Zinc in PDB 4wa6: Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution

All present enzymatic activity of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution:
3.4.19.12;

The structure of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution, PDB code: 4wa6 was solved by C.Wolberger, M.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.076, 68.004, 137.858, 90.00, 106.75, 90.00
R / Rfree (%)	18.3 / 24.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution (pdb code 4wa6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution, PDB code: 4wa6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.6 occ:1.00 ND1 A:HIS6 2.1 50.5 1.0 SG A:CYS99 2.3 50.4 1.0 SG A:CYS4 2.3 49.3 1.0 SG A:CYS96 2.3 48.7 1.0 CE1 A:HIS6 3.0 51.6 1.0 CG A:HIS6 3.2 51.0 1.0 CB A:CYS96 3.3 46.8 1.0 CB A:CYS99 3.3 49.3 1.0 CB A:CYS4 3.3 49.5 1.0 N A:CYS99 3.6 51.6 1.0 CB A:HIS6 3.7 51.4 1.0 CA A:CYS99 4.1 47.9 1.0 CA A:CYS4 4.1 53.1 1.0 CD A:PRO5 4.1 52.6 1.0 N A:HIS6 4.1 50.3 1.0 NE2 A:HIS6 4.1 51.2 1.0 CD2 A:HIS6 4.3 50.6 1.0 N A:PRO5 4.4 51.8 1.0 C A:CYS4 4.5 52.0 1.0 CA A:HIS6 4.5 49.9 1.0 CB A:LYS98 4.6 54.3 1.0 CA A:CYS96 4.7 44.5 1.0 C A:LYS98 4.7 52.7 1.0 CE1 A:PHE85 4.9 44.4 1.0 N A:ILE7 5.0 50.7 1.0

Zinc binding site 2 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:41.5 occ:1.00 ND1 A:HIS73 2.1 41.9 1.0 SG A:CYS49 2.3 41.2 1.0 SG A:CYS46 2.3 39.9 1.0 SG A:CYS68 2.3 43.1 1.0 CB A:CYS46 3.1 40.0 1.0 CG A:HIS73 3.1 41.5 1.0 CE1 A:HIS73 3.1 42.2 1.0 CB A:HIS73 3.4 40.6 1.0 CB A:CYS49 3.4 43.4 1.0 CB A:CYS68 3.5 39.4 1.0 N A:CYS49 3.7 44.4 1.0 N A:CYS68 4.1 39.1 1.0 CA A:CYS49 4.2 44.3 1.0 NE2 A:HIS73 4.2 42.6 1.0 CD2 A:HIS73 4.3 41.7 1.0 ND1 A:HIS71 4.3 47.4 1.0 CB A:HIS71 4.4 44.7 1.0 CA A:CYS68 4.4 38.5 1.0 CB A:THR48 4.5 40.9 1.0 CA A:CYS46 4.5 39.9 1.0 C A:THR48 4.7 44.1 1.0 OG A:SER54 4.8 40.9 1.0 CA A:HIS73 4.8 40.1 1.0 CG A:HIS71 4.8 45.3 1.0 N A:THR48 4.9 41.2 1.0 CB A:SER54 4.9 37.6 1.0 CA A:THR48 4.9 41.3 1.0 C A:CYS49 5.0 43.6 1.0 N A:HIS73 5.0 39.6 1.0

Zinc binding site 3 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:45.9 occ:1.00 NE2 A:HIS77 2.1 43.9 1.0 ND1 A:HIS83 2.2 50.3 1.0 SG A:CYS60 2.3 45.6 1.0 SG A:CYS63 2.3 46.6 1.0 CE1 A:HIS77 3.0 44.6 1.0 CE1 A:HIS83 3.1 49.7 1.0 CG A:HIS83 3.1 48.9 1.0 CD2 A:HIS77 3.2 42.6 1.0 CB A:CYS60 3.3 44.7 1.0 CB A:CYS63 3.3 45.5 1.0 CB A:HIS83 3.4 46.3 1.0 N A:CYS63 3.8 45.7 1.0 CA A:CYS63 4.1 45.4 1.0 ND1 A:HIS77 4.2 44.2 1.0 NE2 A:HIS83 4.2 52.4 1.0 CD2 A:HIS83 4.3 51.3 1.0 CG A:HIS77 4.3 42.1 1.0 C A:GLN62 4.4 46.2 1.0 C A:CYS63 4.6 44.9 1.0 CB A:PHE65 4.7 43.1 1.0 CA A:CYS60 4.7 45.0 1.0 O A:CYS63 4.8 48.5 1.0 CB A:GLN62 4.8 50.9 1.0 N A:GLN62 4.8 46.6 1.0 CG2 A:ILE81 4.9 51.0 1.0 CA A:GLN62 4.9 47.8 1.0 O A:GLN62 4.9 46.2 1.0 CA A:HIS83 5.0 46.0 1.0 CD2 A:PHE65 5.0 40.6 1.0

