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Zinc in PDB 3u9g: Crystal Structure of the Zinc Finger Antiviral Protein

Protein crystallography data

The structure of Crystal Structure of the Zinc Finger Antiviral Protein, PDB code: 3u9g was solved by S.Chen, Y.Xu, K.Zhang, X.Wang, J.Sun, G.Gao, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.49 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.894, 52.894, 138.275, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zinc Finger Antiviral Protein (pdb code 3u9g). 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 the Zinc Finger Antiviral Protein, PDB code: 3u9g:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3u9g

Go back to Zinc Binding Sites List in 3u9g
Zinc binding site 1 out of 4 in the Crystal Structure of the Zinc Finger Antiviral Protein


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 the Zinc Finger Antiviral Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn226

b:30.7
occ:1.00
NE2 A:HIS86 1.9 29.7 1.0
SG A:CYS73 2.3 30.2 1.0
SG A:CYS78 2.3 28.3 1.0
SG A:CYS82 2.4 36.4 1.0
CE1 A:HIS86 2.9 33.4 1.0
CD2 A:HIS86 3.0 30.0 1.0
CB A:CYS73 3.1 29.2 1.0
CB A:CYS78 3.2 28.7 1.0
CB A:CYS82 3.3 38.9 1.0
ND1 A:HIS86 4.0 34.2 1.0
CG A:HIS86 4.1 29.2 1.0
CD A:ARG75 4.2 32.5 1.0
O A:HOH305 4.3 33.7 1.0
O A:HOH361 4.3 39.9 1.0
O A:HOH283 4.4 38.5 1.0
NH1 A:ARG75 4.5 41.2 1.0
CA A:CYS73 4.5 24.1 1.0
CA A:CYS78 4.6 34.1 1.0
CA A:CYS82 4.7 41.1 1.0
NE A:ARG75 4.7 41.9 1.0
CZ A:ARG75 4.8 42.1 1.0
CG A:ARG75 4.9 33.8 1.0
CB A:ARG75 4.9 33.1 1.0

Zinc binding site 2 out of 4 in 3u9g

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Zinc binding site 2 out of 4 in the Crystal Structure of the Zinc Finger Antiviral Protein


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 the Zinc Finger Antiviral Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn227

b:31.0
occ:1.00
NE2 A:HIS110 2.0 21.6 1.0
SG A:CYS96 2.3 30.0 1.0
SG A:CYS88 2.3 26.4 1.0
SG A:CYS106 2.4 30.8 1.0
CD2 A:HIS110 2.8 28.9 1.0
CE1 A:HIS110 3.0 29.2 1.0
CB A:CYS88 3.2 28.6 1.0
CB A:CYS106 3.3 35.6 1.0
CB A:CYS96 3.4 32.6 1.0
CG A:HIS110 4.0 27.4 1.0
ND1 A:HIS110 4.1 30.8 1.0
CB A:ASN91 4.3 27.4 1.0
O A:HOH391 4.5 44.7 1.0
O A:TYR108 4.5 34.1 1.0
CA A:CYS88 4.6 26.5 1.0
CB A:TYR98 4.6 38.2 1.0
CD2 A:TYR98 4.7 39.7 1.0
CA A:CYS106 4.7 32.5 1.0
CA A:CYS96 4.8 36.0 1.0
N A:ASN91 4.8 27.1 1.0
CB A:TYR108 4.9 29.2 1.0

Zinc binding site 3 out of 4 in 3u9g

Go back to Zinc Binding Sites List in 3u9g
Zinc binding site 3 out of 4 in the Crystal Structure of the Zinc Finger Antiviral Protein


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 the Zinc Finger Antiviral Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn228

b:33.2
occ:1.00
NE2 A:HIS172 2.2 31.0 1.0
SG A:CYS168 2.3 31.6 1.0
SG A:CYS150 2.3 31.3 1.0
SG A:CYS162 2.4 33.6 1.0
CD2 A:HIS172 3.1 29.5 1.0
CE1 A:HIS172 3.2 33.2 1.0
CB A:CYS150 3.2 28.1 1.0
CB A:CYS168 3.2 34.7 1.0
CB A:CYS162 3.5 49.4 1.0
CG A:HIS172 4.2 29.8 1.0
ND1 A:HIS172 4.3 31.0 1.0
O A:ARG170 4.5 25.4 1.0
CA A:CYS150 4.6 26.8 1.0
CA A:CYS168 4.7 34.2 1.0
CB A:SER152 4.7 45.7 1.0
CB A:TYR153 4.8 34.4 1.0
O A:HOH409 4.8 44.9 1.0
N A:TYR153 4.9 37.9 1.0
CA A:CYS162 4.9 47.9 1.0
O A:HOH290 4.9 44.2 1.0

Zinc binding site 4 out of 4 in 3u9g

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Zinc binding site 4 out of 4 in the Crystal Structure of the Zinc Finger Antiviral Protein


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 the Zinc Finger Antiviral Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn229

b:23.0
occ:1.00
NE2 A:HIS191 2.1 21.8 1.0
SG A:CYS182 2.3 19.0 1.0
SG A:CYS174 2.3 20.7 1.0
SG A:CYS187 2.4 22.3 1.0
CE1 A:HIS191 3.0 22.0 1.0
CB A:CYS187 3.1 24.4 1.0
CD2 A:HIS191 3.2 20.8 1.0
CB A:CYS174 3.2 20.0 1.0
CB A:CYS182 3.3 19.8 1.0
ND1 A:HIS191 4.2 21.1 1.0
CB A:PHE177 4.3 17.5 1.0
CG A:HIS191 4.3 20.2 1.0
O A:ARG189 4.4 24.5 1.0
CA A:CYS187 4.6 26.2 1.0
N A:PHE177 4.6 20.6 1.0
CA A:CYS174 4.6 20.4 1.0
CA A:CYS182 4.6 19.0 1.0
CB A:ARG189 4.8 24.5 1.0
CA A:PHE177 4.9 19.9 1.0
CD2 A:TYR184 4.9 23.2 1.0

Reference:

S.Chen, Y.Xu, K.Zhang, X.Wang, J.Sun, G.Gao, Y.Liu. Structure of N-Terminal Domain of Zap Indicates How A Zinc-Finger Protein Recognizes Complex Rna. Nat.Struct.Mol.Biol. V. 19 430 2012.
ISSN: ISSN 1545-9993
PubMed: 22407013
DOI: 10.1038/NSMB.2243
Page generated: Wed Dec 16 04:53:51 2020

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