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Table 1 Summary of Zn-binding sites of structures used in the 3D structure modelling in this study

From: Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site

Structure Site 1 Site 2 Site 3 Site 4 Site 5 Coordinated metal ions Substrate Ref.
4f9u Asp99 Glu139 His265 Zn SUB1 [30]
  His82 Asp186   no 2nd ion   
4fwu Asp99 Glu139 His265 Zn no substrate [31]
  His82 Asp186 no 2nd ion   
1f2o   Asp97 Glu132 His247 Zn1 SUB2 [32]
  His85 Asp97 Asp160 Zn2   
1amp   Asp117 Glu152 His256 Zn1 No substrate [28]
  His97 Asp117 Asp179 Zn2   
GAA1Zn Asp153 Asp188 Tyr358 Zn PEP or SUB1 (model / this work)
  *Pro149   Glu226 no 2nd ion   
GAA1Zn1Zn2 Asp153 Asp188 Tyr358 Zn1 PEP or SUB2 (model / this work)
  *Pro149 Asp153 Glu226 Zn2   
  1. This table lists all the amino acid residues involved in the metal ion binding as well as the type of model substrates in the X-ray crystallographic 3D (including references) and model structures used in this work. Residue numbering follows the nomenclature in the published crystal structures and, for GPAA1, in UniProt sequence entry O43292. SUB1 stands for 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]-thiourea [30] and SUB2 is the label for L-leucine [32]. PEP is described in the text and in Fig. 1
  2. *Proline 84 (site 1) does not bind to a Zn ion