS725 4.3 27.1 1.0
CA A:HIS725 4.4 23.3 1.0
CA A:CYS705 4.5 22.9 1.0
O A:HOH1259 4.6 34.3 1.0
CA A:CYS728 4.6 19.6 1.0
CB A:VAL707 4.7 17.3 1.0
C A:CYS708 4.8 25.8 1.0
C A:VAL707 4.9 22.6 1.0
N A:ASN709 5.0 24.1 1.0

Zinc binding site 2 out of 5 in 5pyl

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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 81)


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 81) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:29.7
occ:1.00
SG A:CYS717 2.3 31.4 1.0
SG A:CYS742 2.3 23.5 1.0
SG A:CYS720 2.3 35.1 1.0
SG A:CYS745 2.4 29.3 1.0
CB A:CYS717 3.2 33.1 1.0
CB A:CYS742 3.3 23.9 1.0
CB A:CYS720 3.3 33.1 1.0
CB A:CYS745 3.4 26.6 1.0
N A:CYS742 3.7 27.5 1.0
N A:CYS720 3.8 32.8 1.0
CA A:CYS742 4.0 24.1 1.0
N A:CYS745 4.0 24.6 1.0
CA A:CYS720 4.1 35.3 1.0
OG1 A:THR719 4.1 36.9 1.0
CA A:CYS745 4.3 24.9 1.0
O A:CYS742 4.3 23.1 1.0
C A:CYS742 4.5 24.2 1.0
C A:THR719 4.5 36.0 1.0
O A:CYS720 4.6 37.3 1.0
C A:CYS720 4.6 28.0 1.0
CA A:CYS717 4.6 37.0 1.0
NH1 A:ARG722 4.7 28.7 1.0
C A:SER741 4.8 24.2 1.0
O A:HOH1243 4.8 41.1 1.0
CB A:PHE744 4.9 24.4 1.0
N A:THR719 5.0 39.5 1.0
CA A:SER741 5.0 30.9 1.0

Zinc binding site 3 out of 5 in 5pyl

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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 81)


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 81) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:99.6
occ:0.43
OE2 A:GLU756 2.8 58.7 1.0
SG A:CYS754 2.9 49.4 0.6
OE1 A:GLU756 3.1 44.4 1.0
CD A:GLU756 3.4 47.4 1.0
O A:ARG753 3.5 41.5 1.0
CA A:CYS754 3.5 34.2 0.6
CB A:CYS754 3.5 37.0 0.6
CA A:CYS754 3.5 30.5 0.5
SG A:CYS754 3.7 28.3 0.5
CB A:CYS754 3.8 29.4 0.5
C A:ARG753 4.3 36.1 1.0
CD A:PRO755 4.4 30.5 1.0
N A:CYS754 4.4 33.1 1.0
C A:CYS754 4.5 31.4 1.0
N A:PRO755 4.8 28.8 1.0
CG A:GLU756 4.9 39.9 1.0

Zinc binding site 4 out of 5 in 5pyl

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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 81)


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 81) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:19.6
occ:1.00
ND1 B:HIS725 2.1 20.4 1.0
SG B:CYS728 2.3 19.1 1.0
SG B:CYS708 2.3 20.4 1.0
SG B:CYS705 2.4 18.8 1.0
CE1 B:HIS725 3.0 23.9 1.0
CB B:CYS705 3.1 17.4 1.0
CG B:HIS725 3.1 21.0 1.0
CB B:CYS728 3.2 18.4 1.0
CB B:CYS708 3.4 19.9 1.0
CB B:HIS725 3.5 19.2 1.0
N B:CYS708 3.8 19.5 1.0
CA B:CYS708 4.1 18.7 1.0
NE2 B:HIS725 4.2 22.5 1.0
N B:HIS725 4.2 19.8 1.0
CD2 B:HIS725 4.2 21.5 1.0
CA B:HIS725 4.4 18.3 1.0
CA B:CYS705 4.5 19.4 1.0
O B:HOH1209 4.6 26.5 1.0
CA B:CYS728 4.6 17.6 1.0
CB B:VAL707 4.7 17.6 1.0
C B:CYS708 4.8 23.5 1.0
C B:VAL707 4.9 20.6 1.0

Zinc binding site 5 out of 5 in 5pyl

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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 81)


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 81) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:23.7
occ:1.00
SG B:CYS717 2.3 25.3 1.0
SG B:CYS720 2.3 24.9 1.0
SG B:CYS742 2.3 20.0 1.0
SG B:CYS745 2.4 24.9 1.0
CB B:CYS717 3.2 21.0 1.0
CB B:CYS720 3.3 27.5 1.0
CB B:CYS742 3.4 19.8 1.0
CB B:CYS745 3.5 19.8 1.0
N B:CYS720 3.7 30.4 1.0
N B:CYS742 3.8 20.6 1.0
CA B:CYS720 4.0 28.7 1.0
N B:CYS745 4.0 19.5 1.0
OG1 B:THR719 4.1 25.4 1.0
CA B:CYS742 4.1 19.3 1.0
CA B:CYS745 4.3 22.6 1.0
C B:THR719 4.4 29.3 1.0
O B:HOH1189 4.5 33.3 1.0
O B:CYS742 4.6 18.8 1.0
NH1 B:ARG722 4.6 26.0 1.0
C B:CYS720 4.6 29.5 1.0
C B:CYS742 4.6 19.0 1.0
CA B:CYS717 4.7 22.2 1.0
O B:CYS720 4.7 27.8 1.0
CB B:PHE744 4.9 19.9 1.0
C B:SER741 4.9 22.9 1.0
N B:THR719 4.9 27.8 1.0
CB B:ARG722 5.0 23.0 1.0
CA B:THR719 5.0 28.1 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: Wed Dec 16 06:43:42 2020

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