Zinc binding site 4 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:52.6 occ:1.00 NE2 A:HIS170 2.1 57.6 1.0 SG A:CYS182 2.3 53.9 1.0 SG A:CYS185 2.3 53.6 1.0 SG A:CYS174 2.3 62.6 1.0 CD2 A:HIS170 3.1 55.4 1.0 CE1 A:HIS170 3.1 57.6 1.0 CB A:CYS182 3.2 53.1 1.0 CB A:CYS185 3.3 52.9 1.0 CB A:CYS174 3.4 61.7 1.0 N A:CYS185 3.5 50.6 1.0 CA A:CYS185 3.8 51.2 1.0 ND1 A:HIS170 4.2 54.3 1.0 CG A:HIS170 4.3 55.9 1.0 C A:SER184 4.3 49.0 1.0 CB A:SER184 4.4 47.4 1.0 N A:ARG177 4.5 63.5 1.0 CA A:CYS182 4.5 54.5 1.0 O A:CYS182 4.6 55.6 1.0 CA A:CYS174 4.6 62.5 1.0 CA A:SER184 4.7 47.7 1.0 C A:CYS182 4.8 52.3 1.0 N A:SER184 4.8 48.3 1.0 CB A:VAL176 4.8 59.9 1.0

Zinc binding site 5 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:47.5 occ:1.00 ND1 A:HIS276 2.1 46.5 1.0 ND1 A:HIS250 2.1 50.6 1.0 SG A:CYS273 2.3 44.8 1.0 SG A:CYS271 2.3 51.1 1.0 CE1 A:HIS276 2.8 47.2 1.0 CE1 A:HIS250 2.9 52.6 1.0 CG A:HIS250 3.2 48.3 1.0 CB A:CYS271 3.2 54.8 1.0 CG A:HIS276 3.2 47.9 1.0 CB A:CYS273 3.3 45.1 1.0 CB A:HIS250 3.6 46.7 1.0 CB A:HIS276 3.7 46.4 1.0 NE2 A:HIS276 4.0 48.2 1.0 NE2 A:HIS250 4.1 51.3 1.0 CA A:HIS250 4.1 47.7 1.0 CD2 A:HIS250 4.2 49.7 1.0 N A:CYS273 4.2 49.1 1.0 CD2 A:HIS276 4.2 48.4 1.0 N A:HIS276 4.2 40.4 1.0 CA A:CYS273 4.3 44.2 1.0 CA A:CYS271 4.5 57.1 1.0 CA A:HIS276 4.6 43.4 1.0 C A:CYS271 4.7 56.1 1.0 CD2 A:TYR253 4.8 49.3 1.0 O A:CYS271 4.9 58.3 1.0 C A:CYS273 4.9 43.3 1.0 O A:HIS250 4.9 47.7 1.0 C A:HIS250 4.9 48.0 1.0

Zinc binding site 6 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:70.7 occ:1.00 SG A:CYS292 2.3 76.8 1.0 SG A:CYS339 2.3 74.7 1.0 SG A:CYS336 2.3 75.1 1.0 SG A:CYS289 2.4 68.3 1.0 CB A:CYS336 3.0 70.3 1.0 CB A:CYS339 3.3 74.2 1.0 CB A:CYS292 3.3 76.4 1.0 CB A:CYS289 3.4 68.1 1.0 N A:CYS292 3.8 73.5 1.0 N A:CYS339 3.8 75.8 1.0 CA A:CYS292 4.0 74.9 1.0 CA A:CYS339 4.1 75.4 1.0 CA A:CYS336 4.5 70.9 1.0 C A:CYS292 4.6 72.3 1.0 CB A:GLU338 4.6 79.0 1.0 O A:CYS336 4.7 78.4 1.0 C A:CYS339 4.7 73.6 1.0 C A:GLY291 4.7 76.6 1.0 N A:GLN293 4.8 69.8 1.0 CB A:SER341 4.8 65.8 1.0 C A:CYS336 4.8 75.3 1.0 CA A:CYS289 4.8 65.9 1.0 N A:ASN340 4.8 70.1 1.0 C A:GLU338 4.9 77.2 1.0 CA A:GLY291 5.0 76.0 1.0

