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ZN 262 _

Metal-MACiE entry for ZN 262 _

Although Zn is the physiological metal, studies have shown that cobalt (Co(II)) also yields a product with native-like catalytic properties (PMID9336012).


Metal in MACiE Physiological Metal Site Type
zinc zinc mononuclear

Resting State

nativeState of ZN 262 _
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Representative Structure
PDB code 2cba
MACiE Metal Type
(Identity)
zinc
(ZN262_)
PDB Metal Type (Identity) zinc
(ZN262_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(4)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Water HOH 263 - No monodentate O
Amino Acid Residue HIS 94 AHIS 94 A No monodentate NE2
Amino Acid Residue HIS 119 AHIS 119 A No monodentate ND1
Amino Acid Residue HIS 96 AHIS 96 A No monodentate NE2

Step 01

Metal Functions

Increase Nucleophilicity. Note: Zinc increases the nucleophilicity of the bound water (hydroxide).

Activator. Note: This activates the water to attack the carbon dioxide molecule in a very fast reactio step.

Structural Information


MACiE Metal Type
(Identity)
zinc
(ZN262_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(4)

Geometry assumed to be tetrahedral due to the fact that the zinc ion does not directly bind the carbon dioxide.

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





Right Arrow
product of ZN 262 _
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Representative Structure
PDB code 1cam
MACiE Metal Type
(Identity)
zinc
(ZN262_)
PDB Metal Type (Identity) zinc
(ZN262_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
trigonalBipyramidal
(5)

It is not clear whether the product binds in a bidentate manner, or if the extra zinc ligand is actually water and the product binds in a monodentate manner.

The catalytic His64 appears to be very distant from the catalytic centre in this step.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 94 AHIS 94 A No monodentate NE2
Amino Acid Residue HIS 96 AHIS 96 A No monodentate NE2
Amino Acid Residue HIS 119 AHIS 119 A No monodentate ND1
Reactive Species BCT 500 - No monodentate O3
Note: This is the product of the reaction.
Water HOH 263 - No monodentate O

Step 02

Metal Functions

Increase Acidity. Note: Zinc increases the acidity of water, promoting the loss of a proton and, thus activtaing the enzyme for the next round of catalysis.

Activator

Structural Information


reagent of ZN 262 _
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Representative Structure
PDB code 1ca2
MACiE Metal Type
(Identity)
zinc
(ZN262_)
PDB Metal Type (Identity) zinc
(ZN262_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(4)

The bicarbonate formed as the product in the previous step dissociates from the active site, to be replaced by water, before this step can occur.

PDB structure elucidated at pH 8.5 in which the catalytic His64 is in the in position and able to accept a proton from the water.


First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Water HOH 263 - No monodentate O
Note: This water is activated by the zinc and is a substrate in this step.
Amino Acid Residue HIS 119 AHIS 119 A No monodentate ND1
Amino Acid Residue HIS 96 AHIS 96 A No monodentate NE2
Amino Acid Residue HIS 94 AHIS 94 A No monodentate NE2




Right Arrow
product of ZN 262 _
Download the coordinates file
Representative Structure
PDB code 1ca3
MACiE Metal Type
(Identity)
zinc
(ZN262_)
PDB Metal Type (Identity) zinc
(ZN1_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(4)

PDB structure was elucidated at pH 5.7, in which the catalytic His64 is protonated and in the out configuration. In this configuration it can deliver its proton back to the bulk solvent, possibly via a proton relay chain.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 94 AHIS 94 A No monodentate NE2
Amino Acid Residue HIS 96 AHIS 96 A No monodentate NE2
Amino Acid Residue HIS 119 AHIS 119 A No monodentate ND1
Water HOH 288 - No monodentate O

Step 03

Metal Functions

This metal is not active in this step.

Structural Information


reagent of ZN 262 _
Download the coordinates file
Representative Structure
PDB code 1ca3
MACiE Metal Type
(Identity)
zinc
(ZN262_)
PDB Metal Type (Identity) zinc
(ZN1_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(4)

The zinc is not active in this step.

PDB structure was elucidated at pH 5.7, in which the catalytic His64 is protonated and in the out configuration. In this configuration it can deliver its proton back to the bulk solvent, possibly via a proton relay chain.


First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 94 AHIS 94 A No monodentate NE2
Amino Acid Residue HIS 96 AHIS 96 A No monodentate NE2
Amino Acid Residue HIS 119 AHIS 119 A No monodentate ND1
Water HOH 288 - No monodentate O




Right Arrow
product of ZN 262 _
Download the coordinates file
Representative Structure
PDB code 1ca2
MACiE Metal Type
(Identity)
zinc
(ZN262_)
PDB Metal Type (Identity) zinc
(ZN262_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
tetrahedral
(4)

The catalytic His64 has now lost its proton and thus returns to the in confguration represented by the structure elucidated at pH 8.5


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue HIS 94 AHIS 94 A No monodentate NE2
Amino Acid Residue HIS 96 AHIS 96 A No monodentate NE2
Amino Acid Residue HIS 119 AHIS 119 A No monodentate ND1
Water HOH 263 - No monodentate O


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