Zinc in PDB 4dd8: Adam-8 Metalloproteinase Domain with Bound Batimastat

The structure of Adam-8 Metalloproteinase Domain with Bound Batimastat, PDB code: 4dd8 was solved by T.Hall, H.S.Shieh, J.E.Day, N.Caspers, J.E.Chrencik, J.M.Williams, L.E.Pegg, A.M.Pauley, A.F.Moon, J.M.Krahn, D.H.Fischer, J.R.Kiefer, A.G.Tomasselli, M.D.Zack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.74 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.600, 50.900, 93.500, 90.00, 102.40, 90.00
R / Rfree (%)	18.8 / 25.5

The structure of Adam-8 Metalloproteinase Domain with Bound Batimastat also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Calcium	(Ca)	4 atoms
Chlorine	(Cl)	4 atoms
Sodium	(Na)	8 atoms

The binding sites of Zinc atom in the Adam-8 Metalloproteinase Domain with Bound Batimastat (pdb code 4dd8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Adam-8 Metalloproteinase Domain with Bound Batimastat, PDB code: 4dd8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:18.0 occ:1.00 NE2 A:HIS334 2.1 16.3 1.0 NE2 A:HIS344 2.1 13.9 1.0 O2 A:BAT1000 2.1 17.1 1.0 NE2 A:HIS338 2.2 13.7 1.0 O1 A:BAT1000 2.2 17.2 1.0 C2 A:BAT1000 2.8 19.6 1.0 N1 A:BAT1000 2.9 25.5 1.0 CD2 A:HIS344 3.0 16.1 1.0 CD2 A:HIS334 3.0 15.6 1.0 CE1 A:HIS334 3.1 17.5 1.0 CE1 A:HIS338 3.1 12.1 1.0 CD2 A:HIS338 3.1 14.0 1.0 CE1 A:HIS344 3.2 19.4 1.0 ND1 A:HIS334 4.2 15.6 1.0 OE1 A:GLU335 4.2 12.9 1.0 CG A:HIS334 4.2 16.8 1.0 CG A:HIS344 4.2 17.1 1.0 ND1 A:HIS338 4.2 12.1 1.0 ND1 A:HIS344 4.2 19.8 1.0 C1 A:BAT1000 4.2 23.0 1.0 CG A:HIS338 4.3 10.3 1.0 C9 A:BAT1000 4.5 18.8 1.0 C8 A:BAT1000 4.6 25.6 1.0 CL A:CL1004 4.6 34.9 1.0 CE A:MET364 4.6 9.2 1.0 C11 A:BAT1000 5.0 15.3 1.0 C3 A:BAT1000 5.0 23.7 1.0

Zinc binding site 2 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:18.1 occ:1.00 NE2 B:HIS344 2.1 13.0 1.0 O1 B:BAT1000 2.1 22.7 1.0 NE2 B:HIS338 2.1 13.5 1.0 NE2 B:HIS334 2.2 20.2 1.0 O2 B:BAT1000 2.2 28.3 1.0 C2 B:BAT1000 2.8 23.8 1.0 N1 B:BAT1000 3.0 26.4 1.0 CD2 B:HIS344 3.0 14.7 1.0 CD2 B:HIS338 3.1 17.9 1.0 CE1 B:HIS344 3.1 22.1 1.0 CD2 B:HIS334 3.1 20.2 1.0 CE1 B:HIS338 3.2 16.7 1.0 CE1 B:HIS334 3.2 17.6 1.0 CG B:HIS344 4.2 18.5 1.0 ND1 B:HIS344 4.2 16.8 1.0 C1 B:BAT1000 4.2 26.9 1.0 CG B:HIS338 4.2 15.6 1.0 ND1 B:HIS338 4.2 11.6 1.0 CG B:HIS334 4.3 15.2 1.0 ND1 B:HIS334 4.3 18.9 1.0 OE2 B:GLU335 4.5 17.0 1.0 C9 B:BAT1000 4.5 15.8 1.0 CL B:CL1004 4.5 33.4 1.0 CE B:MET364 4.5 10.5 1.0 OE1 B:GLU335 4.5 30.6 1.0 C8 B:BAT1000 4.5 21.1 1.0 CD B:GLU335 4.8 23.6 1.0 C5 B:BAT1000 4.9 31.5 1.0 C3 B:BAT1000 4.9 30.3 1.0

