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Zinc in PDB 8cx1: Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1

Enzymatic activity of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1

All present enzymatic activity of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1:
3.5.4.38;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 (pdb code 8cx1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1, PDB code: 8cx1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8cx1

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:169.2
occ:1.00
 ND1 A:HIS257 2.2 26.1 1.0
SG A:CYS291 2.3 37.3 1.0
SG A:CYS288 2.3 47.7 1.0
CE1 A:HIS257 3.0 26.1 1.0
CG A:HIS257 3.0 26.1 1.0
CB A:CYS288 3.3 47.7 1.0
CB A:CYS291 3.4 37.3 1.0
CB A:HIS257 3.5 26.1 1.0
OE1 A:GLU259 3.7 22.7 1.0
NE2 A:HIS257 3.8 26.1 1.0
CD2 A:HIS257 3.8 26.1 1.0
N A:CYS288 4.1 47.7 1.0
CD A:GLU259 4.3 22.7 1.0
CA A:CYS288 4.3 47.7 1.0
N A:CYS291 4.3 37.3 1.0
OE2 A:GLU259 4.4 22.7 1.0
CA A:CYS291 4.4 37.3 1.0
CA A:HIS257 4.9 26.1 1.0
C A:CYS288 5.0 47.7 1.0

Zinc binding site 2 out of 6 in 8cx1

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:39.2
occ:1.00
 ND1 A:HIS65 2.3 16.8 1.0
SG A:CYS100 2.3 18.9 1.0
SG A:CYS97 2.3 18.4 1.0
CE1 A:HIS65 3.1 16.8 1.0
CG A:HIS65 3.1 16.8 1.0
CB A:CYS100 3.3 18.9 1.0
CB A:CYS97 3.4 18.4 1.0
CB A:HIS65 3.6 16.8 1.0
OE1 A:GLU67 3.7 21.3 1.0
NE2 A:HIS65 3.9 16.8 1.0
N A:CYS97 4.0 18.4 1.0
CD2 A:HIS65 4.0 16.8 1.0
CA A:CYS97 4.3 18.4 1.0
CA A:CYS100 4.5 18.9 1.0
N A:CYS100 4.5 18.9 1.0
CD A:GLU67 4.5 21.3 1.0
OE2 A:GLU67 4.7 21.3 1.0

Zinc binding site 3 out of 6 in 8cx1

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:88.4
occ:1.00
 NE2 B:HIS139 2.0 29.9 1.0
NE2 B:HIS108 2.0 22.9 1.0
SG B:CYS133 2.3 38.9 1.0
SG B:CYS114 2.3 36.8 1.0
CD2 B:HIS139 2.8 29.9 1.0
CE1 B:HIS108 2.9 22.9 1.0
CD2 B:HIS108 3.0 22.9 1.0
CB B:CYS133 3.1 38.9 1.0
CE1 B:HIS139 3.2 29.9 1.0
CB B:CYS114 3.4 36.8 1.0
ND1 B:HIS108 3.9 22.9 1.0
CA B:CYS133 4.0 38.9 1.0
CG B:HIS108 4.0 22.9 1.0
O B:TYR135 4.1 23.0 1.0
CG B:HIS139 4.1 29.9 1.0
CA B:CYS114 4.1 36.8 1.0
ND1 B:HIS139 4.2 29.9 1.0
O B:ASP113 4.4 32.6 1.0
CG C:ARG151 4.5 35.0 1.0
C B:CYS133 4.8 38.9 1.0
N B:GLU134 4.9 32.0 1.0
C B:TYR135 4.9 23.0 1.0
N B:TYR135 4.9 23.0 1.0

