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MG 401 A

Metal-MACiE entry for MG 401 A

The enzyme is more active in presence of Mn2+ than Mg2+ (PMID11285217). A second metal ion is bound to the enzyme in the substrate-bound form. This ion coordinates two phosphate oxygens of the substrate (PMID12630859).


Metal in MACiE Physiological Metal Site Type
magnesium magnesium/manganese mononuclear

Resting State

nativeState of MG 401 A
Download the coordinates file
Representative Structure
PDB code 1r67
MACiE Metal Type
(Identity)
magnesium
(MG401A)
PDB Metal Type (Identity) magnesium
(MG201A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(4)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue CYS 67 ACYS 67 A Yes monodentate O
Note: Cys67 is involved in proton relay.
Amino Acid Residue GLU 87 A- No monodentate OE1
Water HOH 307 - No monodentate O
Water HOH 364 - No monodentate O

Step 01

Metal Functions

Substrate Binding

Electrostatic Stabiliser

Structural Information


reagent of MG 401 A
Download the coordinates file
Representative Structure
PDB code 1ppw
MACiE Metal Type
(Identity)
magnesium
(MG401A)
PDB Metal Type (Identity) magnesium
(MG401B)
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 CYS 67 ACYS 67 A Yes monodentate O
Note: Cys67 is involved in proton relay.
Amino Acid Residue GLU 87 AGLU 87 A No monodentate OE2
Reactive Species EIP 301 A- No bidentate O3,O7
Note: It is a substrate-analogue inhibitor.
Water HOH 512 - No monodentate O
Water HOH 513 - No monodentate O




Right Arrow
product of MG 401 A
Download the coordinates file
Representative Structure
PDB code 1nfs
MACiE Metal Type
(Identity)
magnesium
(MG401A)
PDB Metal Type (Identity) magnesium
(MG401A)
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 CYS 67 ACYS 67 A Yes monodentate O
Note: Cys67 is involved in proton relay.
Amino Acid Residue GLU 87 AGLU 87 A No monodentate OE2
Reactive Species DED 301 - No bidentate O2,O7
Note: It is a transition state-analogue inhibitor.
Water HOH 508 - No monodentate O
Water HOH 509 - No monodentate O

Step 02

Metal Functions

Substrate Binding

Electrostatic Stabiliser

Structural Information


reagent of MG 401 A
Download the coordinates file
Representative Structure
PDB code 1nfs
MACiE Metal Type
(Identity)
magnesium
(MG401A)
PDB Metal Type (Identity) magnesium
(MG401A)
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 CYS 67 ACYS 67 A Yes monodentate O
Note: Cys67 is involved in proton relay.
Amino Acid Residue GLU 87 AGLU 87 A No monodentate OE2
Reactive Species DED 301 - No bidentate O2,O7
Note: It is a transition-state analogue inhibitor.
Water HOH 508 - No monodentate O
Water HOH 509 - No monodentate O




Right Arrow
MACiE Metal Type
(Identity)
magnesium
(MG401A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
octahedral
(6)

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 MG 401 A
Download the coordinates file
Representative Structure
PDB code 1r67
MACiE Metal Type
(Identity)
magnesium
(MG401A)
PDB Metal Type (Identity) magnesium
(MG201A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(4)

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 CYS 67 ACYS 67 A Yes monodentate O
Note: Cys67 is involved in proton relay.
Amino Acid Residue GLU 87 A- No monodentate OE1
Water HOH 307 - No monodentate O
Water HOH 364 - No monodentate O




Right Arrow
product of MG 401 A
Download the coordinates file
Representative Structure
PDB code 1r67
MACiE Metal Type
(Identity)
magnesium
(MG401A)
PDB Metal Type (Identity) magnesium
(MG201A)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(4)

First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue CYS 67 ACYS 67 A Yes monodentate O
Note: Cys67 is involved in electron relay.
Amino Acid Residue GLU 87 A- No monodentate OE1
Water HOH 307 - No monodentate O
Water HOH 364 - No monodentate O


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