Zinc in PDB 3qqc: Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain

The structure of Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain, PDB code: 3qqc was solved by F.W.Martinez-Rucobo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.70 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.570, 107.040, 51.090, 90.00, 97.10, 90.00
R / Rfree (%)	19.3 / 24.7

The binding sites of Zinc atom in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain (pdb code 3qqc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain, PDB code: 3qqc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:0.9 occ:1.00 SG A:CYS208 2.4 0.6 1.0 SG A:CYS164 2.5 0.5 1.0 SG A:CYS161 2.5 0.6 1.0 CB A:CYS161 3.0 0.8 1.0 CD A:PRO209 3.5 0.8 1.0 CB A:CYS208 3.6 0.9 1.0 CA A:CYS208 3.8 0.3 1.0 N A:PRO209 3.9 0.5 1.0 C A:CYS208 4.1 1.0 1.0 O A:PRO209 4.1 0.9 1.0 CB A:CYS164 4.2 0.0 1.0 CA A:CYS161 4.5 0.6 1.0 CB A:ARG166 4.6 0.6 1.0 O A:ARG162 4.6 0.9 1.0 C A:PRO209 4.6 0.1 1.0 N A:ARG166 4.8 0.8 1.0 CG A:PRO209 4.8 0.5 1.0 CA A:PRO209 4.8 0.8 1.0 O A:CYS208 5.0 0.5 1.0 N A:GLY165 5.0 0.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.7 occ:1.00 NE2 A:HIS134 2.2 0.5 1.0 SG A:CYS131 2.5 0.1 1.0 SG A:CYS121 2.5 0.7 1.0 SG A:CYS124 2.6 0.7 1.0 CD2 A:HIS134 3.0 0.4 1.0 CE1 A:HIS134 3.3 0.9 1.0 CB A:CYS121 3.7 0.4 1.0 O A:PRO132 3.8 0.0 1.0 CB A:CYS131 3.9 0.4 1.0 CG A:HIS134 4.2 0.3 1.0 CB A:CYS124 4.3 0.7 1.0 ND1 A:HIS134 4.4 0.6 1.0 CA A:GLY113 4.4 0.7 1.0 CA A:CYS131 4.7 0.8 1.0 N A:GLU122 4.8 0.4 1.0 N A:VAL114 4.8 0.7 1.0 CG2 A:VAL114 4.8 0.3 1.0 C A:CYS131 4.9 0.5 1.0 C A:PRO132 4.9 1.0 1.0 N A:GLY113 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:0.6 occ:1.00 SG A:CYS11 2.3 89.6 1.0 SG A:CYS26 2.3 0.1 1.0 SG A:CYS8 2.3 0.2 1.0 SG A:CYS29 2.3 0.8 1.0 CB A:CYS26 2.9 99.9 1.0 CB A:CYS8 3.2 99.1 1.0 CB A:CYS29 3.5 96.6 1.0 CB A:CYS11 3.6 85.4 1.0 N A:CYS29 3.9 95.6 1.0 N A:CYS11 3.9 86.3 1.0 CA A:CYS29 4.1 97.0 1.0 CB A:GLU31 4.2 0.2 1.0 CA A:CYS11 4.3 84.4 1.0 CA A:CYS26 4.4 0.9 1.0 CB A:ASN10 4.4 92.5 1.0 CB A:HIS13 4.6 87.2 1.0 C A:CYS29 4.6 0.6 1.0 CA A:CYS8 4.7 98.9 1.0 N A:GLU31 4.7 0.9 1.0 OD1 A:ASN10 4.7 0.7 1.0 C A:CYS11 4.8 85.0 1.0 C A:ASN10 4.9 91.1 1.0 N A:GLY30 4.9 0.3 1.0 N A:HIS13 5.0 84.3 1.0 CB A:VAL28 5.0 95.1 1.0 CA A:ASN10 5.0 90.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn100 b:0.8 occ:1.00 SG E:CYS18 2.4 1.0 1.0 SG E:CYS9 2.4 0.1 1.0 SG E:CYS6 2.4 0.5 1.0 SG E:CYS21 2.5 0.7 1.0 CB E:CYS18 2.8 0.5 1.0 CB E:CYS6 3.1 0.8 1.0 CB E:CYS21 4.1 0.9 1.0 CB E:CYS9 4.1 0.2 1.0 CB E:SER23 4.3 0.8 1.0 CA E:CYS18 4.3 0.8 1.0 N E:CYS9 4.4 0.9 1.0 N E:SER23 4.5 0.0 1.0 CA E:CYS6 4.6 0.6 1.0 N E:CYS21 4.6 0.0 1.0 N E:GLY22 4.7 0.8 1.0 O E:CYS18 4.8 1.0 1.0 CA E:CYS9 4.8 0.1 1.0 CA E:CYS21 4.8 0.3 1.0 C E:CYS18 4.8 0.9 1.0 CB E:TYR11 4.9 0.5 1.0 CA E:SER23 4.9 0.2 1.0

F.W.Martinez-Rucobo, S.Sainsbury, A.C.Cheung, P.Cramer. Architecture of the Rna Polymerase-SPT4/5 Complex and Basis of Universal Transcription Processivity. Embo J. V. 30 1302 2011.
ISSN: ISSN 0261-4189
PubMed: 21386817
DOI: 10.1038/EMBOJ.2011.64