Zinc in PDB 4ogr: Crystal Structure of P-Tefb Complex with AFF4 and Tat

All present enzymatic activity of Crystal Structure of P-Tefb Complex with AFF4 and Tat:
2.7.11.22; 2.7.11.23;

The structure of Crystal Structure of P-Tefb Complex with AFF4 and Tat, PDB code: 4ogr was solved by U.Schulze-Gahmen, T.Alber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.02 / 3.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.908, 184.908, 360.399, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 23.2

The binding sites of Zinc atom in the Crystal Structure of P-Tefb Complex with AFF4 and Tat (pdb code 4ogr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of P-Tefb Complex with AFF4 and Tat, PDB code: 4ogr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of P-Tefb Complex with AFF4 and Tat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P-Tefb Complex with AFF4 and Tat within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:71.8 occ:1.00 ND1 D:HIS33 2.0 62.4 1.0 SG D:CYS22 2.3 66.6 1.0 SG D:CYS37 2.3 72.7 1.0 SG D:CYS34 2.4 64.8 1.0 CE1 D:HIS33 2.8 63.3 1.0 HE1 D:HIS33 2.9 75.9 1.0 HB3 D:HIS33 3.1 78.9 1.0 CG D:HIS33 3.2 64.6 1.0 HB3 D:CYS34 3.3 75.6 1.0 HB2 D:CYS37 3.4 79.8 1.0 CB D:CYS22 3.5 77.9 1.0 HA D:CYS22 3.5 95.5 1.0 HB3 D:CYS22 3.5 93.5 1.0 H D:CYS37 3.5 80.7 1.0 CB D:CYS34 3.5 63.0 1.0 CB D:CYS37 3.5 66.5 1.0 CB D:HIS33 3.6 65.8 1.0 H D:CYS34 3.8 80.9 1.0 HG3 D:PRO18 3.9 85.1 1.0 N D:CYS34 3.9 67.4 1.0 CA D:CYS22 4.0 79.6 1.0 NE2 D:HIS33 4.0 65.7 1.0 HB D:VAL36 4.1 78.7 1.0 N D:CYS37 4.1 67.2 1.0 CD2 D:HIS33 4.2 65.3 1.0 HB3 D:CYS37 4.2 79.8 1.0 HB2 D:CYS34 4.3 75.6 1.0 HB2 D:CYS22 4.3 93.5 1.0 CA D:CYS34 4.3 63.1 1.0 HB2 D:HIS33 4.3 78.9 1.0 C D:HIS33 4.3 67.4 1.0 CA D:CYS37 4.4 66.6 1.0 HE22 B:GLN50 4.4 80.7 1.0 CA D:HIS33 4.6 68.1 1.0 HA D:CYS37 4.6 79.9 1.0 N D:CYS22 4.7 80.8 1.0 HE2 D:HIS33 4.8 78.8 1.0 CG D:PRO18 4.8 71.0 1.0 H D:CYS22 4.8 96.9 1.0 HG2 D:PRO18 4.9 85.1 1.0 C D:CYS34 4.9 62.0 1.0 O D:HIS33 4.9 67.8 1.0 H D:THR23 4.9 92.9 1.0 HG12 D:VAL36 5.0 80.8 1.0 CB D:VAL36 5.0 65.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of P-Tefb Complex with AFF4 and Tat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P-Tefb Complex with AFF4 and Tat within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:0.8 occ:1.00 SG D:CYS30 2.2 0.8 1.0 SG D:CYS27 2.3 78.9 1.0 SG D:CYS25 2.4 0.8 1.0 SG B:CYS261 2.4 0.5 1.0 HB3 D:CYS25 2.9 0.2 1.0 CB D:CYS25 3.1 0.9 1.0 HA B:CYS261 3.4 0.5 1.0 HB2 D:CYS25 3.4 0.2 1.0 HB2 D:CYS30 3.7 0.8 1.0 CB D:CYS30 3.7 97.3 1.0 CB D:CYS27 3.9 93.4 1.0 HB3 D:CYS27 3.9 0.1 1.0 CB B:CYS261 3.9 0.1 1.0 H D:CYS27 3.9 0.4 1.0 HG1 D:THR23 4.0 96.8 1.0 CA B:CYS261 4.1 0.1 1.0 H D:CYS30 4.2 0.5 1.0 HB3 D:CYS30 4.3 0.8 1.0 O B:ALA260 4.4 0.7 1.0 HB3 B:CYS261 4.4 0.1 1.0 HB2 D:CYS27 4.4 0.1 1.0 HB2 B:CYS261 4.5 0.1 1.0 CA D:CYS25 4.6 0.1 1.0 N D:CYS30 4.6 95.4 1.0 N D:CYS27 4.7 89.5 1.0 CA D:CYS30 4.7 94.9 1.0 OG1 D:THR23 4.8 80.7 1.0 HB3 D:LYS29 4.8 0.7 1.0 C D:CYS25 4.8 97.4 1.0 CA D:CYS27 4.8 90.7 1.0 HB2 D:LYS29 4.9 0.7 1.0 HG21 D:THR23 4.9 96.7 1.0 HA D:CYS30 5.0 0.