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Zinc in PDB 5k81: Crystal Structure of A Primate APOBEC3G N-Terminal Domain

Protein crystallography data

The structure of Crystal Structure of A Primate APOBEC3G N-Terminal Domain, PDB code: 5k81 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) 46.01 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.213, 81.297, 106.298, 90.00, 120.03, 90.00
R / Rfree (%) 18.8 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain (pdb code 5k81). 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-Terminal Domain, PDB code: 5k81:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5k81

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Zinc binding site 1 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.8
occ:1.00
 O A:HOH538 2.0 23.6 1.0
ND1 A:HIS65 2.1 35.4 1.0
SG A:CYS100 2.3 25.6 1.0
SG A:CYS97 2.3 27.7 1.0
CE1 A:HIS65 3.0 35.5 1.0
CG A:HIS65 3.2 31.4 1.0
CB A:CYS100 3.2 22.9 1.0
CB A:CYS97 3.4 29.2 1.0
CB A:HIS65 3.6 26.8 1.0
N A:CYS97 3.8 23.5 1.0
N A:CYS100 4.1 22.9 1.0
CA A:CYS97 4.1 23.8 1.0
OE2 A:GLU67 4.1 36.0 1.0
NE2 A:HIS65 4.2 37.2 1.0
OE1 A:GLU67 4.2 27.2 1.0
CA A:CYS100 4.2 24.5 1.0
CD2 A:HIS65 4.3 34.1 1.0
CB A:ALA62 4.3 36.0 1.0
CD A:GLU67 4.4 26.7 1.0
O A:CYS97 4.6 25.1 1.0
C A:CYS97 4.6 22.8 1.0
CA A:ALA62 4.7 39.5 1.0
O A:ALA62 4.8 36.4 1.0
C A:PRO96 4.9 26.4 1.0

Zinc binding site 2 out of 6 in 5k81

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Zinc binding site 2 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:25.0
occ:1.00
 O B:HOH546 1.9 21.9 1.0
ND1 B:HIS65 2.1 33.5 1.0
SG B:CYS100 2.2 25.7 1.0
SG B:CYS97 2.3 27.2 1.0
CE1 B:HIS65 3.0 37.3 1.0
CG B:HIS65 3.2 31.3 1.0
CB B:CYS100 3.2 22.5 1.0
CB B:CYS97 3.4 29.1 1.0
O B:HOH598 3.4 38.8 1.0
CB B:HIS65 3.6 25.5 1.0
N B:CYS97 3.8 25.1 1.0
N B:CYS100 4.0 23.3 1.0
OE2 B:GLU67 4.1 37.1 1.0
CA B:CYS97 4.1 25.9 1.0
NE2 B:HIS65 4.1 36.8 1.0
OE1 B:GLU67 4.2 28.4 1.0
CA B:CYS100 4.2 23.9 1.0
CD2 B:HIS65 4.2 33.5 1.0
CB B:ALA62 4.3 36.8 1.0
CD B:GLU67 4.3 28.5 1.0
O B:HOH551 4.5 38.7 1.0
O B:CYS97 4.6 26.1 1.0
C B:CYS97 4.6 25.8 1.0
CA B:ALA62 4.7 39.2 1.0
O B:ALA62 4.8 33.8 1.0
C B:PRO96 4.9 27.0 1.0

Zinc binding site 3 out of 6 in 5k81

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Zinc binding site 3 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:26.3
occ:1.00
 O C:HOH561 1.9 22.1 1.0
ND1 C:HIS65 2.0 33.9 1.0
SG C:CYS97 2.2 26.6 1.0
SG C:CYS100 2.3 27.4 1.0
CE1 C:HIS65 2.9 37.2 1.0
CG C:HIS65 3.1 30.2 1.0
CB C:CYS100 3.2 23.5 1.0
CB C:CYS97 3.4 28.8 1.0
O C:HOH600 3.5 44.1 1.0
CB C:HIS65 3.5 24.7 1.0
N C:CYS97 3.8 23.3 1.0
NE2 C:HIS65 4.0 39.1 1.0
N C:CYS100 4.1 21.8 1.0
CA C:CYS97 4.1 24.6 1.0
OE1 C:GLU67 4.1 26.9 1.0
CD2 C:HIS65 4.2 37.1 1.0
OE2 C:GLU67 4.2 36.6 1.0
CA C:CYS100 4.2 24.5 1.0
CD C:GLU67 4.4 27.8 1.0
O C:HOH556 4.5 39.3 1.0
O C:CYS97 4.6 23.3 1.0
C C:CYS97 4.6 25.5 1.0
CA C:ALA62 4.7 44.5 1.0
O C:ALA62 4.8 37.9 1.0
C C:PRO96 4.9 26.2 1.0

