Zinc in PDB 5r4t: Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430, PDB code: 5r4t was solved by S.L.Kidd, N.Mateu, R.Talon, T.Krojer, A.Aimon, A.R.Bradley, M.Fairhead, L.Diaz-Saez, H.F.Sore, A.Madin, K.V.M.Huber, F.Von Delft, D.R.Spring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.99 / 1.68
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.010, 59.010, 212.964, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 25.9

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 (pdb code 5r4t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430, PDB code: 5r4t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.3 occ:1.00 NE1 A:TRP149 2.7 42.5 1.0 O A:HOH521 2.9 59.5 1.0 CE A:MET76 3.4 33.4 1.0 ND1 A:HIS171 3.5 35.2 1.0 CD1 A:TRP149 3.7 34.4 1.0 CE2 A:TRP149 3.7 36.0 1.0 CG A:HIS171 3.7 30.1 1.0 CB A:HIS171 3.8 27.9 1.0 SD A:MET76 3.9 34.5 1.0 CZ2 A:TRP149 4.0 42.8 1.0 CE1 A:HIS171 4.2 33.9 1.0 CD2 A:HIS171 4.4 29.9 1.0 O A:HOH437 4.4 41.4 1.0 CD1 A:ILE161 4.5 48.6 1.0 NE2 A:HIS171 4.7 31.1 1.0 CG A:TRP149 4.9 31.3 1.0 CD2 A:TRP149 4.9 34.1 1.0 CG A:PRO168 5.0 36.7 1.0

Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:0.7 occ:1.00 ND1 A:HIS89 2.4 34.4 1.0 CA A:HIS89 3.4 38.1 1.0 CG A:HIS89 3.4 34.2 1.0 CE1 A:HIS89 3.4 36.6 1.0 CB A:HIS89 3.5 35.0 1.0 N A:HIS89 4.2 34.4 1.0 O A:HOH491 4.3 47.6 1.0 C A:HIS89 4.4 38.4 1.0 NE2 A:HIS89 4.6 30.1 1.0 CD2 A:HIS89 4.6 31.5 1.0 O A:HIS89 5.0 39.0 1.0

Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:36.9 occ:1.00 O B:HOH401 1.5 29.1 1.0 OE1 B:GLU88 2.0 37.9 0.3 NE2 B:HIS93 2.1 33.9 1.0 CD B:GLU88 3.0 43.0 0.3 CE1 B:HIS93 3.1 34.7 1.0 CD2 B:HIS93 3.1 33.3 1.0 CG B:GLU88 3.3 42.3 0.3 OE2 B:GLU88 4.1 43.8 0.3 CB B:GLU88 4.2 46.3 0.2 ND1 B:HIS93 4.2 30.6 1.0 CG B:GLU88 4.2 47.7 0.2 CG B:HIS93 4.2 29.7 1.0 CG B:PRO197 4.5 33.4 1.0 O B:GLU88 4.5 47.0 0.3 CB B:PRO197 4.6 32.0 1.0 CD B:PRO197 4.7 33.4 1.0 ND1 B:HIS89 4.7 53.1 0.3 CB B:GLU88 4.8 42.0 0.3 O B:GLU88 4.9 49.7 0.2 O B:HOH472 5.0 54.3 1.0 CE1 B:HIS89 5.0 56.0 0.3

Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:44.8 occ:1.00 NE2 B:HIS164 1.6 36.1 1.0 O B:HOH499 2.5 37.7 1.0 CE1 B:HIS164 2.5 39.8 1.0 CD2 B:HIS164 2.8 41.3 1.0 ND1 B:HIS164 3.7 36.9 1.0 CG B:HIS164 3.8 37.2 1.0

Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:1.0 occ:1.00 ND1 B:HIS164 3.7 36.9 1.0 CE1 B:HIS164 3.9 39.8 1.0 CG B:HIS164 4.8 37.2 1.0

Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Human Cleavage Factor Im in Complex with Sk-430 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:1.0 occ:1.00 CE1 B:HIS171 3.5 38.1 1.0 ND1 B:HIS171 3.9 39.5 1.0 O B:HOH473 4.4 38.7 1.0 NE2 B:HIS171 4.6 39.4 1.0

S.L.Kidd, N.Mateu, R.Talon, T.Krojer, A.Aimon, A.R.Bradley, M.Fairhead, L.Diaz-Saez, H.F.Sore, A.Madin, K.V.M.Huber, F.Von Delft, D.R.Spring. Pandda Analysis Group Deposition To Be Published.