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Zinc in PDB 3f9k: Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd

Protein crystallography data

The structure of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd, PDB code: 3f9k was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.99 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 201.360, 202.500, 280.480, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 23.4

Other elements in 3f9k:

The structure of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd also contains other interesting chemical elements:

Magnesium (Mg) 24 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd (pdb code 3f9k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd, PDB code: 3f9k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 3f9k

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Zinc binding site 1 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:38.7
occ:1.00
 ND1 A:HIS16 2.1 39.2 1.0
NE2 A:HIS12 2.1 37.3 1.0
SG A:CYS43 2.1 50.0 1.0
SG A:CYS40 2.2 42.0 1.0
CD2 A:HIS12 3.0 38.9 1.0
CE1 A:HIS16 3.0 39.5 1.0
CE1 A:HIS12 3.0 37.2 1.0
CG A:HIS16 3.1 38.4 1.0
CB A:CYS40 3.2 42.1 1.0
CB A:CYS43 3.3 51.7 1.0
CB A:HIS16 3.5 37.7 1.0
N A:CYS43 3.9 51.1 1.0
ND1 A:HIS12 4.0 38.9 1.0
CG A:HIS12 4.0 42.6 1.0
NE2 A:HIS16 4.1 39.7 1.0
CA A:HIS16 4.1 37.7 1.0
CA A:CYS43 4.2 52.1 1.0
CD2 A:HIS16 4.2 39.4 1.0
O A:HIS12 4.5 50.5 1.0
CA A:CYS40 4.6 42.2 1.0
CB A:GLN42 4.8 49.5 1.0
C A:GLN42 4.8 50.0 1.0
CD A:ARG164 4.9 46.3 1.0
O A:HIS16 4.9 36.9 1.0
C A:HIS16 4.9 37.0 1.0

Zinc binding site 2 out of 24 in 3f9k

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Zinc binding site 2 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn210

b:46.3
occ:1.00
 ND1 B:HIS16 2.0 50.0 1.0
NE2 B:HIS12 2.1 40.8 1.0
SG B:CYS40 2.1 69.8 1.0
SG B:CYS43 2.4 70.0 1.0
CE1 B:HIS16 2.9 50.4 1.0
CE1 B:HIS12 3.0 40.8 1.0
CD2 B:HIS12 3.1 41.8 1.0
CG B:HIS16 3.1 49.5 1.0
CB B:CYS40 3.3 69.8 1.0
CB B:HIS16 3.6 49.0 1.0
CB B:CYS43 3.6 71.5 1.0
NE2 B:HIS16 4.1 50.4 1.0
ND1 B:HIS12 4.1 42.1 1.0
CA B:HIS16 4.2 48.9 1.0
CG B:HIS12 4.2 45.0 1.0
CD2 B:HIS16 4.2 50.2 1.0
N B:CYS43 4.3 72.3 1.0
C B:GLN42 4.5 72.9 1.0
CA B:CYS43 4.6 71.7 1.0
CA B:CYS40 4.6 69.8 1.0
N B:GLN42 4.7 73.2 1.0
O B:HIS12 4.8 50.6 1.0
CB B:GLN42 4.8 73.7 1.0
CA B:GLN42 4.9 73.4 1.0
O B:GLN42 4.9 73.0 1.0
O B:HIS16 4.9 48.8 1.0
C B:CYS40 4.9 70.6 1.0
CD B:ARG164 4.9 47.8 1.0
C B:HIS16 5.0 48.8 1.0
O B:VAL37 5.0 60.5 1.0

Zinc binding site 3 out of 24 in 3f9k

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Zinc binding site 3 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn210

b:40.0
occ:1.00
 NE2 E:HIS12 2.0 37.3 1.0
ND1 E:HIS16 2.1 39.2 1.0
SG E:CYS40 2.1 42.0 1.0
SG E:CYS43 2.2 50.0 1.0
CD2 E:HIS12 2.9 38.9 1.0
CE1 E:HIS16 3.0 39.5 1.0
CE1 E:HIS12 3.0 37.2 1.0
CB E:CYS40 3.2 42.1 1.0
CG E:HIS16 3.2 38.5 1.0
CB E:CYS43 3.3 51.7 1.0
CB E:HIS16 3.6 37.7 1.0
N E:CYS43 3.9 51.0 1.0
CG E:HIS12 4.0 42.6 1.0
ND1 E:HIS12 4.0 38.8 1.0
NE2 E:HIS16 4.1 39.7 1.0
CA E:HIS16 4.1 37.6 1.0
CA E:CYS43 4.2 52.1 1.0
CD2 E:HIS16 4.2 39.4 1.0
O E:HIS12 4.5 50.5 1.0
CA E:CYS40 4.6 42.2 1.0
CB E:GLN42 4.8 49.5 1.0
C E:GLN42 4.9 50.0 1.0
CD E:ARG164 5.0 46.3 1.0
C E:CYS40 5.0 43.1 1.0
C E:HIS16 5.0 37.0 1.0
O E:HIS16 5.0 36.9 1.0

Zinc binding site 4 out of 24 in 3f9k

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Zinc binding site 4 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn210

b:53.1
occ:1.00
 ND1 F:HIS16 2.0 50.1 1.0
NE2 F:HIS12 2.2 40.7 1.0
SG F:CYS40 2.3 69.7 1.0
SG F:CYS43 2.3 70.0 1.0
CE1 F:HIS16 2.9 50.4 1.0
CE1 F:HIS12 3.1 40.8 1.0
CG F:HIS16 3.1 49.6 1.0
CD2 F:HIS12 3.2 41.8 1.0
CB F:CYS40 3.4 69.8 1.0
CB F:HIS16 3.5 49.0 1.0
CB F:CYS43 3.5 71.5 1.0
NE2 F:HIS16 4.1 50.4 1.0
CA F:HIS16 4.1 48.9 1.0
CD2 F:HIS16 4.2 50.2 1.0
ND1 F:HIS12 4.2 42.1 1.0
N F:CYS43 4.3 72.3 1.0
CG F:HIS12 4.3 45.0 1.0
C F:GLN42 4.4 72.9 1.0
CA F:CYS43 4.5 71.6 1.0
N F:GLN42 4.7 73.2 1.0
CA F:CYS40 4.8 69.8 1.0
CB F:GLN42 4.8 73.7 1.0
CD F:ARG164 4.8 47.8 1.0
O F:GLN42 4.8 73.0 1.0
CA F:GLN42 4.8 73.4 1.0
O F:HIS16 4.9 48.7 1.0
O F:HIS12 4.9 50.6 1.0
C F:HIS16 4.9 48.7 1.0

Zinc binding site 5 out of 24 in 3f9k

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Zinc binding site 5 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn210

b:38.5
occ:1.00
 ND1 I:HIS16 2.1 39.2 1.0
NE2 I:HIS12 2.1 37.3 1.0
SG I:CYS40 2.1 42.0 1.0
SG I:CYS43 2.1 50.0 1.0
CE1 I:HIS16 3.0 39.5 1.0
CD2 I:HIS12 3.0 38.9 1.0
CE1 I:HIS12 3.0 37.2 1.0
CG I:HIS16 3.1 38.4 1.0
CB I:CYS40 3.2 42.1 1.0
CB I:CYS43 3.3 51.8 1.0
CB I:HIS16 3.5 37.7 1.0
N I:CYS43 3.9 51.0 1.0
ND1 I:HIS12 4.1 38.9 1.0
CG I:HIS12 4.1 42.6 1.0
NE2 I:HIS16 4.1 39.7 1.0
CA I:CYS43 4.1 52.1 1.0
CA I:HIS16 4.1 37.6 1.0
CD2 I:HIS16 4.2 39.4 1.0
O I:HIS12 4.6 50.4 1.0
CA I:CYS40 4.6 42.2 1.0
CB I:GLN42 4.7 49.5 1.0
C I:GLN42 4.8 50.0 1.0
CD I:ARG164 4.9 46.3 1.0
O I:HIS16 5.0 36.9 1.0
C I:CYS40 5.0 43.0 1.0
C I:HIS16 5.0 37.0 1.0

