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Magnesium in PDB 3h7k: Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate:
3.5.3.12;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate, PDB code: 3h7k was solved by E.S.Burgie, C.A.Bingman, G.N.Phillips Jr., Center For Eukaryoticstructural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.20 / 1.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.720, 69.560, 50.986, 90.00, 98.52, 90.00
R / Rfree (%) 14.7 / 18.5

Other elements in 3h7k:

The structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate (pdb code 3h7k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate, PDB code: 3h7k:

Magnesium binding site 1 out of 1 in 3h7k

Go back to Magnesium Binding Sites List in 3h7k
Magnesium binding site 1 out of 1 in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg384

b:13.9
occ:1.00
 OD1 A:ASP119 2.2 9.2 1.0
O A:TRP120 2.4 7.9 1.0
O A:HOH528 2.4 14.8 1.0
O A:HOH508 2.5 10.7 1.0
O A:HOH531 2.6 17.3 1.0
CG A:ASP119 3.5 11.1 1.0
C A:TRP120 3.5 8.6 1.0
OG A:SER143 3.5 8.1 1.0
N A:TRP120 3.6 9.7 1.0
O A:HOH451 3.7 10.3 1.0
C A:ASP119 3.9 8.7 1.0
CB A:SER143 3.9 8.8 1.0
O A:SER95 4.0 9.9 1.0
CA A:ASP119 4.1 7.5 1.0
CA A:TRP120 4.1 9.0 1.0
O A:HOH423 4.2 11.7 1.0
OD2 A:ASP119 4.4 11.3 1.0
CB A:ASP119 4.4 5.9 1.0
O A:LEU140 4.6 11.9 1.0
N A:ASN121 4.6 7.8 1.0
O A:ASP119 4.6 7.9 1.0
O A:HOH535 4.7 11.7 0.5
CB A:PHE122 4.7 8.6 1.0
O A:HOH535 4.7 12.1 0.5
CB A:TRP120 4.7 8.5 1.0
CA A:ASN121 4.9 8.7 1.0
C A:ASN121 4.9 8.8 1.0
N A:SER143 4.9 6.4 1.0
C A:SER95 4.9 9.1 1.0
O A:ASP139 4.9 8.0 1.0
O A:ASN121 5.0 6.8 1.0

Reference:

E.S.Burgie, C.A.Bingman, G.N.Phillips Jr.. Structural Insights Into the Catalytic Mechanism of Arabidopsis Thaliana Agmatine Deiminase To Be Published.
Page generated: Sun Aug 10 21:53:52 2025

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