Zinc in PDB 5va4: Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera

Enzymatic activity of Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera

All present enzymatic activity of Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera:
6.1.1.11;

Protein crystallography data

The structure of Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera, PDB code: 5va4 was solved by J.M.Wagner, B.K.Ganser-Pornillos, O.W.Pornillos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.95 / 2.31
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 104.596, 104.596, 104.596, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 28.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera (pdb code 5va4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera, PDB code: 5va4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5va4

Go back to Zinc Binding Sites List in 5va4
Zinc binding site 1 out of 3 in the Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:77.5
occ:1.00
OD2 A:ASP110 2.0 87.8 1.0
ND1 A:HIS124 2.0 84.7 1.0
ND1 A:HIS127 2.0 73.0 1.0
SG A:CYS107 2.2 79.0 1.0
CG A:ASP110 2.9 93.0 1.0
CE1 A:HIS127 2.9 82.8 1.0
HB3 A:HIS124 2.9 86.3 1.0
CE1 A:HIS124 3.0 70.1 1.0
CG A:HIS124 3.0 72.7 1.0
HE1 A:HIS127 3.1 99.3 1.0
CG A:HIS127 3.1 82.9 1.0
HE1 A:HIS124 3.1 84.1 1.0
HB3 A:HIS127 3.3 95.4 1.0
CB A:CYS107 3.3 66.3 1.0
HB2 A:HIS127 3.4 95.4 1.0
HB2 A:CYS107 3.4 79.6 1.0
CB A:HIS124 3.4 72.0 1.0
HA A:HIS124 3.4 97.6 1.0
HB3 A:CYS107 3.5 79.6 1.0
CB A:HIS127 3.5 79.5 1.0
HB2 A:ASP110 3.5 1.0 1.0
HB2 A:GLN109 3.5 0.3 1.0
OD1 A:ASP110 3.6 0.5 1.0
H A:ASP110 3.7 0.2 1.0
CB A:ASP110 3.8 93.3 1.0
CA A:HIS124 3.9 81.3 1.0
NE2 A:HIS127 4.1 80.1 1.0
NE2 A:HIS124 4.1 77.8 1.0
CD2 A:HIS124 4.1 78.6 1.0
CD2 A:HIS127 4.2 86.9 1.0
N A:ASP110 4.2 84.3 1.0
HB2 A:HIS124 4.3 86.3 1.0
CB A:GLN109 4.4 88.6 1.0
HB3 A:GLN109 4.4 0.3 1.0
O A:GLU123 4.4 80.8 1.0
HB3 A:ASP110 4.5 1.0 1.0
HD13 A:ILE114 4.5 88.3 1.0
H A:GLN109 4.6 96.4 1.0
CA A:ASP110 4.7 82.4 1.0
CA A:CYS107 4.7 83.7 1.0
N A:HIS124 4.7 81.4 1.0
HE2 A:HIS127 4.8 96.1 1.0
HE2 A:HIS124 4.9 93.3 1.0
C A:GLU123 4.9 86.6 1.0
HA A:CYS107 5.0 0.4 1.0
C A:GLN109 5.0 86.7 1.0

