Atomistry » Zinc » PDB 5jwl-5k8c » 5k81
Atomistry »
  Zinc »
    PDB 5jwl-5k8c »
      5k81 »

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

Go back to Zinc Binding Sites List in 5k81
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

Go back to Zinc Binding Sites List in 5k81
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

Go back to Zinc Binding Sites List in 5k81
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

Go back to Zinc Binding Sites List in 5k81
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

Go back to Zinc Binding Sites List in 5k81
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: Wed Dec 16 06:26:29 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy