Zinc in PDB 7z1z: Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution

Enzymatic activity of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution

All present enzymatic activity of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution:
2.7.7.49; 3.1.13.2; 3.1.26.13; 3.6.1.23;

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution (pdb code 7z1z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution, PDB code: 7z1z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7z1z

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Zinc binding site 1 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:106.0
occ:1.00
 ND1 A:HIS16 2.0 70.6 1.0
NE2 A:HIS12 2.3 76.1 1.0
SG A:CYS43 2.3 80.2 1.0
SG A:CYS40 2.3 82.3 1.0
CE1 A:HIS16 2.6 70.6 1.0
CE1 A:HIS12 2.9 76.1 1.0
CD2 A:HIS12 3.1 76.1 1.0
CG A:HIS16 3.1 70.6 1.0
CB A:CYS40 3.1 82.3 1.0
NE2 A:HIS16 3.7 70.6 1.0
ND1 A:HIS12 3.8 76.1 1.0
CB A:HIS16 3.8 70.6 1.0
CB A:CYS43 3.9 80.2 1.0
CG A:HIS12 3.9 76.1 1.0
CD2 A:HIS16 4.0 70.6 1.0
CA A:HIS16 4.0 70.6 1.0
O A:HIS12 4.1 76.1 1.0
N A:CYS43 4.6 80.2 1.0
CA A:CYS40 4.6 82.3 1.0
CA A:CYS43 4.8 80.2 1.0
C A:HIS12 4.8 76.1 1.0
CG2 A:VAL37 4.8 88.4 1.0
N A:HIS16 4.9 70.6 1.0

Zinc binding site 2 out of 12 in 7z1z

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Zinc binding site 2 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:365.8
occ:1.00
 ND1 B:HIS16 2.0 222.0 1.0
NE2 B:HIS12 2.0 224.4 1.0
SG B:CYS43 2.3 237.8 1.0
SG B:CYS40 2.3 234.5 1.0
CE1 B:HIS12 2.4 224.4 1.0
CD2 B:HIS12 2.7 224.4 1.0
CE1 B:HIS16 3.0 222.0 1.0
CG B:HIS16 3.0 222.0 1.0
ND1 B:HIS12 3.1 224.4 1.0
O B:HIS12 3.3 224.4 1.0
CG B:HIS12 3.3 224.4 1.0
CA B:HIS16 3.3 222.0 1.0
CB B:HIS16 3.3 222.0 1.0
CB B:CYS40 3.5 234.5 1.0
CB B:CYS43 3.8 237.8 1.0
NE2 B:HIS16 4.0 222.0 1.0
CD2 B:HIS16 4.1 222.0 1.0
C B:HIS12 4.1 224.4 1.0
N B:HIS16 4.2 222.0 1.0
C B:HIS16 4.2 222.0 1.0
CB B:HIS12 4.5 224.4 1.0
N B:CYS43 4.6 237.8 1.0
O B:GLN17 4.6 219.2 1.0
CA B:HIS12 4.7 224.4 1.0
N B:GLN17 4.8 219.2 1.0
CA B:CYS43 4.8 237.8 1.0
CA B:CYS40 4.9 234.5 1.0
O B:HIS16 4.9 222.0 1.0
N B:ASN13 4.9 221.3 1.0

Zinc binding site 3 out of 12 in 7z1z

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Zinc binding site 3 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:211.1
occ:1.00
 ND1 C:HIS16 2.0 107.7 1.0
NE2 C:HIS12 2.0 111.3 1.0
SG C:CYS43 2.3 154.1 1.0
SG C:CYS40 2.3 165.7 1.0
CE1 C:HIS12 2.6 111.3 1.0
CD2 C:HIS12 2.7 111.3 1.0
CE1 C:HIS16 2.8 107.7 1.0
CG C:HIS16 3.0 107.7 1.0
ND1 C:HIS12 3.4 111.3 1.0
CA C:HIS16 3.4 107.7 1.0
CG C:HIS12 3.4 111.3 1.0
O C:HIS12 3.5 111.3 1.0
CB C:HIS16 3.5 107.7 1.0
CB C:CYS40 3.5 165.7 1.0
CB C:CYS43 3.7 154.1 1.0
NE2 C:HIS16 3.9 107.7 1.0
CD2 C:HIS16 4.0 107.7 1.0
C C:HIS12 4.2 111.3 1.0
N C:HIS16 4.3 107.7 1.0
C C:HIS16 4.4 107.7 1.0
N C:CYS43 4.6 154.1 1.0
CB C:HIS12 4.7 111.3 1.0
CA C:CYS43 4.8 154.1 1.0
N C:GLN17 4.8 104.0 1.0
CA C:CYS40 4.9 165.7 1.0
CA C:HIS12 4.9 111.3 1.0
N C:ASN13 5.0 106.1 1.0