Zinc binding site 6 out of 24 in 3f9k

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Zinc binding site 6 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn210

b:49.7
occ:1.00
 ND1 J:HIS16 2.0 50.0 1.0
NE2 J:HIS12 2.2 40.8 1.0
SG J:CYS40 2.2 69.7 1.0
SG J:CYS43 2.3 70.1 1.0
CE1 J:HIS16 2.9 50.4 1.0
CE1 J:HIS12 3.1 40.9 1.0
CG J:HIS16 3.1 49.6 1.0
CD2 J:HIS12 3.2 41.8 1.0
CB J:CYS40 3.3 69.8 1.0
CB J:HIS16 3.5 49.0 1.0
CB J:CYS43 3.6 71.5 1.0
NE2 J:HIS16 4.1 50.4 1.0
CA J:HIS16 4.1 48.9 1.0
ND1 J:HIS12 4.2 42.1 1.0
CD2 J:HIS16 4.2 50.2 1.0
CG J:HIS12 4.3 45.0 1.0
N J:CYS43 4.3 72.3 1.0
C J:GLN42 4.5 72.9 1.0
CA J:CYS43 4.5 71.6 1.0
CA J:CYS40 4.7 69.8 1.0
N J:GLN42 4.7 73.2 1.0
CB J:GLN42 4.8 73.7 1.0
O J:GLN42 4.8 73.0 1.0
O J:HIS12 4.8 50.6 1.0
CA J:GLN42 4.9 73.4 1.0
O J:HIS16 4.9 48.8 1.0
C J:HIS16 4.9 48.8 1.0
CD J:ARG164 4.9 47.8 1.0
C J:CYS40 5.0 70.6 1.0

Zinc binding site 7 out of 24 in 3f9k

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Zinc binding site 7 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn210

b:41.5
occ:1.00
 ND1 M:HIS16 2.1 39.2 1.0
NE2 M:HIS12 2.1 37.3 1.0
SG M:CYS40 2.1 42.0 1.0
SG M:CYS43 2.2 50.1 1.0
CE1 M:HIS16 3.0 39.5 1.0
CD2 M:HIS12 3.0 38.9 1.0
CE1 M:HIS12 3.0 37.2 1.0
CG M:HIS16 3.1 38.5 1.0
CB M:CYS40 3.2 42.1 1.0
CB M:CYS43 3.3 51.7 1.0
CB M:HIS16 3.5 37.7 1.0
N M:CYS43 3.9 51.0 1.0
ND1 M:HIS12 4.0 38.9 1.0
CG M:HIS12 4.1 42.7 1.0
NE2 M:HIS16 4.1 39.7 1.0
CA M:HIS16 4.1 37.7 1.0
CA M:CYS43 4.2 52.1 1.0
CD2 M:HIS16 4.2 39.4 1.0
O M:HIS12 4.5 50.5 1.0
CA M:CYS40 4.6 42.2 1.0
CB M:GLN42 4.8 49.5 1.0
C M:GLN42 4.8 50.0 1.0
CD M:ARG164 5.0 46.3 1.0
C M:CYS40 5.0 43.0 1.0
C M:HIS16 5.0 37.0 1.0
O M:HIS16 5.0 36.9 1.0

Zinc binding site 8 out of 24 in 3f9k

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Zinc binding site 8 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn210

b:52.4
occ:1.00
 ND1 N:HIS16 2.0 50.0 1.0
NE2 N:HIS12 2.2 40.8 1.0
SG N:CYS40 2.2 69.7 1.0
SG N:CYS43 2.3 70.1 1.0
CE1 N:HIS16 2.9 50.4 1.0
CE1 N:HIS12 3.1 40.9 1.0
CG N:HIS16 3.1 49.5 1.0
CD2 N:HIS12 3.2 41.8 1.0
CB N:CYS40 3.4 69.8 1.0
CB N:HIS16 3.5 49.0 1.0
CB N:CYS43 3.6 71.6 1.0
NE2 N:HIS16 4.1 50.4 1.0
CA N:HIS16 4.1 48.9 1.0
ND1 N:HIS12 4.2 42.1 1.0
CD2 N:HIS16 4.2 50.2 1.0
CG N:HIS12 4.2 45.0 1.0
N N:CYS43 4.3 72.3 1.0
C N:GLN42 4.5 72.9 1.0
CA N:CYS43 4.6 71.6 1.0
CA N:CYS40 4.7 69.8 1.0
N N:GLN42 4.7 73.2 1.0
CB N:GLN42 4.8 73.7 1.0
O N:HIS12 4.8 50.6 1.0
O N:GLN42 4.8 73.0 1.0
CA N:GLN42 4.9 73.4 1.0
O N:HIS16 4.9 48.8 1.0
C N:HIS16 4.9 48.8 1.0
CD N:ARG164 5.0 47.8 1.0