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of P-Tefb Complex with AFF4 and Tat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of P-Tefb Complex with AFF4 and Tat within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:71.4 occ:1.00 ND1 H:HIS33 2.0 78.5 1.0 SG H:CYS37 2.3 73.3 1.0 SG H:CYS22 2.3 62.3 1.0 SG H:CYS34 2.3 72.6 1.0 CE1 H:HIS33 2.9 78.0 1.0 HB3 H:HIS33 2.9 94.3 1.0 HE1 H:HIS33 3.1 93.6 1.0 CG H:HIS33 3.1 79.0 1.0 HB3 H:CYS34 3.1 92.3 1.0 HB2 H:CYS37 3.3 78.6 1.0 CB H:CYS34 3.3 76.9 1.0 H H:CYS37 3.4 77.1 1.0 HB3 H:CYS22 3.4 89.7 1.0 CB H:CYS37 3.4 65.5 1.0 CB H:CYS22 3.4 74.7 1.0 H H:CYS34 3.5 95.5 1.0 CB H:HIS33 3.5 78.6 1.0 HA H:CYS22 3.6 92.1 1.0 N H:CYS34 3.6 79.6 1.0 HG3 H:PRO18 3.9 83.3 1.0 CA H:CYS34 4.0 77.3 1.0 CA H:CYS22 4.0 76.7 1.0 C H:HIS33 4.1 77.2 1.0 N H:CYS37 4.1 64.3 1.0 NE2 H:HIS33 4.1 78.9 1.0 HB2 H:CYS34 4.1 92.3 1.0 HB3 H:CYS37 4.1 78.6 1.0 CD2 H:HIS33 4.2 79.3 1.0 HB2 H:CYS22 4.2 89.7 1.0 HB2 H:HIS33 4.2 94.3 1.0 CA H:CYS37 4.3 65.1 1.0 HE22 F:GLN50 4.3 80.6 1.0 HB H:VAL36 4.3 68.4 1.0 CA H:HIS33 4.4 79.0 1.0 C H:CYS34 4.6 75.3 1.0 HA H:CYS37 4.6 78.1 1.0 O H:CYS34 4.7 76.2 1.0 O H:HIS33 4.7 77.4 1.0 CG H:PRO18 4.8 69.4 1.0 HA H:CYS34 4.8 92.7 1.0 N H:CYS22 4.8 78.6 1.0 HE2 H:HIS33 4.8 94.7 1.0 HG2 H:PRO18 4.9 83.3 1.0 H H:THR23 4.9 95.3 1.0 H H:CYS22 5.0 94.3 1.0 H H:VAL36 5.0 71.8 1.0 NE2 F:GLN50 5.0 67.1 1.0 HE21 F:GLN50 5.0 80.6 1.0 H H:HIS33 5.0 96.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of P-Tefb Complex with AFF4 and Tat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of P-Tefb Complex with AFF4 and Tat within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn102 b:95.5 occ:1.00 SG H:CYS27 2.2 75.6 1.0 SG H:CYS30 2.3 76.1 1.0 SG H:CYS25 2.3 79.5 1.0 SG F:CYS261 2.3 0.6 1.0 HB3 H:CYS25 3.0 99.8 1.0 CB H:CYS25 3.2 83.2 1.0 HB3 F:CYS261 3.3 0.3 1.0 HA F:CYS261 3.3 0.9 1.0 CB F:CYS261 3.4 0.1 1.0 HB2 H:CYS25 3.5 99.8 1.0 CB H:CYS30 3.8 92.0 1.0 HB2 H:CYS30 3.8 0.3 1.0 CB H:CYS27 3.8 89.0 1.0 H H:CYS27 3.9 92.8 1.0 HB3 H:CYS27 3.9 0.8 1.0 CA F:CYS261 3.9 0.3 1.0 H H:CYS30 3.9 0.2 1.0 HG1 H:THR23 4.1 96.6 1.0 O F:ALA260 4.2 95.8 1.0 HB2 H:LYS29 4.2 0.8 1.0 HB2 F:CYS261 4.2 0.3 1.0 HB3 H:LYS29 4.2 0.8 1.0 N H:CYS30 4.4 94.4 1.0 HB2 H:CYS27 4.4 0.8 1.0 HB3 H:CYS30 4.4 0.3 1.0 N H:CYS27 4.6 77.3 1.0 CA H:CYS25 4.6 82.2 1.0 CA H:CYS30 4.6 91.0 1.0 CB H:LYS29 4.7 97.3 1.0 CA H:CYS27 4.7 84.3 1.0 HA H:CYS30 4.8 0.2 1.0 C H:CYS25 4.9 78.2 1.0 N F:CYS261 4.9 0.1 1.0 O F:CYS261 4.9 93.1 1.0 C F:CYS261 4.9 99.4 1.0 C F:ALA260 4.9 0.7 1.0 OG1 H:THR23 4.9 80.