Zinc in PDB 8cx2: Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 2

Enzymatic activity of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 2

All present enzymatic activity of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Dimeric Complex in State 2:
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 2 (pdb code 8cx2). 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 2, PDB code: 8cx2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8cx2

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:173.8
occ:1.00
 ND1 A:HIS257 2.3 79.5 1.0
SG A:CYS288 2.3 104.4 1.0
SG A:CYS291 2.3 93.8 1.0
CE1 A:HIS257 3.0 79.5 1.0
CB A:CYS288 3.1 104.4 1.0
CG A:HIS257 3.2 79.5 1.0
N A:CYS288 3.5 104.4 1.0
CB A:CYS291 3.5 93.8 1.0
CB A:HIS257 3.7 79.5 1.0
CA A:CYS288 3.9 104.4 1.0
NE2 A:HIS257 3.9 79.5 1.0
CD2 A:HIS257 4.1 79.5 1.0
OE1 A:GLU259 4.5 77.0 1.0
OE2 A:GLU259 4.6 77.0 1.0
C A:PRO287 4.6 95.5 1.0
CD A:GLU259 4.7 77.0 1.0
N A:CYS291 4.8 93.8 1.0
CA A:CYS291 4.8 93.8 1.0
C A:CYS288 4.8 104.4 1.0
CA A:PRO287 4.9 95.5 1.0

Zinc binding site 2 out of 6 in 8cx2

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:83.6
occ:1.00
 SG A:CYS97 2.3 46.4 1.0
SG A:CYS100 2.3 56.5 1.0
ND1 A:HIS65 2.3 48.8 1.0
CE1 A:HIS65 3.1 48.8 1.0
CB A:CYS97 3.1 46.4 1.0
CG A:HIS65 3.3 48.8 1.0
CB A:CYS100 3.4 56.5 1.0
N A:CYS97 3.6 46.4 1.0
OE2 A:GLU67 3.7 53.1 1.0
CB A:HIS65 3.7 48.8 1.0
OE1 A:GLU67 3.9 53.1 1.0
CA A:CYS97 4.0 46.4 1.0
CD A:GLU67 4.0 53.1 1.0
NE2 A:HIS65 4.2 48.8 1.0
CD2 A:HIS65 4.3 48.8 1.0
CA A:CYS100 4.7 56.5 1.0
C A:PRO96 4.7 43.1 1.0
N A:CYS100 4.7 56.5 1.0
C A:CYS97 4.9 46.4 1.0
CA A:PRO96 4.9 43.1 1.0

Zinc binding site 3 out of 6 in 8cx2

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:114.1
occ:1.00
 NE2 B:HIS139 2.0 84.2 1.0
NE2 B:HIS108 2.0 74.8 1.0
SG B:CYS114 2.3 94.6 1.0
SG B:CYS133 2.3 90.4 1.0
CE1 B:HIS139 2.7 84.2 1.0
CE1 B:HIS108 2.8 74.8 1.0
CD2 B:HIS108 3.1 74.8 1.0
CD2 B:HIS139 3.3 84.2 1.0
CB B:CYS114 3.3 94.6 1.0
CB B:CYS133 3.4 90.4 1.0
ND1 B:HIS108 3.9 74.8 1.0
ND1 B:HIS139 3.9 84.2 1.0
CG B:HIS108 4.1 74.8 1.0
CA B:CYS114 4.1 94.6 1.0
O B:TYR135 4.2 72.5 1.0
CG B:HIS139 4.2 84.2 1.0
CG C:GLU152 4.3 99.9 1.0
CA B:CYS133 4.3 90.4 1.0
OE2 C:GLU152 4.6 99.9 1.0
CG C:ARG151 4.8 89.0 1.0
CD C:GLU152 4.8 99.9 1.0
N B:PHE115 4.9 102.0 1.0

Zinc binding site 4 out of 6 in 8cx2

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:199.1
occ:1.00
 SG F:CYS291 2.3 124.2 1.0
ND1 F:HIS257 2.3 104.7 1.0
SG F:CYS288 2.3 132.8 1.0
CE1 F:HIS257 2.6 104.7 1.0
CB F:CYS288 3.0 132.8 1.0
CG F:HIS257 3.1 104.7 1.0
NE2 F:HIS257 3.4 104.7 1.0
CD2 F:HIS257 3.7 104.7 1.0
CB F:CYS291 3.7 124.2 1.0
CB F:HIS257 3.8 104.7 1.0
N F:CYS288 3.8 132.8 1.0
CA F:CYS288 4.0 132.8 1.0
N F:CYS291 4.6 124.2 1.0
C F:CYS288 4.7 132.8 1.0
CA F:CYS291 4.8 124.2 1.0

Zinc binding site 5 out of 6 in 8cx2

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:91.3
occ:1.00
 ND1 F:HIS65 2.3 57.8 1.0
SG F:CYS100 2.3 58.8 1.0
SG F:CYS97 2.3 49.5 1.0
OE1 F:GLU67 3.0 55.4 1.0
OE2 F:GLU67 3.2 55.4 1.0
CG F:HIS65 3.2 57.8 1.0
CE1 F:HIS65 3.3 57.8 1.0
CB F:CYS100 3.4 58.8 1.0
CD F:GLU67 3.4 55.4 1.0
CB F:HIS65 3.5 57.8 1.0
CB F:CYS97 3.6 49.5 1.0
N F:CYS97 3.7 49.5 1.0
CA F:CYS97 4.3 49.5 1.0
NE2 F:HIS65 4.3 57.8 1.0
CD2 F:HIS65 4.4 57.8 1.0
CA F:CYS100 4.6 58.8 1.0
CG F:GLU67 4.7 55.4 1.0
C F:PRO96 4.8 45.3 1.0
N F:CYS100 4.8 58.8 1.0
CA F:PRO96 4.8 45.3 1.0
CA F:HIS65 4.9 57.8 1.0

Zinc binding site 6 out of 6 in 8cx2

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:202.3
occ:1.00
 NE2 G:HIS139 2.0 162.0 1.0
NE2 G:HIS108 2.0 137.0 1.0
SG G:CYS114 2.3 162.6 1.0
SG G:CYS133 2.3 156.4 1.0
CE1 G:HIS108 2.7 137.0 1.0
CE1 G:HIS139 2.9 162.0 1.0
CB G:CYS114 3.1 162.6 1.0
CD2 G:HIS139 3.1 162.0 1.0
CD2 G:HIS108 3.2 137.0 1.0
CB G:CYS133 3.5 156.4 1.0
CA G:CYS114 3.7 162.6 1.0
O G:TYR135 3.8 125.1 1.0
ND1 G:HIS108 3.8 137.0 1.0
ND1 G:HIS139 4.0 162.0 1.0
CG G:HIS108 4.1 137.0 1.0
CG G:HIS139 4.2 162.0 1.0
O G:ASP113 4.2 143.0 1.0
CA G:CYS133 4.3 156.4 1.0
C G:TYR135 4.6 125.1 1.0
N G:CYS114 4.6 162.6 1.0
CG H:ARG151 4.7 166.0 1.0
N G:TYR135 4.8 125.1 1.0
C G:ASP113 4.8 143.0 1.0
N G:PHE115 4.8 174.1 1.0
C G:CYS114 4.8 162.6 1.0
CB G:TYR135 5.0 125.1 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 18:58:13 2024

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