spacer

CA 2 A

Metal-MACiE entry for CA 2 A

The catalityc calcium ion is involved in substrate binding (PMID9048554).


Metal in MACiE Physiological Metal Site Type
calcium calcium mononuclear

Resting State

nativeState of CA 2 A
Download the coordinates file
Representative Structure
PDB code 1dji
MACiE Metal Type
(Identity)
calcium
(CA2A)
PDB Metal Type (Identity) calcium
(CA1A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
squarePyramidal
(6)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue ASN 312 AASN 312 A Yes monodentate OD1
Note: Asn312 stabilizes the negative charge of the deprotonated 2-hydroxyl throughout the reaction course and the transition state.
Amino Acid Residue GLU 341 AGLU 341 A No monodentate OE1
Amino Acid Residue ASP 343 AASP 343 A No bidentate OD1,OD2
Water HOH 754 - No monodentate O
Water HOH 757 - No monodentate O

Step 01

Metal Functions

Substrate Binding

Electrostatic Stabiliser. Note: It stabilizes the negative charge of the deprotonated 2-hydroxyl throughout the reaction course and the transition state.

Increase Electrophilicity. Note: It increases the electrophilicity of the substrate

Activator. Note: It polarizes P-O bonds

Structural Information


MACiE Metal Type
(Identity)
calcium
(CA2A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(9999)

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 CA 2 A
Download the coordinates file
Representative Structure
PDB code 1djw
MACiE Metal Type
(Identity)
calcium
(CA2A)
PDB Metal Type (Identity) calcium
(CA2A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
cappedTrigonalPrism
(8)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue ASN 312 AASN 312 A Yes monodentate OD1
Note: Asn312 stabilizes the negative charge of the deprotonated 2-hydroxyl throughout the reaction course and the transition state.
Amino Acid Residue GLU 341 AGLU 341 A No monodentate OE1
Amino Acid Residue ASP 343 AASP 343 A No bidentate OD1,OD2
Amino Acid Residue GLU 390 AGLU 390 A Yes monodentate OE1
Note: Glu390 is tentatively identified as general base.
Reactive Species CIP 1 A- No bidentate O1P,O2P
Water HOH 218 - No monodentate O

Step 02

Metal Functions

Substrate Binding

Electrostatic Stabiliser. Note: It stabilizes the negative charge of the deprotonated 2-hydroxyl throughout the reaction course and the transition state.

Activator

Increase Electrophilicity. Note: It polarizes the P-O bond

Structural Information


reagent of CA 2 A
Download the coordinates file
Representative Structure
PDB code 1djw
MACiE Metal Type
(Identity)
calcium
(CA2A)
PDB Metal Type (Identity) calcium
(CA2A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
cappedTrigonalPrism
(8)

First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue ASN 312 AASN 312 A Yes monodentate OD1
Note: Asn312 stabilizes the negative charge of the deprotonated 2-hydroxyl throughout the reaction course and the transition state.
Amino Acid Residue GLU 341 AGLU 341 A No monodentate OE1
Amino Acid Residue ASP 343 AASP 343 A No bidentate OD1,OD2
Amino Acid Residue GLU 390 AGLU 390 A Yes monodentate OE1
Note: Glu390 is tentatively identified as general base.
Reactive Species CIP 1 A- No bidentate O1P,O2P
Water HOH 218 - No monodentate O




Right Arrow
product of CA 2 A
Download the coordinates file
Representative Structure
PDB code 1djx
MACiE Metal Type
(Identity)
calcium
(CA2A)
PDB Metal Type (Identity) calcium
(CA2A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
octahedral
(7)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue ASN 312 AASN 312 A Yes monodentate OD1
Note: Asn312 stabilizes the negative charge of the deprotonated 2-hydroxyl throughout the reaction course and the transition state.
Amino Acid Residue GLU 341 AGLU 341 A No monodentate OE2
Amino Acid Residue ASP 343 AASP 343 A No bidentate OD1,OD2
Amino Acid Residue GLU 390 AGLU 390 A Yes monodentate OE1
Note: Glu390 is tentatively identified as general base.
Reactive Species I3P 1 A- No monodentate O2
Water HOH 784 - No monodentate O


spacer
spacer