Zinc binding site 9 out of 24 in 3f9k

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Zinc binding site 9 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn210

b:39.3
occ:1.00
 NE2 Q:HIS12 2.1 37.3 1.0
SG Q:CYS43 2.1 50.0 1.0
ND1 Q:HIS16 2.1 39.2 1.0
SG Q:CYS40 2.2 42.0 1.0
CE1 Q:HIS12 3.0 37.2 1.0
CD2 Q:HIS12 3.0 38.9 1.0
CE1 Q:HIS16 3.0 39.5 1.0
CG Q:HIS16 3.1 38.5 1.0
CB Q:CYS40 3.3 42.1 1.0
CB Q:CYS43 3.3 51.8 1.0
CB Q:HIS16 3.5 37.7 1.0
N Q:CYS43 3.9 51.0 1.0
ND1 Q:HIS12 4.0 38.9 1.0
CG Q:HIS12 4.1 42.7 1.0
CA Q:HIS16 4.1 37.6 1.0
CA Q:CYS43 4.1 52.1 1.0
NE2 Q:HIS16 4.1 39.7 1.0
CD2 Q:HIS16 4.2 39.4 1.0
O Q:HIS12 4.6 50.5 1.0
CA Q:CYS40 4.7 42.3 1.0
CB Q:GLN42 4.8 49.5 1.0
C Q:GLN42 4.8 50.0 1.0
CD Q:ARG164 4.9 46.3 1.0
O Q:HIS16 4.9 36.8 1.0
C Q:HIS16 4.9 37.0 1.0

Zinc binding site 10 out of 24 in 3f9k

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Zinc binding site 10 out of 24 in the Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Two Domain Fragment of Hiv-2 Integrase in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn210

b:47.3
occ:1.00
 ND1 R:HIS16 2.0 50.0 1.0
NE2 R:HIS12 2.1 40.7 1.0
SG R:CYS43 2.3 70.0 1.0
SG R:CYS40 2.3 69.7 1.0
CE1 R:HIS16 2.9 50.4 1.0
CE1 R:HIS12 3.0 40.8 1.0
CG R:HIS16 3.0 49.6 1.0
CD2 R:HIS12 3.1 41.8 1.0
CB R:HIS16 3.4 49.0 1.0
CB R:CYS40 3.5 69.8 1.0
CB R:CYS43 3.6 71.6 1.0
CA R:HIS16 4.0 48.9 1.0
NE2 R:HIS16 4.0 50.4 1.0
ND1 R:HIS12 4.1 42.1 1.0
CD2 R:HIS16 4.1 50.2 1.0
CG R:HIS12 4.2 45.0 1.0
N R:CYS43 4.4 72.3 1.0
C R:GLN42 4.5 72.9 1.0
CA R:CYS43 4.6 71.6 1.0
O R:HIS12 4.7 50.6 1.0
CD R:ARG164 4.7 47.8 1.0
O R:HIS16 4.8 48.7 1.0
C R:HIS16 4.8 48.7 1.0
CB R:GLN42 4.8 73.7 1.0
CA R:CYS40 4.8 69.8 1.0
N R:GLN42 4.9 73.2 1.0
O R:GLN42 4.9 73.0 1.0
CA R:GLN42 5.0 73.4 1.0

Reference:

S.Hare, M.C.Shun, S.S.Gupta, E.Valkov, A.Engelman, P.Cherepanov. A Novel Co-Crystal Structure Affords the Design of Gain-of-Function Lentiviral Integrase Mutants in the Presence of Modified PSIP1/Ledgf/P75 Plos Pathog. V. 5 E1000 2009.
ISSN: ISSN 1553-7366
PubMed: 19132083
DOI: 10.1371/JOURNAL.PPAT.1000259
Page generated: Thu Oct 24 13:05:38 2024

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