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of P-Tefb Complex with AFF4 and Tat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of P-Tefb Complex with AFF4 and Tat within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn101 b:0.0 occ:1.00 ND1 M:HIS33 2.1 86.1 1.0 SG M:CYS37 2.2 0.5 1.0 SG M:CYS22 2.3 0.7 1.0 SG M:CYS34 2.3 0.3 1.0 HB3 M:HIS33 2.9 0.8 1.0 CE1 M:HIS33 3.0 86.9 1.0 CG M:HIS33 3.1 0.4 1.0 HE1 M:HIS33 3.2 0.3 1.0 HB3 M:CYS34 3.2 0.6 1.0 HB2 M:CYS37 3.2 0.6 1.0 H M:CYS37 3.2 1.0 1.0 CB M:CYS34 3.3 99.7 1.0 CB M:CYS37 3.4 99.7 1.0 HB3 M:CYS22 3.4 0.4 1.0 CB M:CYS22 3.5 0.0 1.0 CB M:HIS33 3.5 0.9 1.0 H M:CYS34 3.5 0.5 1.0 N M:CYS34 3.6 0.7 1.0 HA M:CYS22 3.8 0.3 1.0 N M:CYS37 3.9 100.0 1.0 CA M:CYS34 4.0 99.8 1.0 HB M:VAL36 4.0 0.2 1.0 C M:HIS33 4.1 97.8 1.0 HB3 M:CYS37 4.1 0.6 1.0 HB2 M:CYS34 4.1 0.6 1.0 NE2 M:HIS33 4.1 88.3 1.0 HG3 M:PRO18 4.2 0.2 1.0 CA M:CYS37 4.2 98.7 1.0 HB2 M:HIS33 4.2 0.8 1.0 HB2 M:CYS22 4.2 0.4 1.0 CD2 M:HIS33 4.2 88.7 1.0 CA M:CYS22 4.2 0.3 1.0 CA M:HIS33 4.4 1.0 1.0 HA M:CYS37 4.5 0.4 1.0 C M:CYS34 4.6 99.8 1.0 O M:CYS34 4.7 0.1 1.0 O M:HIS33 4.7 98.7 1.0 HG12 M:VAL36 4.8 0.3 1.0 H M:VAL36 4.9 0.1 1.0 HA M:CYS34 4.9 0.7 1.0 CB M:VAL36 4.9 0.8 1.0 HE2 M:HIS33 4.9 0.9 1.0 H M:HIS33 4.9 0.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of P-Tefb Complex with AFF4 and Tat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of P-Tefb Complex with AFF4 and Tat within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn102 b:0.4 occ:1.00 SG K:CYS261 2.3 0.4 1.0 SG M:CYS27 2.4 0.4 1.0 SG M:CYS30 2.4 0.1 1.0 SG M:CYS25 2.5 0.0 1.0 HA K:CYS261 2.7 0.8 1.0 HB3 M:CYS25 3.2 0.9 1.0 CB M:CYS25 3.4 0.6 1.0 CB K:CYS261 3.4 0.6 1.0 CA K:CYS261 3.4 0.0 1.0 HB2 M:CYS25 3.5 0.9 1.0 HB3 K:CYS261 3.7 1.0 1.0 CB M:CYS27 4.0 0.7 1.0 HB3 M:CYS27 4.0 0.0 1.0 N K:CYS261 4.0 0.9 1.0 CB M:CYS30 4.1 0.3 1.0 HB2 K:CYS261 4.2 1.0 1.0 O K:ALA260 4.2 0.1 1.0 HG1 M:THR23 4.2 0.1 1.0 H M:CYS27 4.3 0.9 1.0 HB2 M:CYS30 4.3 0.9 1.0 C K:ALA260 4.4 0.7 1.0 HB2 M:CYS27 4.4 0.0 1.0 H M:CYS30 4.4 0.7 1.0 H K:CYS261 4.5 0.3 1.0 HB2 M:LYS29 4.6 0.4 1.0 HB3 M:LYS29 4.6 0.4 1.0 HB3 M:CYS30 4.6 0.9 1.0 C K:CYS261 4.7 0.3 1.0 N M:CYS30 4.8 0.9 1.0 CA M:CYS25 4.8 0.3 1.0 N M:CYS27 5.0 0.7 1.0 CA M:CYS30 5.0 0.9 1.0

U.Schulze-Gahmen, H.Lu, Q.Zhou, T.Alber. AFF4 Binding to Tat-P-Tefb Indirectly Stimulates Tar Recognition of Super Elongation Complexes at the Hiv Promoter. Elife V. 3 02375 2014.
ISSN: ESSN 2050-084X
PubMed: 24843025
DOI: 10.7554/ELIFE.02375