Zinc in PDB 3lpe: Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii

All present enzymatic activity of Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii:
2.7.7.6;

The structure of Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii, PDB code: 3lpe was solved by A.Hirtreiter, G.E.Damsma, A.C.M.Cheung, D.Klose, D.Grohmann, E.Vojnic, A.C.R.Martin, P.Cramer, F.Werner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.36 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.360, 63.970, 83.040, 90.00, 106.98, 90.00
R / Rfree (%)	20.8 / 25.5

The binding sites of Zinc atom in the Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii (pdb code 3lpe). 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 SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii, PDB code: 3lpe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii


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 SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn60 b:23.4 occ:1.00 SG B:CYS7 2.3 24.9 1.0 SG B:CYS16 2.3 21.2 1.0 SG B:CYS4 2.3 20.6 1.0 SG B:CYS19 2.4 21.1 1.0 CB B:CYS4 3.0 20.3 1.0 CB B:CYS16 3.2 21.2 1.0 CB B:CYS7 3.4 25.7 1.0 CB B:CYS19 3.5 30.6 1.0 N B:CYS7 3.8 26.2 1.0 N B:CYS19 3.9 25.6 1.0 CA B:CYS7 4.1 29.6 1.0 CA B:CYS19 4.2 29.6 1.0 CB B:ILE18 4.5 24.0 1.0 CA B:CYS4 4.5 20.3 1.0 O B:HOH122 4.6 35.5 1.0 OG B:SER21 4.6 66.9 1.0 CA B:CYS16 4.6 28.5 1.0 C B:CYS7 4.6 21.2 1.0 CB B:TYR9 4.7 21.8 1.0 N B:LYS8 4.7 20.9 1.0 CB B:LYS6 4.8 34.6 1.0 C B:CYS19 4.8 26.7 1.0 C B:LYS6 4.9 39.5 1.0 C B:ILE18 4.9 27.9 1.0 N B:TYR9 5.0 20.5 1.0 N B:HIS20 5.0 20.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii


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 SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn60 b:46.6 occ:1.00 O D:HOH225 2.3 48.7 1.0 SG D:CYS16 2.3 46.9 1.0 SG D:CYS7 2.3 46.1 1.0 SG D:CYS4 2.4 50.5 1.0 SG D:CYS19 2.4 57.9 1.0 CB D:CYS4 3.0 41.3 1.0 CB D:CYS16 3.1 44.7 1.0 CB D:CYS7 3.4 38.4 1.0 CB D:CYS19 3.5 44.5 1.0 N D:CYS7 3.8 47.0 1.0 N D:CYS19 3.9 49.7 1.0 CA D:CYS7 4.1 44.7 1.0 CA D:CYS19 4.2 44.6 1.0 CB D:ILE18 4.4 46.9 1.0 CA D:CYS4 4.5 42.6 1.0 CA D:CYS16 4.6 49.7 1.0 CB D:TYR9 4.6 35.3 1.0 C D:CYS7 4.7 35.9 1.0 OG D:SER21 4.7 71.2 1.0 CB D:LYS6 4.8 54.7 1.0 C D:CYS19 4.8 47.4 1.0 N D:LYS8 4.8 37.2 1.0 C D:ILE18 4.9 41.7 1.0 C D:LYS6 4.9 51.2 1.0 N D:HIS20 4.9 52.2 1.0 N D:TYR9 4.9 37.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii


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 SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn60 b:26.1 occ:1.00 SG F:CYS19 2.3 25.8 1.0 SG F:CYS4 2.3 24.9 1.0 SG F:CYS16 2.4 25.4 1.0 SG F:CYS7 2.4 24.2 1.0 CB F:CYS16 3.1 22.4 1.0 CB F:CYS4 3.1 24.0 1.0 CB F:CYS7 3.4 25.9 1.0 CB F:CYS19 3.5 23.1 1.0 N F:CYS19 3.8 23.8 1.0 N F:CYS7 3.9 28.8 1.0 CA F:CYS7 4.1 30.9 1.0 CA F:CYS19 4.2 35.2 1.0 CB F:ILE18 4.4 31.4 1.0 CA F:CYS16 4.6 31.6 1.0 CA F:CYS4 4.6 23.5 1.0 CB F:TYR9 4.6 32.2 1.0 C F:CYS7 4.7 22.1 1.0 OG F:SER21 4.7 58.7 1.0 C F:CYS19 4.7 28.7 1.0 O F:HOH308 4.8 47.4 1.0 CB F:LYS6 4.8 40.6 1.0 N F:LYS8 4.8 21.9 1.0 C F:ILE18 4.8 23.4 1.0 N F:HIS20 4.9 32.2 1.0 C F:LYS6 4.9 47.8 1.0 CG2 F:ILE18 5.0 25.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii


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 SPT4/5NGN Heterodimer Complex From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn60 b:47.9 occ:1.00 SG H:CYS4 2.3 47.0 1.0 SG H:CYS16 2.3 47.5 1.0 SG H:CYS7 2.4 51.5 1.0 SG H:CYS19 2.4 58.9 1.0 O H:HOH316 2.5 59.8 1.0 CB H:CYS4 3.1 43.5 1.0 CB H:CYS16 3.1 50.9 1.0 CB H:CYS7 3.4 40.7 1.0 CB H:CYS19 3.5 54.2 1.0 N H:CYS19 3.8 48.8 1.0 N H:CYS7 3.8 52.6 1.0 CA H:CYS7 4.1 46.0 1.0 CA H:CYS19 4.2 52.9 1.0 CB H:ILE18 4.4 42.1 1.0 CA H:CYS4 4.6 44.8 1.0 CA H:CYS16 4.6 49.5 1.0 CB H:TYR9 4.7 36.4 1.0 C H:CYS7 4.7 39.6 1.0 OG H:SER21 4.7 77.5 1.0 CB H:LYS6 4.7 51.7 1.0 C H:CYS19 4.8 56.5 1.0 N H:LYS8 4.8 45.5 1.0 C H:ILE18 4.9 45.5 1.0 C H:LYS6 4.9 52.8 1.0 N H:HIS20 5.0 55.6 1.0 CG2 H:ILE18 5.0 41.5 1.0

A.Hirtreiter, G.E.Damsma, A.C.Cheung, D.Klose, D.Grohmann, E.Vojnic, A.C.Martin, P.Cramer, F.Werner. SPT4/5 Stimulates Transcription Elongation Through the Rna Polymerase Clamp Coiled-Coil Motif. Nucleic Acids Res. V. 38 4040 2010.
ISSN: ISSN 0305-1048
PubMed: 20197319
DOI: 10.1093/NAR/GKQ135