Zinc binding site 4 out of 12 in 7z1z

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Zinc binding site 4 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:235.4
occ:1.00
 NE2 E:HIS12 2.0 138.8 1.0
ND1 E:HIS16 2.0 146.5 1.0
SG E:CYS43 2.3 192.6 1.0
SG E:CYS40 2.3 201.7 1.0
CD2 E:HIS12 2.6 138.8 1.0
CE1 E:HIS12 2.7 138.8 1.0
CE1 E:HIS16 2.8 146.5 1.0
CG E:HIS16 3.0 146.5 1.0
CG E:HIS12 3.4 138.8 1.0
ND1 E:HIS12 3.4 138.8 1.0
O E:HIS12 3.4 138.8 1.0
CB E:CYS40 3.5 201.7 1.0
CB E:HIS16 3.6 146.5 1.0
CB E:CYS43 3.6 192.6 1.0
CA E:HIS16 3.6 146.5 1.0
NE2 E:HIS16 3.9 146.5 1.0
CD2 E:HIS16 4.0 146.5 1.0
C E:HIS12 4.2 138.8 1.0
N E:CYS43 4.4 192.6 1.0
N E:HIS16 4.5 146.5 1.0
CA E:CYS43 4.6 192.6 1.0
C E:HIS16 4.6 146.5 1.0
CB E:HIS12 4.7 138.8 1.0
CA E:CYS40 4.9 201.7 1.0
CA E:HIS12 4.9 138.8 1.0
N E:ASN13 5.0 132.6 1.0

Zinc binding site 5 out of 12 in 7z1z

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Zinc binding site 5 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:364.9
occ:1.00
 ND1 F:HIS16 2.0 239.5 1.0
NE2 F:HIS12 2.0 244.3 1.0
SG F:CYS43 2.3 254.4 1.0
SG F:CYS40 2.3 254.9 1.0
CD2 F:HIS12 2.6 244.3 1.0
CE1 F:HIS12 2.6 244.3 1.0
CE1 F:HIS16 2.9 239.5 1.0
CG F:HIS16 3.0 239.5 1.0
CA F:HIS16 3.2 239.5 1.0
ND1 F:HIS12 3.2 244.3 1.0
CG F:HIS12 3.3 244.3 1.0
O F:HIS12 3.4 244.3 1.0
CB F:CYS40 3.4 254.9 1.0
CB F:HIS16 3.5 239.5 1.0
CB F:CYS43 3.7 254.4 1.0
NE2 F:HIS16 4.0 239.5 1.0
CD2 F:HIS16 4.1 239.5 1.0
C F:HIS12 4.1 244.3 1.0
C F:HIS16 4.1 239.5 1.0
N F:HIS16 4.2 239.5 1.0
CB F:HIS12 4.5 244.3 1.0
N F:GLN17 4.6 241.0 1.0
N F:CYS43 4.7 254.4 1.0
O F:GLN17 4.7 241.0 1.0
CA F:HIS12 4.7 244.3 1.0
CA F:CYS43 4.8 254.4 1.0
CA F:CYS40 4.8 254.9 1.0
O F:HIS16 4.9 239.5 1.0
N F:ASN13 4.9 241.2 1.0

