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Zinc in PDB 3hph: Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd

Protein crystallography data

The structure of Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd, PDB code: 3hph was solved by S.Hare, J.Wang, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.01 / 2.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.870, 83.150, 115.300, 90.00, 101.96, 90.00
R / Rfree (%) 22.6 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd (pdb code 3hph). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd, PDB code: 3hph:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3hph

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Zinc binding site 1 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) 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 Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn220

b:30.6
occ:1.00
NE2 A:HIS12 2.1 23.1 1.0
ND1 A:HIS16 2.2 24.1 1.0
SG A:CYS40 2.4 37.4 1.0
SG A:CYS43 2.4 38.0 1.0
CE1 A:HIS12 3.0 23.9 1.0
CD2 A:HIS12 3.1 23.8 1.0
CG A:HIS16 3.1 24.4 1.0
CE1 A:HIS16 3.3 24.8 1.0
CB A:HIS16 3.3 23.5 1.0
CB A:CYS40 3.6 38.4 1.0
CB A:CYS43 3.7 37.6 1.0
ND1 A:HIS12 4.0 24.5 1.0
CA A:HIS16 4.0 23.5 1.0
CG A:HIS12 4.1 25.4 1.0
N A:CYS43 4.1 37.8 1.0
CD2 A:HIS16 4.3 24.6 1.0
NE2 A:HIS16 4.3 24.9 1.0
CA A:CYS43 4.4 37.7 1.0
O A:HIS12 4.4 26.0 1.0
CB A:VAL42 4.5 38.4 1.0
C A:VAL42 4.7 38.1 1.0
C A:HIS16 4.9 23.8 1.0
CA A:CYS40 4.9 38.4 1.0
CA A:VAL42 5.0 38.5 1.0

Zinc binding site 2 out of 4 in 3hph

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Zinc binding site 2 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) 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 Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn220

b:19.0
occ:1.00
NE2 B:HIS12 2.0 17.2 1.0
ND1 B:HIS16 2.1 18.2 1.0
SG B:CYS43 2.2 38.4 1.0
SG B:CYS40 2.4 36.8 1.0
CE1 B:HIS12 2.8 19.5 1.0
CE1 B:HIS16 3.0 17.8 1.0
CD2 B:HIS12 3.1 19.8 1.0
CG B:HIS16 3.2 18.7 1.0
CB B:CYS40 3.3 39.1 1.0
CB B:CYS43 3.5 39.5 1.0
CB B:HIS16 3.6 17.1 1.0
ND1 B:HIS12 3.9 20.7 1.0
N B:CYS43 3.9 39.7 1.0
CG B:HIS12 4.0 21.0 1.0
CA B:HIS16 4.1 17.7 1.0
NE2 B:HIS16 4.2 17.9 1.0
CA B:CYS43 4.3 39.7 1.0
CD2 B:HIS16 4.3 18.5 1.0
O B:HIS12 4.4 23.1 1.0
CB B:VAL42 4.6 40.7 1.0
CA B:CYS40 4.8 39.3 1.0
O B:HOH242 4.8 16.7 1.0
C B:VAL42 4.8 40.2 1.0
C B:HIS16 4.9 17.5 1.0

Zinc binding site 3 out of 4 in 3hph

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Zinc binding site 3 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) 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 Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn220

b:20.7
occ:1.00
NE2 C:HIS12 2.0 17.0 1.0
ND1 C:HIS16 2.1 18.1 1.0
SG C:CYS43 2.1 37.8 1.0
SG C:CYS40 2.4 37.0 1.0
CE1 C:HIS12 2.7 19.6 1.0
CE1 C:HIS16 3.0 17.7 1.0
CD2 C:HIS12 3.1 19.9 1.0
CG C:HIS16 3.2 18.6 1.0
CB C:CYS40 3.4 39.2 1.0
CB C:CYS43 3.4 39.5 1.0
CB C:HIS16 3.5 17.2 1.0
ND1 C:HIS12 3.8 21.0 1.0
N C:CYS43 3.9 39.7 1.0
CG C:HIS12 4.0 21.2 1.0
CA C:HIS16 4.0 17.8 1.0
NE2 C:HIS16 4.2 17.8 1.0
CD2 C:HIS16 4.2 18.7 1.0
CA C:CYS43 4.3 39.6 1.0
O C:HIS12 4.5 23.2 1.0
CB C:VAL42 4.6 40.7 1.0
CA C:CYS40 4.8 39.3 1.0
C C:VAL42 4.8 40.2 1.0
C C:HIS16 4.9 17.6 1.0
O C:HOH244 5.0 8.2 1.0
O C:HIS16 5.0 18.0 1.0

Zinc binding site 4 out of 4 in 3hph

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Zinc binding site 4 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) 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 Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn220

b:34.4
occ:1.00
NE2 D:HIS12 2.2 23.2 1.0
ND1 D:HIS16 2.2 24.2 1.0
SG D:CYS40 2.3 37.5 1.0
SG D:CYS43 2.5 38.2 1.0
CD2 D:HIS12 3.0 23.9 1.0
CE1 D:HIS12 3.1 23.8 1.0
CG D:HIS16 3.1 24.4 1.0
CE1 D:HIS16 3.2 24.9 1.0
CB D:HIS16 3.4 23.6 1.0
CB D:CYS40 3.5 38.5 1.0
CB D:CYS43 3.7 37.7 1.0
N D:CYS43 4.1 37.8 1.0
ND1 D:HIS12 4.1 24.4 1.0
CG D:HIS12 4.1 25.5 1.0
CA D:HIS16 4.1 23.6 1.0
CD2 D:HIS16 4.3 24.6 1.0
NE2 D:HIS16 4.3 24.9 1.0
CA D:CYS43 4.4 37.7 1.0
O D:HIS12 4.4 26.1 1.0
CB D:VAL42 4.5 38.5 1.0
C D:VAL42 4.7 38.1 1.0
CA D:CYS40 4.9 38.4 1.0
CA D:VAL42 4.9 38.5 1.0
N D:VAL42 5.0 39.1 1.0

Reference:

S.Hare, F.Di Nunzio, A.Labeja, J.Wang, A.Engelman, P.Cherepanov. Structural Basis For Functional Tetramerization of Lentiviral Integrase Plos Pathog. V. 5 E1000 2009.
ISSN: ISSN 1553-7366
PubMed: 19609359
DOI: 10.1371/JOURNAL.PPAT.1000515
Page generated: Sat Sep 26 10:42:52 2020
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