Zinc binding site 3 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:18.1 occ:1.00 NE2 C:HIS344 2.1 14.1 1.0 O2 C:BAT1000 2.1 23.5 1.0 NE2 C:HIS338 2.1 16.5 1.0 NE2 C:HIS334 2.2 19.5 1.0 O1 C:BAT1000 2.2 21.1 1.0 C2 C:BAT1000 2.8 22.7 1.0 N1 C:BAT1000 2.9 25.4 1.0 CD2 C:HIS344 3.0 14.3 1.0 CD2 C:HIS338 3.0 16.0 1.0 CD2 C:HIS334 3.0 18.7 1.0 CE1 C:HIS344 3.1 17.8 1.0 CE1 C:HIS338 3.2 15.8 1.0 CE1 C:HIS334 3.3 14.4 1.0 CG C:HIS344 4.2 17.5 1.0 ND1 C:HIS344 4.2 18.3 1.0 CG C:HIS338 4.2 14.3 1.0 C1 C:BAT1000 4.2 21.8 1.0 CG C:HIS334 4.2 17.4 1.0 ND1 C:HIS338 4.2 14.0 1.0 ND1 C:HIS334 4.3 12.2 1.0 CL C:CL1004 4.4 37.3 1.0 OE2 C:GLU335 4.5 22.1 1.0 C9 C:BAT1000 4.5 18.7 1.0 CE C:MET364 4.5 12.3 1.0 OE1 C:GLU335 4.5 22.4 1.0 C8 C:BAT1000 4.6 16.2 1.0 C5 C:BAT1000 4.8 28.9 1.0 CD C:GLU335 4.9 20.0 1.0 C3 C:BAT1000 4.9 23.3 1.0 C4 C:BAT1000 5.0 35.4 1.0

Zinc binding site 4 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:17.1 occ:1.00 NE2 D:HIS344 2.0 12.4 1.0 O1 D:BAT1000 2.1 21.0 1.0 NE2 D:HIS334 2.2 21.8 1.0 NE2 D:HIS338 2.2 16.1 1.0 O2 D:BAT1000 2.2 22.2 1.0 C2 D:BAT1000 2.8 23.4 1.0 CE1 D:HIS344 2.9 18.4 1.0 N1 D:BAT1000 2.9 28.3 1.0 CD2 D:HIS344 3.0 12.8 1.0 CD2 D:HIS334 3.0 23.3 1.0 CD2 D:HIS338 3.1 17.0 1.0 CE1 D:HIS334 3.2 19.3 1.0 CE1 D:HIS338 3.2 19.6 1.0 O D:HOH1147 4.0 23.0 1.0 ND1 D:HIS344 4.0 18.6 1.0 CG D:HIS344 4.1 18.4 1.0 C1 D:BAT1000 4.2 27.8 1.0 CG D:HIS334 4.2 18.9 1.0 ND1 D:HIS334 4.2 16.5 1.0 CG D:HIS338 4.2 11.9 1.0 ND1 D:HIS338 4.3 14.2 1.0 OE1 D:GLU335 4.4 24.3 1.0 C9 D:BAT1000 4.5 24.8 1.0 OE2 D:GLU335 4.5 25.9 1.0 C8 D:BAT1000 4.5 24.6 1.0 CL D:CL1004 4.6 32.7 1.0 CE D:MET364 4.7 11.9 1.0 CD D:GLU335 4.8 22.9 1.0 C3 D:BAT1000 4.9 30.5 1.0

T.Hall, H.S.Shieh, J.E.Day, N.Caspers, J.E.Chrencik, J.M.Williams, L.E.Pegg, A.M.Pauley, A.F.Moon, J.M.Krahn, D.H.Fischer, J.R.Kiefer, A.G.Tomasselli, M.D.Zack. Structure of Human Adam-8 Catalytic Domain Complexed with Batimastat. Acta Crystallogr.,Sect.F V. 68 616 2012.
ISSN: ESSN 1744-3091
PubMed: 22684055
DOI: 10.1107/S1744309112015618