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MG 161 x

Metal-MACiE entry for MG 161 x

Two Mg2+ ions are required for the catalysis. Six catalytic roles were proposed for these metal ions: (i) they induce the conformational changes to bring catalytic residues into the active site, (ii) they orient substrates (iii) they activate ATP for the nucleophilic attack (iv) they lower the pKa of the substrate (v) they stabilize the negative charge developed in the transition state (vi) they facilitate the departure of AMP (PMID11080626).


Metal in MACiE Physiological Metal Site Type
magnesium magnesium mononuclear

Resting State

nativeState of MG 161 x
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Representative Structure
PDB code 1tmj
MACiE Metal Type
(Identity)
magnesium
(MG161x)
PDB Metal Type (Identity) magnesium
(MG161_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
squarePyramidal
(5)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue ASP 95 AASP 95 A No monodentate OD1
Amino Acid Residue ASP 97 AASP 97 A No monodentate OD1
Water HOH 215 - No monodentate O
Water HOH 257 - No monodentate O
Water HOH 258 - No monodentate O

Step 01

Metal Functions

Substrate Binding

Activator. Note: It activates ATP.

Increase Electrophilicity. Note: It increases nucleophilicity of ATP.

Electrostatic Stabiliser. Note: It stabilizes the negative charge of the transition state.

Structural Information


reagent of MG 161 x
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Representative Structure
PDB code 1q0n
MACiE Metal Type
(Identity)
magnesium
(MG161x)
PDB Metal Type (Identity) magnesium
(MG161_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
octahedral
(6)

First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue ASP 95 AASP 95 A No monodentate OD1
Amino Acid Residue ASP 97 AASP 97 A No monodentate OD1
Reactive Species APC 171 - No bidentate O1B,O1A
Water HOH 212 - No monodentate O
Water HOH 226 - No monodentate O




Right Arrow
product of MG 161 x
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Representative Structure
PDB code 1rao
MACiE Metal Type
(Identity)
magnesium
(MG161x)
PDB Metal Type (Identity) none
(none0none)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(9999)

This structure does not contain any metal: all the coordinating information are derived from the reaction model in MACiE.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms


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