Zinc in PDB 5bqk: Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1

Protein crystallography data

The structure of Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1, PDB code: 5bqk was solved by V.Patel, V.Rajakannan, S.Dahlroth, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.80 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.983, 120.335, 79.037, 90.00, 100.46, 90.00
R / Rfree (%) 21.7 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1 (pdb code 5bqk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1, PDB code: 5bqk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5bqk

Go back to Zinc Binding Sites List in 5bqk
Zinc binding site 1 out of 3 in the Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1


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 C-Terminal Domain of ICP27 Protein From Hsv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:33.5
occ:1.00
NE2 A:HIS479 2.0 30.4 1.0
SG A:CYS400 2.1 33.4 1.0
SG A:CYS488 2.4 33.0 1.0
SG A:CYS483 2.4 35.8 1.0
CD2 A:HIS479 2.9 33.4 1.0
CE1 A:HIS479 3.0 26.6 1.0
CB A:CYS488 3.1 29.0 1.0
CB A:CYS400 3.2 33.6 1.0
CB A:CYS483 3.4 37.7 1.0
CG A:HIS479 4.1 28.5 1.0
ND1 A:HIS479 4.1 25.2 1.0
CA A:CYS400 4.4 33.6 1.0
O A:HOH807 4.5 27.0 1.0
C A:CYS400 4.5 32.5 1.0
CA A:CYS488 4.6 30.6 1.0
N A:TYR401 4.7 30.2 1.0
O A:HOH782 4.7 40.2 1.0
CA A:CYS483 4.8 37.5 1.0
CB A:SER485 4.9 36.7 1.0
O A:CYS400 5.0 33.8 1.0

Zinc binding site 2 out of 3 in 5bqk

Go back to Zinc Binding Sites List in 5bqk
Zinc binding site 2 out of 3 in the Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1


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 C-Terminal Domain of ICP27 Protein From Hsv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:35.8
occ:1.00
SG B:CYS400 1.9 32.6 1.0
NE2 B:HIS479 2.0 31.7 1.0
SG B:CYS488 2.4 39.1 1.0
SG B:CYS483 2.5 42.0 1.0
CE1 B:HIS479 2.7 31.7 1.0
CD2 B:HIS479 3.2 36.2 1.0
CB B:CYS400 3.2 34.9 1.0
CB B:CYS488 3.2 39.5 1.0
CB B:CYS483 3.3 43.6 1.0
ND1 B:HIS479 3.9 36.3 1.0
CG B:HIS479 4.2 31.4 1.0
CA B:CYS400 4.4 35.4 1.0
O B:HOH787 4.4 31.1 1.0
C B:CYS400 4.4 35.8 1.0
O B:HOH783 4.5 36.3 1.0
N B:TYR401 4.6 34.6 1.0
O B:HOH778 4.6 42.0 1.0
CA B:CYS488 4.6 39.0 1.0
CA B:CYS483 4.8 44.5 1.0
O B:CYS400 4.9 34.1 1.0

Zinc binding site 3 out of 3 in 5bqk

Go back to Zinc Binding Sites List in 5bqk
Zinc binding site 3 out of 3 in the Crystal Structure of C-Terminal Domain of ICP27 Protein From Hsv-1


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 C-Terminal Domain of ICP27 Protein From Hsv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:37.8
occ:1.00
NE2 C:HIS479 2.0 37.0 1.0
SG C:CYS400 2.2 36.9 1.0
SG C:CYS488 2.3 33.7 1.0
SG C:CYS483 2.4 38.6 1.0
CE1 C:HIS479 3.0 38.4 1.0
CD2 C:HIS479 3.0 35.6 1.0
CB C:CYS488 3.2 32.6 1.0
CB C:CYS483 3.3 40.9 1.0
CB C:CYS400 3.4 35.5 1.0
ND1 C:HIS479 4.1 38.5 1.0
CG C:HIS479 4.1 35.2 1.0
O C:HOH770 4.4 33.4 1.0
CA C:CYS400 4.6 37.4 1.0
C C:CYS400 4.6 37.3 1.0
CA C:CYS488 4.6 31.5 1.0
N C:TYR401 4.7 37.7 1.0
O C:HOH759 4.7 36.5 1.0
O C:HOH755 4.8 32.7 1.0
CA C:CYS483 4.8 40.7 1.0
CB C:SER485 4.8 37.3 1.0
O C:CYS400 5.0 36.7 1.0

Reference:

V.Patel, S.L.Dahlroth, V.Rajakannan, H.T.Ho, T.Cornvik, P.Nordlund. Structure of the C-Terminal Domain of the Multifunctional ICP27 Protein From Herpes Simplex Virus 1. J.Virol. V. 89 8828 2015.
ISSN: ESSN 1098-5514
PubMed: 26085142
DOI: 10.1128/JVI.00441-15
Page generated: Wed Dec 16 06:04:56 2020

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