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ZN 401 A

Metal-MACiE entry for ZN 401 A

The enzyme binds zinc in a dinuclear site. Zinc ions are directly involved in catalysis (substrate binding and activation) (PMID12144777).


Metal in MACiE Physiological Metal Site Type
zinc zinc dinuclear

Resting State

nativeState of ZN 401 A
Download the coordinates file
Representative Structure
PDB code 1itq
MACiE Metal Type
(Identity)
zinc
(ZN401A)
PDB Metal Type (Identity) zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalBipyramidal
(6)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 20 AHIS 20 A No monodentate NE2
Amino Acid Residue ASP 22 AASP 22 A No monodentate OD1
Amino Acid Residue GLU 125 AGLU 125 A No monodentate OE1
Water HOH 421 - No monodentate O
Water HOH 422 - No monodentate O

Step 01

Metal Functions

Activator. Note: It activates a water molecule.

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

Substrate Binding

Structural Information


reagent of ZN 401 A
Download the coordinates file
Representative Structure
PDB code 1itu
MACiE Metal Type
(Identity)
zinc
(ZN401A)
PDB Metal Type (Identity) zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalPyramidal
(5)

First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 20 AHIS 20 A No monodentate NE2
Amino Acid Residue ASP 22 AASP 22 A No bidentate OD1,OD2
Amino Acid Residue GLU 125 AGLU 125 A No monodentate OE1
Water HOH 421 - No monodentate O




Right Arrow
product of ZN 401 A
Download the coordinates file
Representative Structure
PDB code 1itu
MACiE Metal Type
(Identity)
zinc
(ZN401A)
PDB Metal Type (Identity) zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalPyramidal
(5)

In this stage the coordination of the metal is the same as in the reagent status.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 20 AHIS 20 A No monodentate NE2
Amino Acid Residue ASP 22 AASP 22 A No bidentate OD1,OD2
Amino Acid Residue GLU 125 AGLU 125 A No monodentate OE1
Water HOH 421 - No monodentate O

Step 02

Metal Functions

Substrate Binding

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

Activator

Structural Information


MACiE Metal Type
(Identity)
zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalPyramidal
(4)

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





Right Arrow
MACiE Metal Type
(Identity)
zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalPyramidal
(4)

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


MACiE Metal Type
(Identity)
zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalPyramidal
(4)

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





Right Arrow
MACiE Metal Type
(Identity)
zinc
(ZN401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalPyramidal
(4)

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



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