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Zinc in PDB 3csq: Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail

Protein crystallography data

The structure of Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail, PDB code: 3csq was solved by Y.Xiang, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.842, 133.963, 85.725, 90.00, 89.99, 90.00
R / Rfree (%) 23.8 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail (pdb code 3csq). 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 and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail, PDB code: 3csq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3csq

Go back to Zinc Binding Sites List in 3csq
Zinc binding site 1 out of 4 in the Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn335

b:28.2
occ:1.00
OD1 A:ASP195 1.9 19.2 1.0
ND1 A:HIS280 2.0 17.1 1.0
NE2 A:HIS188 2.1 15.5 1.0
O A:HOH359 2.3 29.9 1.0
CG A:ASP195 2.7 17.2 1.0
OD2 A:ASP195 2.9 17.8 1.0
CE1 A:HIS280 2.9 16.5 1.0
CE1 A:HIS188 3.0 13.8 1.0
CG A:HIS280 3.1 15.7 1.0
CD2 A:HIS188 3.2 18.6 1.0
CB A:HIS280 3.5 15.2 1.0
NE2 A:HIS280 4.1 18.2 1.0
CB A:ASP195 4.1 14.3 1.0
ND1 A:HIS188 4.2 16.2 1.0
CD2 A:HIS280 4.2 17.3 1.0
NE2 A:GLN180 4.2 17.9 1.0
OG A:SER187 4.3 23.5 1.0
CG A:HIS188 4.3 19.6 1.0
CA A:HIS280 4.4 13.9 1.0
NE2 A:HIS278 4.5 26.9 1.0
N A:ASP195 4.5 13.2 1.0
CA A:ASP195 4.6 14.1 1.0
NE2 A:HIS247 4.8 29.2 1.0
CB A:CYS193 4.8 14.2 1.0
C A:ILE194 4.9 12.5 1.0
CD2 A:HIS278 5.0 27.6 1.0

Zinc binding site 2 out of 4 in 3csq

Go back to Zinc Binding Sites List in 3csq
Zinc binding site 2 out of 4 in the Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn335

b:23.4
occ:1.00
ND1 B:HIS280 1.8 13.9 1.0
OD1 B:ASP195 2.0 16.3 1.0
NE2 B:HIS188 2.1 8.8 1.0
O B:HOH376 2.3 29.7 1.0
OD2 B:ASP195 2.7 17.1 1.0
CG B:ASP195 2.7 14.5 1.0
CG B:HIS280 2.8 13.6 1.0
CE1 B:HIS280 2.8 16.0 1.0
CE1 B:HIS188 3.1 9.7 1.0
CD2 B:HIS188 3.1 12.9 1.0
CB B:HIS280 3.2 13.1 1.0
NE2 B:HIS280 3.9 16.4 1.0
CD2 B:HIS280 3.9 14.7 1.0
CB B:ASP195 4.2 13.2 1.0
ND1 B:HIS188 4.2 8.8 1.0
OG B:SER187 4.3 17.8 1.0
CA B:HIS280 4.3 12.4 1.0
CG B:HIS188 4.3 10.9 1.0
NE2 B:HIS278 4.4 25.4 1.0
NE2 B:GLN180 4.4 14.5 1.0
NE2 B:HIS247 4.6 22.2 1.0
CA B:ASP195 4.7 12.2 1.0
CD2 B:HIS278 4.7 22.1 1.0
N B:ASP195 4.8 11.5 1.0
CB B:CYS193 4.8 9.2 1.0
C B:ILE194 5.0 11.4 1.0

Zinc binding site 3 out of 4 in 3csq

Go back to Zinc Binding Sites List in 3csq
Zinc binding site 3 out of 4 in the Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn335

b:25.2
occ:1.00
ND1 C:HIS280 2.0 13.9 1.0
OD1 C:ASP195 2.1 12.1 1.0
NE2 C:HIS188 2.2 12.5 1.0
O C:HOH355 2.2 22.6 1.0
CG C:ASP195 2.7 15.6 1.0
OD2 C:ASP195 2.7 18.4 1.0
CG C:HIS280 3.0 13.1 1.0
CE1 C:HIS188 3.0 12.3 1.0
CE1 C:HIS280 3.1 15.3 1.0
CD2 C:HIS188 3.2 16.1 1.0
CB C:HIS280 3.3 12.3 1.0
NE2 C:HIS278 4.1 26.4 1.0
CD2 C:HIS280 4.1 15.6 1.0
NE2 C:HIS280 4.1 14.8 1.0
CB C:ASP195 4.2 14.1 1.0
ND1 C:HIS188 4.2 13.8 1.0
CG C:HIS188 4.3 15.2 1.0
CA C:HIS280 4.3 11.5 1.0
OG C:SER187 4.4 21.6 1.0
NE2 C:GLN180 4.4 13.1 1.0
CD2 C:HIS278 4.7 23.1 1.0
CA C:ASP195 4.7 13.7 1.0
N C:ASP195 4.8 11.8 1.0
CB C:CYS193 4.8 10.1 1.0
NE2 C:HIS247 4.8 21.7 1.0

Zinc binding site 4 out of 4 in 3csq

Go back to Zinc Binding Sites List in 3csq
Zinc binding site 4 out of 4 in the Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn335

b:28.6
occ:1.00
NE2 D:HIS188 2.0 12.8 1.0
ND1 D:HIS280 2.1 17.7 1.0
OD1 D:ASP195 2.1 25.0 1.0
O D:HOH371 2.1 35.6 1.0
CG D:ASP195 2.7 18.9 1.0
OD2 D:ASP195 2.8 15.9 1.0
CE1 D:HIS280 2.8 18.1 1.0
CE1 D:HIS188 3.0 12.6 1.0
CD2 D:HIS188 3.1 13.3 1.0
CG D:HIS280 3.2 17.5 1.0
CB D:HIS280 3.8 14.5 1.0
NE2 D:HIS280 4.0 19.0 1.0
ND1 D:HIS188 4.1 12.4 1.0
OG D:SER187 4.2 15.4 1.0
NE2 D:GLN180 4.2 12.0 1.0
CG D:HIS188 4.2 13.3 1.0
CB D:ASP195 4.2 15.9 1.0
CD2 D:HIS280 4.2 19.0 1.0
NE2 D:HIS278 4.4 23.8 1.0
CA D:HIS280 4.6 13.9 1.0
N D:ASP195 4.7 14.1 1.0
CA D:ASP195 4.8 16.4 1.0
CB D:CYS193 4.8 13.5 1.0
NE2 D:HIS247 4.9 25.9 1.0
CD2 D:HIS278 4.9 25.5 1.0

Reference:

Y.Xiang, M.C.Morais, D.N.Cohen, V.D.Bowman, D.L.Anderson, M.G.Rossmann. Crystal and Cryoem Structural Studies of A Cell Wall Degrading Enzyme in the Bacteriophage PHI29 Tail. Proc.Natl.Acad.Sci.Usa V. 105 9552 2008.
ISSN: ISSN 0027-8424
PubMed: 18606992
DOI: 10.1073/PNAS.0803787105
Page generated: Wed Dec 16 04:11:22 2020

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