Zinc in PDB 7uu5: Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna

Protein crystallography data

The structure of Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna, PDB code: 7uu5 was solved by H.J.Yang, S.-X.Li, X.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.51 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.305, 71.559, 72.71, 119.39, 111, 90.08
R / Rfree (%) 18.7 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna (pdb code 7uu5). 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 APOBEC3G Complex with 5'-Overhang Dsrna, PDB code: 7uu5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7uu5

Go back to Zinc Binding Sites List in 7uu5
Zinc binding site 1 out of 4 in the Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna


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 APOBEC3G Complex with 5'-Overhang Dsrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:129.5
occ:1.00
ND1 A:HIS65 2.0 149.7 1.0
SG A:CYS97 2.3 122.8 1.0
SG A:CYS100 2.3 85.7 1.0
CE1 A:HIS65 2.6 147.7 1.0
CG A:HIS65 3.1 139.5 1.0
CB A:CYS97 3.4 118.6 1.0
CB A:CYS100 3.6 79.6 1.0
NE2 A:HIS65 3.7 146.9 1.0
CB A:HIS65 3.8 118.1 1.0
CD2 A:HIS65 4.0 146.4 1.0
OE2 A:GLU67 4.0 115.1 1.0
CB A:ALA62 4.1 103.2 1.0
N A:CYS97 4.1 108.1 1.0
N A:CYS100 4.2 92.2 1.0
CA A:CYS97 4.3 111.9 1.0
CA A:CYS100 4.6 81.4 1.0
CD A:GLU67 4.7 110.3 1.0
CA A:ALA62 4.8 107.2 1.0
OE1 A:GLU67 4.8 115.5 1.0
C A:CYS97 4.8 108.3 1.0

Zinc binding site 2 out of 4 in 7uu5

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Zinc binding site 2 out of 4 in the Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna


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 APOBEC3G Complex with 5'-Overhang Dsrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:96.1
occ:0.68
SG A:CYS287 2.3 75.9 1.0
SG A:CYS290 2.3 94.4 1.0
CB A:CYS287 3.1 74.7 1.0
N A:CYS287 3.3 68.5 1.0
CG A:HIS257 3.3 90.2 1.0
CB A:CYS290 3.5 86.9 1.0
CB A:HIS257 3.5 77.5 1.0
CD2 A:HIS257 3.5 94.6 1.0
ND1 A:HIS257 3.7 93.4 1.0
CA A:CYS287 3.8 70.8 1.0
NE2 A:HIS257 4.0 95.4 1.0
CE1 A:HIS257 4.1 95.8 1.0
C A:PRO286 4.4 64.3 1.0
CA A:PRO286 4.5 58.9 1.0
N A:CYS290 4.5 82.7 1.0
CA A:CYS290 4.6 82.4 1.0
C A:CYS287 4.6 71.3 1.0
O A:CYS287 4.9 68.8 1.0
CA A:HIS257 4.9 67.7 1.0

Zinc binding site 3 out of 4 in 7uu5

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Zinc binding site 3 out of 4 in the Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna


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 APOBEC3G Complex with 5'-Overhang Dsrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:124.1
occ:1.00
ND1 B:HIS65 2.0 139.0 1.0
OE1 B:GLU67 2.0 154.4 1.0
SG B:CYS100 2.2 84.0 1.0
SG B:CYS97 2.7 106.5 1.0
CE1 B:HIS65 2.8 135.6 1.0
CG B:HIS65 2.8 127.1 1.0
CD B:GLU67 3.0 139.8 1.0
CB B:HIS65 3.3 104.7 1.0
CB B:CYS100 3.3 71.7 1.0
OE2 B:GLU67 3.4 151.2 1.0
CB B:CYS97 3.6 106.3 1.0
NE2 B:HIS65 3.7 134.6 1.0
CD2 B:HIS65 3.8 133.7 1.0
N B:CYS97 3.9 102.0 1.0
CG B:GLU67 4.3 111.0 1.0
CA B:CYS97 4.3 102.6 1.0
N B:CYS100 4.5 88.7 1.0
CA B:CYS100 4.5 78.7 1.0
CA B:HIS65 4.8 90.5 1.0
CB B:GLU67 4.9 92.0 1.0
C B:PRO96 5.0 109.4 1.0
C B:CYS97 5.0 102.1 1.0

Zinc binding site 4 out of 4 in 7uu5

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Zinc binding site 4 out of 4 in the Crystal Structure of APOBEC3G Complex with 5'-Overhang Dsrna


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 APOBEC3G Complex with 5'-Overhang Dsrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:82.0
occ:0.58
ND1 B:HIS257 1.9 110.5 1.0
SG B:CYS290 2.3 88.3 1.0
SG B:CYS287 2.4 114.3 1.0
CE1 B:HIS257 2.6 107.3 1.0
CG B:HIS257 2.8 99.4 1.0
CB B:CYS287 2.8 106.6 1.0
CB B:HIS257 3.3 85.8 1.0
CB B:CYS290 3.5 87.6 1.0
NE2 B:HIS257 3.6 104.5 1.0
CD2 B:HIS257 3.7 102.9 1.0
N B:CYS287 3.7 95.2 1.0
CA B:CYS287 3.8 99.3 1.0
OG B:SER289 4.0 107.4 1.0
N B:CYS290 4.1 86.8 1.0
CA B:CYS290 4.4 86.7 1.0
C B:CYS287 4.5 97.0 1.0
CA B:HIS257 4.8 77.2 1.0
C B:PRO286 4.9 78.6 1.0
O B:CYS287 4.9 100.5 1.0

Reference:

H.Yang, K.Kim, S.Li, J.Pacheco, X.S.Chen. Structural Basis of Sequence-Specific Rna Recognition By the Antiviral Factor APOBEC3G. Nat Commun V. 13 7498 2022.
ISSN: ESSN 2041-1723
PubMed: 36470880
DOI: 10.1038/S41467-022-35201-9
Page generated: Sat Apr 8 04:28:59 2023

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