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ZN 1308 A

Metal-MACiE entry for ZN 1308 A

The enzyme uses zinc to perform the reaction. The metal ion is directly involved in the catalytic mechanism (substrate binding and activation) (PMID3463986)


Metal in MACiE Physiological Metal Site Type
zinc zinc mononuclear

Resting State

nativeState of ZN 1308 A
Download the coordinates file
Representative Structure
PDB code 1m4l
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
PDB Metal Type (Identity) zinc
(ZN1308A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(5)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 69 AHIS 69 A No monodentate ND1
Amino Acid Residue GLU 72 AGLU 72 A No bidentate OE1,OE2
Amino Acid Residue HIS 196 AHIS 196 A No monodentate ND1
Water HOH 1016 - No monodentate O

Step 01

Metal Functions

Substrate Binding

Activator. Note: It activates both the substrates.

Increase Nucleophilicity. Note: It increases nucleophilicity of a water molecule.

Increase Electrophilicity. Note: I increases electrophilicity of the substrate polarizing the carbonyl group.

Structural Information


reagent of ZN 1308 A
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Representative Structure
PDB code 3cpa
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
PDB Metal Type (Identity) zinc
(ZN1_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalBipyramidal
(6)

In this structure the enzyme is in complex with a dipeptide which coordinates zinc in a bidentate mode whereas the substrate is supposed to coordinate zinc in a monodentate mode. Water should be the fifth ligand (PMID3463986).


First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 69 HIS 69 A No monodentate ND1
Amino Acid Residue GLU 72 GLU 72 A No bidentate OE1,OE2
Amino Acid Residue HIS 196 HIS 196 A No monodentate ND1
Reactive Species GLY 1 S- No bidentate N,O
Note: Dipeptides are probably poor substrates because of bidentate coordination of zinc that removes the activated water from the zinc coordination sphere (PMID3463986).




Right Arrow
product of ZN 1308 A
Download the coordinates file
Representative Structure
PDB code 6cpa
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
PDB Metal Type (Identity) zinc
(ZN308_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(5)

In this structure the enzyme is in complex with a transition-state analogue inhibitor.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 69 HIS 69 A No monodentate ND1
Amino Acid Residue GLU 72 GLU 72 A No bidentate OE1,OE2
Amino Acid Residue HIS 196 HIS 196 A No monodentate ND1
Reactive Species ZAF 1 - No monodentate O3A
Note: This is a transition-state analogue inhibitor.

Step 02

Metal Functions

Substrate Binding

Electrostatic Stabiliser

Structural Information


reagent of ZN 1308 A
Download the coordinates file
Representative Structure
PDB code 6cpa
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
PDB Metal Type (Identity) zinc
(ZN308_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(5)

In this structure the enzyme is in complex with a transition-state analogue inhibitor.


First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 69 HIS 69 A No monodentate ND1
Amino Acid Residue GLU 72 GLU 72 A No bidentate OE1,OE2
Amino Acid Residue HIS 196 HIS 196 A No monodentate ND1
Reactive Species ZAF 1 - No monodentate O3A
Note: This is a transition-state analogue inhibitor.




Right Arrow
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(5)

This step has no available structures in the PDB: all the coordinating information are derived from the reaction model in MACiE.


Step 03

Metal Functions

This metal is not active in this step.

Structural Information


reagent of ZN 1308 A
Download the coordinates file
Representative Structure
PDB code 1m4l
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
PDB Metal Type (Identity) zinc
(ZN1308A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(5)

This is an inferred step. In this stage the coordination of the metal is the same as in the resting state.


First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 69 AHIS 69 A No monodentate ND1
Amino Acid Residue GLU 72 AGLU 72 A No bidentate OE1,OE2
Amino Acid Residue HIS 196 AHIS 196 A No monodentate ND1
Water HOH 1016 - No monodentate O




Right Arrow
product of ZN 1308 A
Download the coordinates file
Representative Structure
PDB code 1m4l
MACiE Metal Type
(Identity)
zinc
(ZN1308A)
PDB Metal Type (Identity) zinc
(ZN1308A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(5)

In this stage the coordination of the metal is the same as in the resting state.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 69 AHIS 69 A No monodentate ND1
Amino Acid Residue GLU 72 AGLU 72 A No bidentate OE1,OE2
Amino Acid Residue HIS 196 AHIS 196 A No monodentate ND1
Water HOH 1016 - No monodentate O


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