Zinc binding site 7 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:90.1 occ:1.00 NE2 C:HIS88 2.1 82.2 1.0 SG C:CYS92 2.3 68.4 1.0 CD2 C:HIS88 3.1 79.6 1.0 CE1 C:HIS88 3.1 83.5 1.0 CB C:CYS92 3.3 72.4 1.0 ND1 C:HIS88 4.1 80.5 1.0 CG C:HIS88 4.2 78.8 1.0 CA C:CYS92 4.7 77.9 1.0

Zinc binding site 8 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn101 b:63.1 occ:1.00 NE2 E:HIS93 2.1 68.2 1.0 O E:HOH203 2.2 83.5 1.0 SG E:CYS81 2.3 64.8 1.0 SG E:CYS78 2.3 59.4 1.0 CE1 E:HIS93 2.8 69.0 1.0 CB E:CYS78 3.2 57.2 1.0 CD2 E:HIS93 3.3 68.4 1.0 CB E:CYS81 3.3 63.9 1.0 N E:CYS81 3.5 67.4 1.0 CA E:CYS81 4.0 64.1 1.0 ND1 E:HIS93 4.0 69.7 1.0 CB E:LYS80 4.1 76.1 1.0 CG E:HIS93 4.3 68.1 1.0 C E:LYS80 4.5 70.4 1.0 CA E:CYS78 4.6 57.1 1.0 CA E:LYS80 4.7 71.6 1.0 C E:CYS81 4.8 58.8 1.0 N E:LYS80 4.9 67.6 1.0 N E:GLY82 4.9 55.9 1.0

Zinc binding site 9 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:78.2 occ:1.00 ND1 D:HIS6 2.1 74.0 1.0 SG D:CYS4 2.3 68.3 1.0 SG D:CYS99 2.3 81.7 1.0 SG D:CYS96 2.4 65.8 1.0 CE1 D:HIS6 3.0 74.2 1.0 CG D:HIS6 3.1 75.0 1.0 CB D:CYS96 3.2 66.2 1.0 CB D:CYS99 3.4 77.6 1.0 CB D:CYS4 3.4 68.2 1.0 CB D:HIS6 3.6 74.7 1.0 N D:HIS6 3.9 72.5 1.0 N D:CYS99 3.9 76.8 1.0 CA D:CYS4 4.0 69.2 1.0 NE2 D:HIS6 4.1 76.2 1.0 CD D:PRO5 4.1 68.2 1.0 CA D:CYS99 4.1 76.3 1.0 CD2 D:HIS6 4.2 77.2 1.0 N D:PRO5 4.2 70.2 1.0 C D:CYS4 4.3 71.1 1.0 CA D:HIS6 4.4 75.2 1.0 CA D:CYS96 4.7 63.4 1.0 C D:LYS98 4.8 76.6 1.0 CG D:PRO5 4.8 70.0 1.0 CB D:LYS98 4.8 79.3 1.0 N D:ILE7 4.9 76.1 1.0 C D:PRO5 5.0 72.5 1.0

Zinc binding site 10 out of 15 in the Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:65.5 occ:1.00 ND1 D:HIS73 2.1 65.1 1.0 SG D:CYS46 2.3 64.3 1.0 SG D:CYS49 2.3 61.0 1.0 SG D:CYS68 2.4 63.5 1.0 CE1 D:HIS73 3.0 66.7 1.0 CG D:HIS73 3.1 66.3 1.0 CB D:CYS46 3.3 62.5 1.0 CB D:CYS49 3.3 68.3 1.0 CB D:CYS68 3.5 56.2 1.0 CB D:HIS73 3.5 65.3 1.0 N D:CYS49 3.7 73.1 1.0 ND1 D:HIS71 3.8 78.0 1.0 NE2 D:HIS73 4.1 69.7 1.0 N D:CYS68 4.1 56.6 1.0 CA D:CYS49 4.1 72.7 1.0 CD2 D:HIS73 4.1 67.6 1.0 CB D:HIS71 4.2 68.2 1.0 CA D:CYS68 4.3 55.9 1.0 CB D:THR48 4.5 74.0 1.0 CG D:HIS71 4.5 70.9 1.0 OG D:SER54 4.7 62.2 1.0 CA D:CYS46 4.7 62.3 1.0 C D:THR48 4.7 73.0 1.0 CA D:HIS73 4.8 67.5 1.0 CB D:SER54 4.8 57.0 1.0 N D:HIS73 4.9 66.7 1.0 CE1 D:HIS71 4.9 79.0 1.0 C D:CYS68 5.0 58.6 1.0 CA D:THR48 5.0 73.6 1.0

C.Wolberger, M.Yan. Structure of Yeast Saga Dubm with SGF73 N59D Mutant at 2.36 Angstroms Resolution To Be Published.