Zinc binding site 6 out of 12 in 7z1z

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Zinc binding site 6 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:341.1
occ:1.00
 ND1 G:HIS16 2.0 229.6 1.0
NE2 G:HIS12 2.0 233.6 1.0
SG G:CYS43 2.3 234.8 1.0
SG G:CYS40 2.3 236.1 1.0
CD2 G:HIS12 2.6 233.6 1.0
CE1 G:HIS12 2.7 233.6 1.0
CG G:HIS16 2.9 229.6 1.0
CE1 G:HIS16 3.0 229.6 1.0
CB G:HIS16 3.3 229.6 1.0
CA G:HIS16 3.3 229.6 1.0
CG G:HIS12 3.4 233.6 1.0
ND1 G:HIS12 3.4 233.6 1.0
O G:HIS12 3.5 233.6 1.0
CB G:CYS40 3.5 236.1 1.0
CB G:CYS43 3.7 234.8 1.0
CD2 G:HIS16 4.0 229.6 1.0
NE2 G:HIS16 4.0 229.6 1.0
C G:HIS16 4.2 229.6 1.0
N G:HIS16 4.3 229.6 1.0
C G:HIS12 4.3 233.6 1.0
N G:CYS43 4.5 234.8 1.0
CB G:HIS12 4.6 233.6 1.0
N G:GLN17 4.7 228.1 1.0
CA G:CYS43 4.7 234.8 1.0
O G:GLN17 4.8 228.1 1.0
O G:HIS16 4.8 229.6 1.0
CA G:HIS12 4.9 233.6 1.0
CA G:CYS40 4.9 236.1 1.0

Zinc binding site 7 out of 12 in 7z1z

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Zinc binding site 7 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:106.0
occ:1.00
 ND1 I:HIS16 2.0 70.6 1.0
NE2 I:HIS12 2.3 76.1 1.0
SG I:CYS43 2.3 80.2 1.0
SG I:CYS40 2.3 82.3 1.0
CE1 I:HIS16 2.6 70.6 1.0
CE1 I:HIS12 2.9 76.1 1.0
CD2 I:HIS12 3.1 76.1 1.0
CG I:HIS16 3.1 70.6 1.0
CB I:CYS40 3.1 82.3 1.0
NE2 I:HIS16 3.7 70.6 1.0
ND1 I:HIS12 3.8 76.1 1.0
CB I:HIS16 3.8 70.6 1.0
CB I:CYS43 3.9 80.2 1.0
CG I:HIS12 3.9 76.1 1.0
CD2 I:HIS16 4.0 70.6 1.0
CA I:HIS16 4.0 70.6 1.0
O I:HIS12 4.1 76.1 1.0
N I:CYS43 4.6 80.2 1.0
CA I:CYS40 4.6 82.3 1.0
CA I:CYS43 4.8 80.2 1.0
C I:HIS12 4.8 76.1 1.0
CG2 I:VAL37 4.8 88.4 1.0
N I:HIS16 4.9 70.6 1.0

Zinc binding site 8 out of 12 in 7z1z

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Zinc binding site 8 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:365.8
occ:1.00
 ND1 J:HIS16 2.0 222.0 1.0
NE2 J:HIS12 2.0 224.4 1.0
SG J:CYS43 2.3 237.8 1.0
SG J:CYS40 2.3 234.5 1.0
CE1 J:HIS12 2.4 224.4 1.0
CD2 J:HIS12 2.7 224.4 1.0
CG J:HIS16 3.0 222.0 1.0
CE1 J:HIS16 3.0 222.0 1.0
ND1 J:HIS12 3.1 224.4 1.0
O J:HIS12 3.3 224.4 1.0
CG J:HIS12 3.3 224.4 1.0
CA J:HIS16 3.3 222.0 1.0
CB J:HIS16 3.3 222.0 1.0
CB J:CYS40 3.5 234.5 1.0
CB J:CYS43 3.8 237.8 1.0
NE2 J:HIS16 4.0 222.0 1.0
CD2 J:HIS16 4.1 222.0 1.0
C J:HIS12 4.1 224.4 1.0
C J:HIS16 4.2 222.0 1.0
N J:HIS16 4.2 222.0 1.0
CB J:HIS12 4.5 224.4 1.0
N J:CYS43 4.6 237.8 1.0
O J:GLN17 4.6 219.2 1.0
CA J:HIS12 4.7 224.4 1.0
N J:GLN17 4.7 219.2 1.0
CA J:CYS43 4.8 237.8 1.0
CA J:CYS40 4.9 234.5 1.0
O J:HIS16 4.9 222.0 1.0
N J:ASN13 4.9 221.3 1.0