Zinc binding site 2 out of 3 in 5va4

Go back to Zinc Binding Sites List in 5va4
Zinc binding site 2 out of 3 in the Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:66.2
occ:1.00
ND1 A:HIS99 2.0 84.5 1.0
SG A:CYS118 2.2 70.9 1.0
SG A:CYS96 2.2 66.9 1.0
SG A:CYS115 2.2 78.1 1.0
CE1 A:HIS99 2.9 76.0 1.0
HB2 A:HIS99 2.9 91.7 1.0
H A:CYS118 3.0 81.1 1.0
HE1 A:HIS99 3.0 91.2 1.0
CG A:HIS99 3.1 75.1 1.0
CB A:CYS96 3.2 65.4 1.0
HB2 A:CYS96 3.2 78.5 1.0
HB3 A:CYS115 3.3 83.6 1.0
HB3 A:CYS96 3.3 78.5 1.0
H A:CYS115 3.4 78.8 1.0
CB A:CYS115 3.4 69.7 1.0
CB A:CYS118 3.5 54.6 1.0
CB A:HIS99 3.5 76.4 1.0
HB2 A:CYS118 3.5 65.5 1.0
N A:CYS118 3.7 67.6 1.0
H A:HIS99 3.7 89.9 1.0
HB2 A:LEU117 3.9 89.0 1.0
HB2 A:HIS98 3.9 75.1 1.0
CA A:CYS118 4.0 60.8 1.0
NE2 A:HIS99 4.0 78.0 1.0
N A:CYS115 4.1 65.7 1.0
HA A:CYS118 4.1 73.0 1.0
HB2 A:CYS115 4.1 83.6 1.0
CD2 A:HIS99 4.1 65.1 1.0
HB3 A:HIS99 4.2 91.7 1.0
N A:HIS99 4.2 74.9 1.0
HB3 A:CYS118 4.2 65.5 1.0
CA A:CYS115 4.3 67.5 1.0
HB2 A:GLU101 4.5 71.4 1.0
CA A:HIS99 4.5 74.5 1.0
CA A:CYS96 4.6 74.1 1.0
H A:LEU117 4.6 68.7 1.0
C A:LEU117 4.7 66.8 1.0
C A:CYS115 4.7 59.0 1.0
CB A:LEU117 4.8 74.1 1.0
HD21 A:LEU103 4.8 75.8 1.0
HE2 A:HIS99 4.8 93.6 1.0
HD23 A:LEU103 4.8 75.8 1.0
H A:HIS98 4.8 82.1 1.0
O A:CYS115 4.8 60.8 1.0
H A:GLU101 4.8 0.2 1.0
HB A:ILE114 4.8 75.1 1.0
HA A:CYS96 4.8 88.9 1.0
CB A:HIS98 4.8 62.6 1.0
HB3 A:LEU117 5.0 89.0 1.0

Zinc binding site 3 out of 3 in 5va4

Go back to Zinc Binding Sites List in 5va4
Zinc binding site 3 out of 3 in the Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Trim-Cyclophilin A B-Box 2 and Coiled-Coil Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:95.5
occ:1.00
OE1 A:GLU158 2.0 0.0 1.0
SG A:CYS186 2.4 92.9 1.0
SG A:CYS161 2.4 0.3 1.0
HB2 A:CYS161 2.8 0.2 1.0
HB3 A:CYS161 2.8 0.2 1.0
CB A:CYS161 2.9 0.2 1.0
CD A:GLU158 3.0 0.7 1.0
OE2 A:GLU158 3.3 0.1 1.0
HA A:GLU158 3.6 0.5 1.0
HB3 A:CYS186 3.7 0.6 1.0
CB A:CYS186 3.8 91.3 1.0
HB2 A:CYS186 4.3 0.6 1.0
CG A:GLU158 4.4 0.0 1.0
CA A:CYS161 4.4 98.0 1.0
CA A:GLU158 4.5 0.9 1.0
HB3 A:GLU158 4.6 0.7 1.0
C A:CYS186 4.6 90.6 1.0
HA2 A:GLY187 4.6 0.5 1.0
CB A:GLU158 4.7 0.6 1.0
HA A:CYS161 4.7 0.6 1.0
N A:GLY187 4.8 97.8 1.0
HG3 A:GLU158 4.8 0.6 1.0
CA A:CYS186 4.8 93.1 1.0
O A:CYS186 4.8 83.2 1.0
H A:CYS161 4.9 0.9 1.0
H A:GLY187 4.9 0.3 1.0
HG2 A:GLU158 5.0 0.6 1.0
O A:GLY183 5.0 93.7 1.0

Reference:

J.M.Wagner, D.E.Christensen, A.Bhattacharya, D.M.Dawidziak, M.D.Roganowicz, Y.Wan, R.A.Pumroy, B.Demeler, D.N.Ivanov, B.K.Ganser-Pornillos, W.I.Sundquist, O.Pornillos. General Model For Retroviral Capsid Pattern Recognition By TRIM5 Proteins. J. Virol. V. 92 2018.
ISSN: ESSN 1098-5514
PubMed: 29187540
DOI: 10.1128/JVI.01563-17
Page generated: Wed Dec 16 11:07:47 2020

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