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Yttrium in PDB 4or5: Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4

Enzymatic activity of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4

All present enzymatic activity of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4:
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4, PDB code: 4or5 was solved by J.Gu, N.D.Babayeva, Y.Suwa, A.G.Baranovskiy, D.H.Price, T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.90 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.862, 186.739, 108.661, 90.00, 120.24, 90.00
R / Rfree (%) 22.5 / 26.7

Other elements in 4or5:

The structure of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Yttrium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Yttrium atom in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 (pdb code 4or5). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 16 binding sites of Yttrium where determined in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4, PDB code: 4or5:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Yttrium binding site 1 out of 16 in 4or5

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Yttrium binding site 1 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y401

b:65.9
occ:1.00
 O A:HOH521 2.4 20.1 1.0
OD2 A:ASP167 2.4 48.5 1.0
O A:HOH527 2.5 23.1 1.0
OD2 A:ASP149 2.5 51.7 1.0
CG A:ASP167 3.5 54.6 1.0
CG A:ASP149 3.6 50.2 1.0
OD1 A:ASP167 3.9 56.4 1.0
OD1 A:ASP149 4.1 50.8 1.0
NZ A:LYS151 4.3 55.3 1.0
CE A:LYS151 4.4 55.4 1.0
ND2 A:ASN154 4.5 58.8 1.0
CB A:ASP167 4.8 56.7 1.0
CB A:ASP149 4.8 43.1 1.0

Yttrium binding site 2 out of 16 in 4or5

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Yttrium binding site 2 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y402

b:87.0
occ:1.00
 OD2 A:ASP305 2.7 63.9 1.0
O A:HOH514 2.8 25.3 1.0
OD2 A:ASP308 2.9 64.4 1.0
OD1 A:ASP305 3.0 73.0 1.0
CG A:ASP305 3.2 63.8 1.0
CG A:ASP308 3.4 62.7 1.0
OD1 A:ASP308 3.6 66.2 1.0
OD2 A:ASP307 3.7 82.5 1.0
CG A:ASP307 4.1 77.8 1.0
CB A:ASP307 4.1 62.8 1.0
N A:ASP308 4.5 48.7 1.0
CB A:ASP308 4.5 58.0 1.0
CB A:ASP305 4.6 56.5 1.0
OD1 A:ASP307 4.9 86.0 1.0

Yttrium binding site 3 out of 16 in 4or5

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Yttrium binding site 3 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y403

b:76.5
occ:1.00
 O A:HOH505 2.5 13.7 1.0
O A:HOH502 3.2 19.8 1.0
OE1 A:GLU266 3.2 80.3 1.0
OE2 A:GLU266 3.4 73.0 1.0
NZ A:LYS269 3.5 67.1 1.0
CD A:GLU266 3.7 72.8 1.0
OH A:TYR262 4.7 72.9 1.0
CE A:LYS269 4.9 67.8 1.0
OE2 A:GLU263 4.9 24.0 1.0

Yttrium binding site 4 out of 16 in 4or5

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Yttrium binding site 4 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y301

b:27.8
occ:1.00
 O B:HOH410 2.1 14.0 1.0
OD2 B:ASP169 2.2 12.2 1.0
OXT E:ARG69 2.4 32.3 1.0
O E:ARG69 2.6 39.8 1.0
OE1 B:GLN172 2.7 44.7 1.0
C E:ARG69 2.9 41.8 1.0
CG B:ASP169 3.2 42.3 1.0
Y E:YT3101 3.4 46.2 1.0
CD B:GLN172 3.6 45.9 1.0
OD1 B:ASP169 3.6 59.3 1.0
NE2 B:GLN172 3.8 47.5 1.0
Y B:YT3302 4.2 57.1 1.0
O E:ILE66 4.4 42.1 1.0
CA E:ARG69 4.4 45.8 1.0
CB B:ASP169 4.4 41.7 1.0
O E:LYS63 4.8 33.6 1.0
CA B:ASP169 4.8 44.8 1.0
CG B:GLN172 4.9 45.9 1.0
CB E:ARG69 4.9 45.0 1.0