Zinc binding site 9 out of 12 in 7z1z

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Zinc binding site 9 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:211.1
occ:1.00
 ND1 K:HIS16 2.0 107.7 1.0
NE2 K:HIS12 2.0 111.3 1.0
SG K:CYS43 2.3 154.1 1.0
SG K:CYS40 2.3 165.7 1.0
CE1 K:HIS12 2.6 111.3 1.0
CD2 K:HIS12 2.7 111.3 1.0
CE1 K:HIS16 2.8 107.7 1.0
CG K:HIS16 3.0 107.7 1.0
ND1 K:HIS12 3.4 111.3 1.0
CA K:HIS16 3.4 107.7 1.0
CG K:HIS12 3.4 111.3 1.0
O K:HIS12 3.5 111.3 1.0
CB K:HIS16 3.5 107.7 1.0
CB K:CYS40 3.5 165.7 1.0
CB K:CYS43 3.7 154.1 1.0
NE2 K:HIS16 3.9 107.7 1.0
CD2 K:HIS16 4.0 107.7 1.0
C K:HIS12 4.2 111.3 1.0
N K:HIS16 4.3 107.7 1.0
C K:HIS16 4.4 107.7 1.0
N K:CYS43 4.6 154.1 1.0
CB K:HIS12 4.7 111.3 1.0
CA K:CYS43 4.8 154.1 1.0
N K:GLN17 4.8 104.0 1.0
CA K:CYS40 4.9 165.7 1.0
CA K:HIS12 4.9 111.3 1.0
N K:ASN13 4.9 106.1 1.0

Zinc binding site 10 out of 12 in 7z1z

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Zinc binding site 10 out of 12 in the Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Mvv Strand Transfer Complex (Stc) Intasome in Complex with Ledgf/P75 at 3.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn301

b:235.4
occ:1.00
 ND1 M:HIS16 2.0 146.5 1.0
NE2 M:HIS12 2.0 138.8 1.0
SG M:CYS43 2.3 192.6 1.0
SG M:CYS40 2.3 201.7 1.0
CD2 M:HIS12 2.6 138.8 1.0
CE1 M:HIS12 2.7 138.8 1.0
CE1 M:HIS16 2.8 146.5 1.0
CG M:HIS16 3.0 146.5 1.0
CG M:HIS12 3.4 138.8 1.0
ND1 M:HIS12 3.4 138.8 1.0
O M:HIS12 3.4 138.8 1.0
CB M:CYS40 3.5 201.7 1.0
CB M:HIS16 3.6 146.5 1.0
CB M:CYS43 3.6 192.6 1.0
CA M:HIS16 3.6 146.5 1.0
NE2 M:HIS16 3.9 146.5 1.0
CD2 M:HIS16 4.0 146.5 1.0
C M:HIS12 4.2 138.8 1.0
N M:CYS43 4.4 192.6 1.0
N M:HIS16 4.5 146.5 1.0
CA M:CYS43 4.6 192.6 1.0
C M:HIS16 4.6 146.5 1.0
CB M:HIS12 4.7 138.8 1.0
CA M:CYS40 4.9 201.7 1.0
CA M:HIS12 4.9 138.8 1.0
N M:ASN13 5.0 132.6 1.0

Reference:

A.Ballandras-Colas, V.Chivukula, D.T.Gruszka, Z.Shan, P.K.Singh, V.E.Pye, R.K.Mclean, G.J.Bedwell, W.Li, A.Nans, N.J.Cook, H.J.Fadel, E.M.Poeschla, D.J.Griffiths, J.Vargas, I.A.Taylor, D.Lyumkis, H.Yardimci, A.N.Engelman, P.Cherepanov. Multivalent Interactions Essential For Lentiviral Integrase Function. Nat Commun V. 13 2416 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-29928-8
Page generated: Wed Oct 30 16:10:40 2024

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