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Zinc in PDB 1pyi: Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster

Protein crystallography data

The structure of Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster, PDB code: 1pyi was solved by R.Marmorstein, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 53.800, 92.600, 174.700, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 33

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster (pdb code 1pyi). 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 A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster, PDB code: 1pyi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1pyi

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Zinc binding site 1 out of 4 in the Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster


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 A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn21

b:26.7
occ:1.00
SG A:CYS61 2.2 31.1 1.0
SG A:CYS54 2.3 34.1 1.0
SG A:CYS34 2.3 30.0 1.0
SG A:CYS51 2.4 30.1 1.0
CB A:CYS54 2.9 38.6 1.0
ZN A:ZN22 3.1 26.8 1.0
CB A:CYS34 3.2 26.6 1.0
CB A:CYS61 3.4 34.3 1.0
CB A:CYS51 3.7 31.5 1.0
CA A:CYS61 3.8 35.9 1.0
CA A:CYS54 4.2 42.7 1.0
N A:CYS51 4.2 35.3 1.0
O A:CYS51 4.3 41.5 1.0
N A:CYS54 4.3 45.7 1.0
CA A:CYS51 4.4 37.2 1.0
SG A:CYS37 4.5 27.9 1.0
CA A:CYS34 4.6 25.8 1.0
SG A:CYS44 4.7 26.5 1.0
C A:CYS61 4.7 35.2 1.0
C A:CYS51 4.7 41.3 1.0
CB A:ARG36 4.8 33.7 1.0
OG A:SER50 4.8 34.0 1.0
N A:CYS61 4.9 37.7 1.0
N A:VAL62 4.9 34.3 1.0

Zinc binding site 2 out of 4 in 1pyi

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Zinc binding site 2 out of 4 in the Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster


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 A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn22

b:26.8
occ:1.00
SG A:CYS44 2.2 26.5 1.0
SG A:CYS37 2.2 27.9 1.0
SG A:CYS51 2.3 30.1 1.0
SG A:CYS34 2.5 30.0 1.0
CB A:CYS44 3.1 28.7 1.0
ZN A:ZN21 3.1 26.7 1.0
CB A:CYS37 3.3 27.8 1.0
CB A:CYS51 3.3 31.5 1.0
CB A:CYS34 3.4 26.6 1.0
CA A:CYS44 3.4 31.7 1.0
N A:CYS34 3.9 26.6 1.0
N A:ASP45 4.2 37.2 1.0
CA A:CYS34 4.2 25.8 1.0
C A:CYS44 4.2 33.6 1.0
N A:CYS44 4.4 34.1 1.0
N A:CYS37 4.5 26.8 1.0
CA A:CYS37 4.5 27.4 1.0
SG A:CYS61 4.6 31.1 1.0
O A:CYS34 4.7 26.1 1.0
SG A:CYS54 4.7 34.1 1.0
CA A:CYS51 4.8 37.2 1.0
C A:CYS34 4.9 25.6 1.0
C A:ALA33 4.9 28.3 1.0

Zinc binding site 3 out of 4 in 1pyi

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Zinc binding site 3 out of 4 in the Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster


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 A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn321

b:12.7
occ:1.00
SG B:CYS54 2.2 19.9 1.0
SG B:CYS61 2.3 16.3 1.0
SG B:CYS51 2.3 16.1 1.0
SG B:CYS34 2.4 18.2 1.0
CB B:CYS61 2.8 11.8 1.0
ZN B:ZN322 3.0 16.5 1.0
CB B:CYS54 3.2 22.2 1.0
CB B:CYS34 3.5 17.5 1.0
CB B:CYS51 3.6 21.3 1.0
N B:CYS51 3.8 21.9 1.0
O B:CYS51 3.9 32.3 1.0
CA B:CYS61 4.1 8.7 1.0
CA B:CYS51 4.2 24.7 1.0
N B:CYS54 4.2 27.2 1.0
CA B:CYS54 4.3 26.3 1.0
C B:CYS51 4.5 28.9 1.0
C B:SER50 4.6 20.9 1.0
SG B:CYS44 4.7 19.6 1.0
SG B:CYS37 4.8 17.9 1.0
C B:CYS61 4.8 7.3 1.0
CA B:SER50 4.9 20.0 1.0
CG B:ARG36 5.0 13.8 1.0
CA B:CYS34 5.0 16.0 1.0

Zinc binding site 4 out of 4 in 1pyi

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Zinc binding site 4 out of 4 in the Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster


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 A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn322

b:16.5
occ:1.00
SG B:CYS44 2.3 19.6 1.0
SG B:CYS37 2.3 17.9 1.0
SG B:CYS34 2.3 18.2 1.0
SG B:CYS51 2.3 16.1 1.0
ZN B:ZN321 3.0 12.7 1.0
CB B:CYS44 3.2 19.3 1.0
CB B:CYS51 3.6 21.3 1.0
CB B:CYS37 3.8 13.1 1.0
CB B:CYS34 3.8 17.5 1.0
SG B:CYS54 4.0 19.9 1.0
CA B:CYS44 4.1 19.5 1.0
N B:CYS34 4.2 17.5 1.0
N B:CYS37 4.3 13.6 1.0
CA B:CYS34 4.5 16.0 1.0
CA B:CYS37 4.6 13.1 1.0
C B:CYS44 4.8 22.7 1.0
CB B:ARG53 4.9 30.2 1.0
NE B:ARG53 4.9 32.7 1.0
N B:ASP45 4.9 25.4 1.0
CD B:ARG53 4.9 30.4 1.0
SG B:CYS61 4.9 16.3 1.0
CA B:CYS51 5.0 24.7 1.0
OD1 B:ASP45 5.0 21.6 1.0

Reference:

R.Marmorstein, S.C.Harrison. Crystal Structure of A PPR1-Dna Complex: Dna Recognition By Proteins Containing A ZN2CYS6 Binuclear Cluster. Genes Dev. V. 8 2504 1994.
ISSN: ISSN 0890-9369
PubMed: 7958913
Page generated: Fri Sep 25 23:03:41 2020
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