Zinc binding site 4 out of 6 in 5k81

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Zinc binding site 4 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:36.7
occ:1.00
 SG D:CYS100 2.0 37.6 1.0
ND1 D:HIS65 2.0 46.0 1.0
O D:HOH536 2.2 30.4 1.0
SG D:CYS97 2.4 35.6 1.0
CE1 D:HIS65 3.0 45.0 1.0
CG D:HIS65 3.1 39.6 1.0
CB D:CYS100 3.1 36.4 1.0
CB D:HIS65 3.4 36.6 1.0
CB D:CYS97 3.4 39.3 1.0
N D:CYS97 3.8 35.3 1.0
OE2 D:GLU67 3.8 40.7 1.0
N D:CYS100 4.1 37.2 1.0
NE2 D:HIS65 4.1 48.9 1.0
CA D:CYS97 4.1 39.2 1.0
CD2 D:HIS65 4.2 42.8 1.0
CA D:CYS100 4.2 31.9 1.0
CD D:GLU67 4.2 29.5 1.0
OE1 D:GLU67 4.2 39.9 1.0
CB D:ALA62 4.6 50.3 1.0
O D:CYS97 4.6 33.7 1.0
C D:CYS97 4.7 32.5 1.0
O D:ALA62 4.9 47.5 1.0
CA D:HIS65 4.9 38.0 1.0
O D:HOH528 4.9 35.9 1.0
C D:PRO96 4.9 34.7 1.0
CA D:ALA62 5.0 54.7 1.0

Zinc binding site 5 out of 6 in 5k81

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Zinc binding site 5 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:37.6
occ:1.00
 SG E:CYS100 2.0 35.4 1.0
ND1 E:HIS65 2.0 48.5 1.0
O E:HOH548 2.1 33.8 1.0
SG E:CYS97 2.4 35.9 1.0
CE1 E:HIS65 3.0 49.0 1.0
CG E:HIS65 3.0 39.9 1.0
CB E:CYS100 3.1 36.0 1.0
CB E:HIS65 3.3 35.7 1.0
CB E:CYS97 3.5 38.5 1.0
N E:CYS97 3.8 34.6 1.0
OE2 E:GLU67 3.9 43.4 1.0
NE2 E:HIS65 4.1 50.0 1.0
N E:CYS100 4.1 38.5 1.0
OE1 E:GLU67 4.1 36.9 1.0
CD2 E:HIS65 4.1 41.3 1.0
CA E:CYS97 4.2 37.4 1.0
CA E:CYS100 4.2 29.9 1.0
CD E:GLU67 4.2 31.9 1.0
O E:CYS97 4.7 32.4 1.0
C E:CYS97 4.7 31.6 1.0
CB E:ALA62 4.8 54.0 1.0
O E:ALA62 4.8 46.4 1.0
CA E:HIS65 4.9 40.7 1.0
C E:PRO96 4.9 33.9 1.0

Zinc binding site 6 out of 6 in 5k81

Go back to Zinc Binding Sites List in 5k81
Zinc binding site 6 out of 6 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:36.9
occ:1.00
 SG F:CYS100 1.9 34.6 1.0
ND1 F:HIS65 2.0 44.7 1.0
O F:HOH541 2.1 33.2 1.0
SG F:CYS97 2.4 36.1 1.0
CE1 F:HIS65 3.0 48.0 1.0
CG F:HIS65 3.0 39.8 1.0
CB F:CYS100 3.2 35.7 1.0
CB F:HIS65 3.3 34.5 1.0
CB F:CYS97 3.5 38.1 1.0
N F:CYS97 3.8 36.9 1.0
OE1 F:GLU67 3.9 39.5 1.0
NE2 F:HIS65 4.1 49.5 1.0
CD2 F:HIS65 4.1 44.0 1.0
N F:CYS100 4.1 38.2 1.0
CA F:CYS97 4.2 37.2 1.0
OE2 F:GLU67 4.2 34.9 1.0
CA F:CYS100 4.2 30.6 1.0
CD F:GLU67 4.3 33.2 1.0
CB F:ALA62 4.6 54.4 1.0
O F:CYS97 4.7 33.3 1.0
C F:CYS97 4.7 34.1 1.0
O F:ALA62 4.8 75.5 1.0
CA F:HIS65 4.8 39.1 1.0
CA F:ALA62 4.9 62.9 1.0
C F:PRO96 4.9 34.1 1.0
O F:HOH525 5.0 38.1 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 20:09:38 2024

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