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Zinc in PDB 5k83: Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna

Protein crystallography data

The structure of Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna, PDB code: 5k83 was solved by X.Xiao, S.-X.Li, H.Yang, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.79 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.720, 83.311, 105.754, 90.00, 120.00, 90.00
R / Rfree (%) 18.7 / 25.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna (pdb code 5k83). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna, PDB code: 5k83:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5k83

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Zinc binding site 1 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna


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 Primate APOBEC3G N-Domain, in Complex with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:48.7
occ:1.00
 ND1 D:HIS65 1.9 56.4 1.0
SG D:CYS100 2.0 42.2 1.0
SG D:CYS97 2.4 54.0 1.0
O D:HOH517 2.5 44.0 1.0
CE1 D:HIS65 2.8 57.3 1.0
CG D:HIS65 3.0 51.5 1.0
CB D:CYS97 3.4 47.5 1.0
CB D:CYS100 3.4 49.8 1.0
CB D:HIS65 3.4 41.0 1.0
N D:CYS97 3.9 45.1 1.0
OE2 D:GLU67 4.0 45.0 1.0
NE2 D:HIS65 4.0 59.8 1.0
CD2 D:HIS65 4.1 53.5 1.0
N D:CYS100 4.1 55.7 1.0
CA D:CYS97 4.1 46.1 1.0
OE1 D:GLU67 4.2 39.3 1.0
CD D:GLU67 4.2 42.1 1.0
CA D:CYS100 4.4 46.7 1.0
O D:HOH529 4.5 51.8 1.0
O D:ALA62 4.6 60.6 1.0
CB D:ALA62 4.6 60.7 1.0
O D:CYS97 4.7 44.4 1.0
C D:CYS97 4.7 48.4 1.0
CA D:ALA62 4.9 61.9 1.0
CA D:HIS65 4.9 50.7 1.0

Zinc binding site 2 out of 6 in 5k83

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Zinc binding site 2 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna


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 Primate APOBEC3G N-Domain, in Complex with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:32.9
occ:1.00
 O I:HOH103 1.9 30.0 1.0
ND1 C:HIS65 2.1 29.2 1.0
SG C:CYS97 2.2 26.1 1.0
SG C:CYS100 2.2 28.1 1.0
CE1 C:HIS65 2.9 34.1 1.0
CG C:HIS65 3.1 30.8 1.0
CB C:CYS100 3.2 25.5 1.0
CB C:CYS97 3.5 24.9 1.0
CB C:HIS65 3.5 28.8 1.0
O C:HOH514 3.7 39.3 1.0
N C:CYS97 3.7 21.8 1.0
O2 I:DT11 3.8 36.3 1.0
OE2 C:GLU67 3.9 31.9 1.0
NE2 C:HIS65 4.1 33.4 1.0
N C:CYS100 4.1 26.6 1.0
CA C:CYS97 4.1 29.8 1.0
CD2 C:HIS65 4.2 36.7 1.0
CA C:CYS100 4.2 26.4 1.0
CD C:GLU67 4.3 27.9 1.0
OE1 C:GLU67 4.3 27.4 1.0
CZ2 C:TRP94 4.6 28.3 1.0
C C:CYS97 4.7 28.7 1.0
O C:CYS97 4.7 27.7 1.0
C C:PRO96 4.9 27.1 1.0

Zinc binding site 3 out of 6 in 5k83

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Zinc binding site 3 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna


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 Primate APOBEC3G N-Domain, in Complex with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:50.6
occ:1.00
 ND1 F:HIS65 2.0 55.9 1.0
SG F:CYS100 2.0 40.7 1.0
O F:HOH513 2.4 46.2 1.0
SG F:CYS97 2.5 55.2 1.0
CE1 F:HIS65 2.9 59.3 1.0
CG F:HIS65 3.0 53.9 1.0
CB F:CYS100 3.3 49.8 1.0
CB F:HIS65 3.4 43.6 1.0
CB F:CYS97 3.5 51.3 1.0
N F:CYS97 3.9 44.0 1.0
NE2 F:HIS65 4.0 62.0 1.0
OE2 F:GLU67 4.0 44.6 1.0
CD2 F:HIS65 4.1 56.2 1.0
OE1 F:GLU67 4.1 41.0 1.0
N F:CYS100 4.2 56.4 1.0
CA F:CYS97 4.2 47.6 1.0
CD F:GLU67 4.3 46.0 1.0
CB F:ALA62 4.3 63.4 1.0
CA F:CYS100 4.3 47.5 1.0
O F:HOH541 4.3 52.6 1.0
O F:ALA62 4.6 61.5 1.0
CA F:ALA62 4.7 64.2 1.0
O F:CYS97 4.7 48.5 1.0
C F:CYS97 4.7 49.4 1.0
CA F:HIS65 4.9 53.9 1.0
O F:HOH530 5.0 53.1 1.0
C F:PRO96 5.0 44.5 1.0

