Table I.
Summary of zinc binding site designs and experimental results
| Name | Scaffold | Scaffold type | Mutations | Zinc binding residues | Second-shell hydrogen bond residues | Experimental outcome | Zinc binding affinity | |
|---|---|---|---|---|---|---|---|---|
| Phase 1 | ZE1 | 4fua | Hydrolase-like (α/β) | G37A | H92, H94, H155 | N/A | Destabilized by zinc | ND |
| ZE2 | 1a53 | TIM barrel (α/β) | K109A, E158G, N179H, R181A, L183H, E209A, S210H | H179, H183, H210 | N/A | Soluble, binds zinc | 1.4 µM | |
| ZE3 | 1dl3 | TIM barrel (α/β) | L130G, E158H, M79C, R181S, E209H | H7, C7, H79 | N/A | Soluble aggregates | ND | |
| Phase 2 | 1473 | 1icm | Lipocalin-like (Beta barrel) | L36S, E51H, R56H, V60H, Y70N | H51, H56, H60 | S36, N70 | Soluble aggregates | ND |
| 225 | 1q7f | 6-bladed beta propeller | A32N, R79H, T120H, V163S, V164S, I207H | H79, H120, H207 | N32, S164 | Did not express | ND | |
| 255 | 1m4w | Jelly roll (Beta sandwich) | Y78H, W80H, E87H, Y89N, D169G | H78, H80, H87 | N89, S126 | Soluble aggregates | ND | |
| 339 | 1f5j | Jelly roll (Beta sandwich) | Y81H, W83H, E90H, Y92T, S130T | H81, H83, H90 | D92, T130 | Soluble aggregates | ND | |
| 548 | 1lbm | TIM barrel (α/β) | K5H, A25G, F55H, V57H, Q81I, I101E, L124I, A165N, D167G | H5, H55, H57 | E10, N165 | Soluble aggregates | ND | |
| 1032 | 1suu | 6-bladed beta propeller | V186T, K187H, D239H, I241T, V287A, S288H, V289A | H187, H239, H288 | T24, T186 | Aggregated after cleavage | ND | |
| 289 | 2h13 | 6-bladed beta propeller | K21R, D61H, C103H, N105D, F232H | H61, H103, H232 | S60, D105 | Soluble aggregates | ND | |
| Phase 3 | Alpha1 | 1ovk | Lysozyme-like (α+β) | T21Q, N101A, Q105E, M106D, W118H, T122H, R125G | E105, H138, H142 | N21, D106 | Did not express | ND |
| AlphaBeta1 | 6cpa | Hydrolase-like (α/β) | R71A, E72H, R127H, E163Q, H196D, E270H, F279H | H72, H127, H279 | Q163, D196 | Did not express | ND | |
| TIM1 | 1igs | TIM barrel (α/β) | W7E, S55H, P56A, S57G, F87N, R181E, L186H | H55, E181, H186 | E7, S210 | Low expression, bound zinc | ∼50 µM | |
| TIM2 | 1tml | 7-stranded TIM barrel (α/β) | F42E, N46T, Q53H, L57K | E42, H44, H53 | T46, K57 | Did not express | ND | |
| Hinge1 | 1abe | Periplasmic binding protein (α/β) | W16F, D88H, M107Q, T146H, R150M, M203S, N204H, T207Q | H88, H146, H204 | E107, D231 | Expressed, bound zinc | 6.5 µM | |
| Hinge2 | 1gca | Periplasmic binding protein (α/β) | F16D, N91G, T110H, D154E, N256H, Q261E, Y295C | H110, H256, E261 | D16, E154 | Expressed, bound zinc | 1.1 µM | |
| Beta1 | 1cbs | Lipocalin-like (Beta barrel) | F15H, L18S, L19A, A32H, A36S, V76E | H15, H32, E76 | S18, S36 | Did not express | ND | |
| Beta2 | 1cbs | Lipocalin-like (Beta barrel) | F15A, L18E, A32D, A36H, T56N, V76H | D32, H36, H76 | E18, N56 | Did not express | ND | |
| Beta3 | 1ifc | Lipocalin-like (Beta barrel) | L36S, E51H, F55S, R56H, I58E, V60H | H51, H56, H60 | S36, S55 | Soluble aggregates | ND | |
| Beta4 | 1cbs | Lipocalin-like (Beta barrel) | F15A, L18Q, A32D, A36H, T56N, V76H | D32, H36, H76 | E18, N56 | Did not express | ND | |
| Pocket1 | 1f5j | Jelly roll (Beta sandwich) | N43E, L45D, Q128R, E180H, Y182H | E43, H180, H182 | D45, R128 | Soluble aggregates | ND | |
| Pocket2 | 1m4w | Jelly roll (Beta sandwich) | Y78H, W80H,Y89D, I127D, D169G | H78, H80, E87 | D89, D127 | Soluble aggregates | ND |