Yttrium binding site 5 out of 16 in 4or5

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Yttrium binding site 5 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y302

b:57.1
occ:1.00
 OD1 B:ASP169 2.5 59.3 1.0
OD1 E:ASP64 2.8 52.4 1.0
CG B:ASP169 3.3 42.3 1.0
Y E:YT3101 3.4 46.2 1.0
OD2 B:ASP169 3.6 12.2 1.0
CG E:ASP64 3.6 51.7 1.0
OD2 E:ASP64 4.2 54.8 1.0
Y B:YT3301 4.2 27.8 1.0
O B:HOH410 4.3 14.0 1.0
CG E:LYS63 4.5 48.3 1.0
CB B:ASP169 4.6 41.7 1.0
CB E:ASP64 4.6 49.3 1.0
CA E:ASP64 4.7 41.9 1.0
CD E:LYS63 4.7 54.8 1.0
O3 B:SO4304 4.9 78.5 1.0

Yttrium binding site 6 out of 16 in 4or5

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Yttrium binding site 6 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y303

b:41.9
occ:1.00
 OE1 B:GLU240 2.1 41.8 1.0
OE1 B:GLN243 2.2 34.2 1.0
CD B:GLU240 2.8 45.8 1.0
OE2 B:GLU240 2.8 42.1 1.0
CD B:GLN243 3.4 34.4 1.0
NE2 B:GLN243 4.1 23.2 1.0
CG B:GLU240 4.3 37.6 1.0
CG B:GLN243 4.6 38.7 1.0
NE2 B:HIS239 4.9 49.3 1.0

Yttrium binding site 7 out of 16 in 4or5

Go back to Yttrium Binding Sites List in 4or5
Yttrium binding site 7 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 7 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Y101

b:46.2
occ:1.00
 OXT E:ARG69 2.8 32.3 1.0
Y B:YT3302 3.4 57.1 1.0
Y B:YT3301 3.4 27.8 1.0
C E:ARG69 3.7 41.8 1.0
O B:HOH410 4.0 14.0 1.0
OD1 E:ASP64 4.1 52.4 1.0
O E:ARG69 4.2 39.8 1.0
OD2 B:ASP169 4.6 12.2 1.0
CA E:ARG69 4.7 45.8 1.0
OD1 B:ASP169 4.8 59.3 1.0
O E:ASP64 4.8 47.7 1.0

Yttrium binding site 8 out of 16 in 4or5

Go back to Yttrium Binding Sites List in 4or5
Yttrium binding site 8 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 8 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Y102

b:93.0
occ:1.00
 OE1 E:GLU37 2.1 80.7 1.0
CD E:GLU37 2.8 77.8 1.0
OE2 E:GLU37 2.8 78.7 1.0
CG E:GLU37 4.3 75.0 1.0

Yttrium binding site 9 out of 16 in 4or5

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Yttrium binding site 9 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 9 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Y401

b:42.3
occ:1.00
 OD2 F:ASP305 1.9 38.6 1.0
CG F:ASP305 2.6 43.1 1.0
OD2 F:ASP308 2.7 57.8 1.0
OD1 F:ASP305 2.7 43.8 1.0
OD1 F:ASP308 3.2 65.8 1.0
CG F:ASP308 3.2 60.6 1.0
OD1 F:ASP307 3.4 51.6 1.0
O F:HOH511 3.5 25.5 1.0
CG F:ASP307 3.6 58.4 1.0
OD2 F:ASP307 3.6 67.1 1.0
CB F:ASP305 4.1 42.2 1.0
CB F:ASP307 4.5 54.1 1.0
N F:ASP308 4.6 59.5 1.0
CB F:ASP308 4.6 55.9 1.0

Yttrium binding site 10 out of 16 in 4or5

Go back to Yttrium Binding Sites List in 4or5
Yttrium binding site 10 out of 16 in the Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 10 of Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Y402

b:59.6
occ:1.00
 O F:HOH501 2.3 10.2 1.0
OD2 F:ASP167 2.4 60.7 1.0
O F:HOH502 2.4 19.1 1.0
OD2 F:ASP149 2.5 58.8 1.0
CG F:ASP167 3.4 55.6 1.0
CG F:ASP149 3.5 56.5 1.0
OD1 F:ASP167 3.8 50.7 1.0
OD1 F:ASP149 3.9 58.6 1.0
ND2 F:ASN154 4.3 59.3 1.0
CB F:ASP167 4.6 50.8 1.0
OD1 F:ASN154 4.8 57.5 1.0
CB F:ASP149 4.8 51.6 1.0

Reference:

J.Gu, N.D.Babayeva, Y.Suwa, A.G.Baranovskiy, D.H.Price, T.H.Tahirov. Crystal Structure of Hiv-1 Tat Complexed with Human P-Tefb and AFF4. Cell Cycle V. 13 1788 2014.
ISSN: ISSN 1538-4101
PubMed: 24727379
DOI: 10.4161/CC.28756
Page generated: Sat Oct 12 20:41:41 2024

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