Zinc binding site 4 out of 6 in 5k83

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Zinc binding site 4 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna


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 Primate APOBEC3G N-Domain, in Complex with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:29.1
occ:1.00
 ND1 E:HIS65 2.0 29.0 1.0
O E:HOH507 2.0 33.6 1.0
SG E:CYS100 2.2 25.9 1.0
SG E:CYS97 2.2 60.9 1.0
CE1 E:HIS65 2.9 32.0 1.0
CG E:HIS65 3.1 34.6 1.0
CB E:CYS100 3.2 24.0 1.0
CB E:CYS97 3.4 30.8 1.0
CB E:HIS65 3.5 29.6 1.0
O E:HOH533 3.6 40.4 1.0
O2 J:DT11 3.7 38.8 1.0
N E:CYS97 3.8 21.7 1.0
OE2 E:GLU67 3.9 29.7 1.0
NE2 E:HIS65 4.0 35.0 1.0
N E:CYS100 4.1 26.0 1.0
CD2 E:HIS65 4.1 37.8 1.0
CA E:CYS97 4.2 31.4 1.0
CA E:CYS100 4.2 26.1 1.0
OE1 E:GLU67 4.2 28.4 1.0
CD E:GLU67 4.3 27.6 1.0
O E:CYS97 4.7 25.7 1.0
C E:CYS97 4.7 28.8 1.0
CZ2 E:TRP94 4.7 30.4 1.0
C2 J:DT11 4.9 39.1 1.0
C E:PRO96 5.0 29.9 1.0

Zinc binding site 5 out of 6 in 5k83

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Zinc binding site 5 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:50.7
occ:1.00
 ND1 B:HIS65 2.0 57.4 1.0
SG B:CYS100 2.1 42.0 1.0
SG B:CYS97 2.4 55.1 1.0
O B:HOH505 2.5 46.0 1.0
CE1 B:HIS65 2.9 56.7 1.0
CG B:HIS65 3.0 53.3 1.0
CB B:CYS97 3.3 51.2 1.0
CB B:HIS65 3.4 44.3 1.0
CB B:CYS100 3.4 49.2 1.0
OE2 B:GLU67 3.9 46.5 1.0
N B:CYS97 3.9 45.4 1.0
NE2 B:HIS65 4.0 64.0 1.0
CD2 B:HIS65 4.0 55.1 1.0
CA B:CYS97 4.1 48.8 1.0
OE1 B:GLU67 4.2 41.0 1.0
CD B:GLU67 4.2 43.3 1.0
N B:CYS100 4.3 55.5 1.0
CA B:CYS100 4.4 46.9 1.0
CB B:ALA62 4.5 62.3 1.0
O B:ALA62 4.6 58.4 1.0
C B:CYS97 4.7 50.5 1.0
O B:CYS97 4.8 46.9 1.0
CA B:ALA62 4.9 64.0 1.0
CA B:HIS65 4.9 54.1 1.0

Zinc binding site 6 out of 6 in 5k83

Go back to Zinc Binding Sites List in 5k83
Zinc binding site 6 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Primate APOBEC3G N-Domain, in Complex with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:27.5
occ:1.00
 O A:HOH510 2.0 24.3 1.0
ND1 A:HIS65 2.1 30.9 1.0
SG A:CYS100 2.2 26.9 1.0
SG A:CYS97 2.2 29.3 1.0
CE1 A:HIS65 2.9 32.6 1.0
CB A:CYS100 3.2 25.4 1.0
CG A:HIS65 3.2 32.5 1.0
CB A:CYS97 3.4 28.7 1.0
CB A:HIS65 3.6 29.8 1.0
O A:HOH521 3.7 36.7 1.0
N A:CYS97 3.8 25.0 1.0
O2 H:DT11 3.8 39.4 1.0
OE2 A:GLU67 3.9 29.5 1.0
N A:CYS100 4.1 26.1 1.0
NE2 A:HIS65 4.1 34.0 1.0
CA A:CYS97 4.1 30.8 1.0
CA A:CYS100 4.2 26.2 1.0
CD2 A:HIS65 4.2 38.1 1.0
CD A:GLU67 4.3 26.8 1.0
OE1 A:GLU67 4.3 29.2 1.0
C A:CYS97 4.7 28.7 1.0
O A:CYS97 4.7 27.9 1.0
CZ2 A:TRP94 4.7 38.3 1.0
O H:HOH102 4.9 45.8 1.0
C A:PRO96 4.9 27.0 1.0

Reference:

X.Xiao, S.X.Li, H.Yang, X.S.Chen. Crystal Structures of APOBEC3G N-Domain Alone and Its Complex with Dna. Nat Commun V. 7 12193 2016.
ISSN: ESSN 2041-1723
PubMed: 27480941
DOI: 10.1038/NCOMMS12193
Page generated: Sun Oct 27 20:10:34 2024

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