Zinc in PDB 4i7d: SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr

The structure of SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr, PDB code: 4i7d was solved by E.Santelli, J.L.Stebbins, Y.Feng, S.K.De, A.Purves, K.Motamedchaboki, B.Wu, Z.A.Ronai, R.C.Liddington, M.Pellecchia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	160.977, 160.977, 160.977, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.2

The binding sites of Zinc atom in the SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr (pdb code 4i7d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr, PDB code: 4i7d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:61.9 occ:1.00 NE2 A:HIS147 2.0 64.8 1.0 SG A:CYS135 2.1 65.7 1.0 NE2 A:HIS152 2.2 59.5 1.0 SG A:CYS128 2.3 57.6 1.0 CD2 A:HIS147 3.0 56.1 1.0 CE1 A:HIS147 3.0 62.1 1.0 CB A:CYS135 3.1 67.9 1.0 CD2 A:HIS152 3.1 64.0 1.0 CE1 A:HIS152 3.3 65.0 1.0 CB A:CYS128 3.3 62.0 1.0 ND1 A:HIS147 4.1 63.6 1.0 CG A:HIS147 4.2 57.9 1.0 CG A:HIS152 4.3 67.1 1.0 ND1 A:HIS152 4.4 64.3 1.0 CB A:TRP137 4.5 72.4 1.0 CA A:CYS135 4.5 75.9 1.0 CA A:CYS128 4.6 55.7 1.0 C A:CYS135 4.8 76.2 1.0 O A:CYS135 4.9 75.6 1.0 CB A:GLN151 4.9 87.8 1.0

Zinc binding site 2 out of 4 in the SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:58.1 occ:1.00 NE2 A:HIS117 2.0 63.4 1.0 SG A:CYS105 2.2 53.6 1.0 SG A:CYS98 2.3 55.9 1.0 SG A:CYS121 2.4 63.7 1.0 CD2 A:HIS117 3.0 57.0 1.0 CE1 A:HIS117 3.0 64.2 1.0 CB A:CYS98 3.1 51.2 1.0 CB A:CYS121 3.2 64.1 1.0 CB A:CYS105 3.2 51.4 1.0 ND1 A:HIS117 4.1 67.8 1.0 CG A:HIS117 4.1 65.0 1.0 CA A:CYS121 4.4 67.1 1.0 CB A:TYR100 4.4 50.6 1.0 CB A:ILE107 4.5 65.8 1.0 CA A:CYS98 4.6 50.3 1.0 CD1 A:TYR100 4.6 52.6 1.0 CA A:CYS105 4.7 53.5 1.0 CG1 A:ILE107 4.8 69.5 1.0 CD1 A:PHE123 4.9 63.6 1.0

Zinc binding site 3 out of 4 in the SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:54.7 occ:1.00 NE2 C:HIS152 2.0 54.9 1.0 NE2 C:HIS147 2.1 49.7 1.0 SG C:CYS128 2.3 49.2 1.0 SG C:CYS135 2.3 57.2 1.0 CE1 C:HIS147 2.7 54.5 1.0 CD2 C:HIS152 3.0 56.8 1.0 CE1 C:HIS152 3.0 59.6 1.0 CB C:CYS135 3.1 59.7 1.0 CB C:CYS128 3.2 50.6 1.0 CD2 C:HIS147 3.3 47.5 1.0 ND1 C:HIS147 3.9 52.2 1.0 ND1 C:HIS152 4.1 55.9 1.0 CG C:HIS152 4.2 60.7 1.0 O C:HOH744 4.2 55.5 1.0 CG C:HIS147 4.3 52.2 1.0 CB C:TRP137 4.3 54.9 1.0 CA C:CYS128 4.6 48.2 1.0 CA C:CYS135 4.6 61.7 1.0 NE2 C:GLN151 4.8 0.4 1.0 CB C:CYS130 4.8 50.5 1.0 SG C:CYS130 4.9 56.6 1.0 C C:CYS135 4.9 57.0 1.0

Zinc binding site 4 out of 4 in the SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SIAH1 Bound to Synthetic Peptide (Ace)Klrpvamvrp(Prk)Vr within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:57.0 occ:1.00 NE2 C:HIS117 2.0 62.3 1.0 SG C:CYS98 2.3 60.2 1.0 SG C:CYS105 2.3 61.2 1.0 SG C:CYS121 2.3 59.7 1.0 CD2 C:HIS117 2.9 61.1 1.0 CB C:CYS98 3.0 61.9 1.0 CE1 C:HIS117 3.0 67.2 1.0 CB C:CYS105 3.2 62.9 1.0 CB C:CYS121 3.2 65.3 1.0 CG C:HIS117 4.1 69.0 1.0 ND1 C:HIS117 4.1 70.7 1.0 CA C:CYS121 4.3 69.1 1.0 CA C:CYS98 4.5 60.7 1.0 CA C:CYS105 4.6 70.2 1.0 CB C:ILE107 4.7 62.1 1.0 CB C:TYR100 4.7 65.1 1.0 CD1 C:TYR100 4.8 68.7 1.0 CD1 C:PHE123 5.0 68.5 1.0

J.L.Stebbins, E.Santelli, Y.Feng, S.K.De, A.Purves, K.Motamedchaboki, B.Wu, Z.A.Ronai, R.C.Liddington, M.Pellecchia. Structure-Based Design of Covalent Siah Inhibitors. Chem.Biol. V. 20 973 2013.
ISSN: ISSN 1074-5521
PubMed: 23891150
DOI: 10.1016/J.CHEMBIOL.2013.06.008