Zinc binding site 4 out of 6 in 8cx1

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:226.8
occ:1.00
 SG F:CYS288 2.3 69.5 1.0
ND1 F:HIS257 2.3 48.4 1.0
SG F:CYS291 2.3 57.7 1.0
CE1 F:HIS257 2.9 48.4 1.0
CB F:CYS288 3.1 69.5 1.0
CG F:HIS257 3.3 48.4 1.0
N F:CYS288 3.5 69.5 1.0
CB F:CYS291 3.6 57.7 1.0
CB F:HIS257 3.8 48.4 1.0
CA F:CYS288 3.9 69.5 1.0
NE2 F:HIS257 4.0 48.4 1.0
OE1 F:GLU259 4.2 43.6 1.0
CD2 F:HIS257 4.2 48.4 1.0
OE2 F:GLU259 4.3 43.6 1.0
CD F:GLU259 4.4 43.6 1.0
N F:CYS291 4.6 57.7 1.0
C F:CYS288 4.7 69.5 1.0
C F:PRO287 4.7 60.1 1.0
CA F:CYS291 4.7 57.7 1.0
CA F:PRO287 4.9 60.1 1.0

Zinc binding site 5 out of 6 in 8cx1

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:129.7
occ:1.00
 SG F:CYS100 2.3 34.3 1.0
SG F:CYS97 2.3 32.3 1.0
ND1 F:HIS65 2.3 37.0 1.0
OE1 F:GLU67 2.9 32.5 1.0
CE1 F:HIS65 3.1 37.0 1.0
CG F:HIS65 3.3 37.0 1.0
CB F:CYS100 3.4 34.3 1.0
CB F:CYS97 3.5 32.3 1.0
CD F:GLU67 3.6 32.5 1.0
OE2 F:GLU67 3.6 32.5 1.0
N F:CYS97 3.7 32.3 1.0
CB F:HIS65 3.7 37.0 1.0
CA F:CYS97 4.2 32.3 1.0
NE2 F:HIS65 4.3 37.0 1.0
CD2 F:HIS65 4.4 37.0 1.0
CD1 F:LEU62 4.6 37.6 1.0
C F:PRO96 4.7 23.6 1.0
CA F:CYS100 4.7 34.3 1.0
CA F:PRO96 4.7 23.6 1.0
N F:CYS100 4.8 34.3 1.0
CG F:GLU67 5.0 32.5 1.0

Zinc binding site 6 out of 6 in 8cx1

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:132.1
occ:1.00
 NE2 G:HIS139 2.0 66.4 1.0
NE2 G:HIS108 2.0 55.4 1.0
SG G:CYS133 2.3 73.7 1.0
SG G:CYS114 2.3 74.5 1.0
CE1 G:HIS139 2.9 66.4 1.0
CD2 G:HIS139 3.0 66.4 1.0
CE1 G:HIS108 3.0 55.4 1.0
CD2 G:HIS108 3.0 55.4 1.0
CB G:CYS114 3.3 74.5 1.0
O G:TYR135 3.3 50.3 1.0
CB G:CYS133 3.3 73.7 1.0
O G:ASP113 3.5 63.2 1.0
CA G:CYS114 3.9 74.5 1.0
CA G:CYS133 4.0 73.7 1.0
ND1 G:HIS139 4.0 66.4 1.0
CG G:HIS139 4.1 66.4 1.0
ND1 G:HIS108 4.1 55.4 1.0
CG G:HIS108 4.2 55.4 1.0
C G:TYR135 4.3 50.3 1.0
C G:ASP113 4.3 63.2 1.0
N G:TYR135 4.5 50.3 1.0
N G:CYS114 4.5 74.5 1.0
N G:GLU134 4.6 57.0 1.0
C G:CYS133 4.7 73.7 1.0
CB G:TYR135 4.8 50.3 1.0
CA G:TYR135 4.8 50.3 1.0

Reference:

Y.Li, C.Langley, C.M.Azumaya, I.Echeverria, N.M.Chesarino, M.Emerman, Y.Cheng, J.D.Gross. The Structural Basis of Hiv-1 Vif Antagonism of Human APOBEC3G Nature 2023.
ISSN: ESSN 1476-4687
Page generated: Wed Oct 30 18:58:09 2024

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