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ZN 500 x

Metal-MACiE entry for ZN 500 x

Mg2+ is required for enzyme activity (PMID14725765).


Metal in MACiE Physiological Metal Site Type
magnesium magnesium mononuclear

Resting State

nativeState of ZN 500 x
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Representative Structure
PDB code 2fuc
MACiE Metal Type
(Identity)
magnesium
(ZN500x)
PDB Metal Type (Identity) magnesium
(MG500_)
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 19 A- No monodentate OD2
Amino Acid Residue ASP 21 A- No monodentate O
Amino Acid Residue ASN 218 A- No monodentate OD1
Water HOH 1114 - No monodentate O
Water HOH 1118 - No monodentate O
Water HOH 1127 - No monodentate O

Step 01

Metal Functions

Increase Electrophilicity. Note: It increases electrophilicity of P polarizing the P-O bond of the phosphate

Activator

Electrostatic Stabiliser

Structural Information


reagent of ZN 500 x
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Representative Structure
PDB code 1pcm
MACiE Metal Type
(Identity)
magnesium
(ZN500x)
PDB Metal Type (Identity) zinc
(ZN500_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(4)

In this structure Mg2+ is substituted by Zn2+ which inactivates the enzyme. The Mg2+ coordination sphere could be quite different from that of Zn2+.


First Coordination Sphere


Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue SEP 108 X- Yes monodentate O3P
Note: It is the phosphoserine.
Amino Acid Residue ASP 242 XASP 242 X No monodentate OD2
Amino Acid Residue ASP 244 XASP 244 X No monodentate OD2
Amino Acid Residue ASP 246 XASP 246 X No monodentate OD1




Right Arrow
MACiE Metal Type
(Identity)
magnesium
(ZN500x)
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.


Step 02

Metal Functions

Electrostatic Stabiliser

Structural Information


MACiE Metal Type
(Identity)
magnesium
(ZN500x)
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 ZN 500 x
Download the coordinates file
Representative Structure
PDB code 1pcj
MACiE Metal Type
(Identity)
magnesium
(ZN500x)
PDB Metal Type (Identity) zinc
(ZN500_)
Oxidation State 2
Coordination Geometry
(Number of ligands)
unknownGeometry
(5)

In this structure Mg2+ is substituted by Zn2+ which inactivates the enzyme. The Mg2+ coordination sphere could be quite different from that of Zn2+.


First Coordination Sphere

Ligand Type Ligand (PDB) Ligand (MACiE) Catalytic Binding Mode Contacting Atoms
Amino Acid Residue SEP 108 X- Yes bidentate OG,O3P
Note: It is a phosphoserine.
Amino Acid Residue ASP 242 XASP 242 X No monodentate OD2
Amino Acid Residue ASP 244 XASP 244 X No monodentate OD2
Amino Acid Residue ASP 246 XASP 246 X No monodentate OD1


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