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Sodium 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:

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase Complexed with A Covalently Bound Reaction Intermediate, PDB code: 3h7k:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3h7k

Go back to Sodium Binding Sites List in 3h7k
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na385

b:6.1
occ:1.00
O A:TRP125 2.6 9.5 1.0
O A:ASP220 2.8 11.1 1.0
O A:ASP130 2.8 19.1 1.0
O A:HOH513 2.9 25.9 1.0
OD1 A:ASN222 2.9 11.7 1.0
O A:HOH558 2.9 19.4 1.0
O A:GLU219 3.3 19.4 1.0
C A:ASP220 3.5 8.4 1.0
CG A:ASN222 3.7 13.2 1.0
ND2 A:ASN222 3.8 13.9 1.0
C A:TRP125 3.9 9.1 1.0
C A:ASP130 4.0 17.9 1.0
ND2 A:ASN185 4.1 11.9 1.0
CB A:TRP125 4.3 8.1 1.0
CA A:ASP220 4.3 10.8 1.0
N A:THR221 4.4 9.3 1.0
CG A:ASP130 4.4 28.1 1.0
OD1 A:ASP130 4.4 28.9 1.0
C A:GLU219 4.5 16.6 1.0
N A:ASN222 4.5 9.3 1.0
CA A:GLY131 4.6 14.5 1.0
OD2 A:ASP130 4.6 30.4 1.0
C A:THR221 4.6 10.0 1.0
CA A:THR221 4.6 8.2 1.0
CA A:TRP125 4.7 7.2 1.0
CA A:GLY126 4.7 11.2 1.0
N A:GLY126 4.8 11.1 1.0
SG A:CYS132 4.8 14.2 1.0
N A:GLY131 4.8 14.2 1.0
NH1 A:ARG186 4.8 8.9 1.0
N A:ASP220 4.9 10.5 1.0
CB A:ASP130 4.9 23.6 1.0
C A:GLY131 4.9 13.9 1.0
CB A:ASN222 4.9 9.9 1.0

Sodium binding site 2 out of 3 in 3h7k

Go back to Sodium Binding Sites List in 3h7k
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na binding site number 2 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:Na386

b:12.0
occ:1.00
OH5 A:1PE391 2.5 47.9 1.0
OH3 A:1PE391 2.8 26.4 1.0
OH4 A:1PE391 2.8 31.9 1.0
OH6 A:1PE391 2.8 37.9 1.0
C25 A:1PE391 3.2 42.2 1.0
C15 A:1PE391 3.4 38.9 1.0
C12 A:1PE391 3.4 29.1 1.0
C14 A:1PE391 3.5 37.3 1.0
C22 A:1PE391 3.6 26.1 1.0
C13 A:1PE391 3.7 31.2 1.0
C24 A:1PE391 3.7 35.6 1.0
C23 A:1PE391 3.7 23.5 1.0
C26 A:1PE391 4.0 38.7 1.0
CA A:GLY304 4.6 10.8 1.0

Sodium binding site 3 out of 3 in 3h7k

Go back to Sodium Binding Sites List in 3h7k
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na binding site number 3 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:Na387

b:24.5
occ:1.00
O A:HOH452 2.2 13.6 1.0
O A:ARG306 2.5 10.3 1.0
O A:HOH593 2.5 22.3 1.0
O A:GLY217 2.7 16.8 1.0
OG1 A:THR305 3.0 6.0 0.5
C A:GLY217 3.6 13.6 1.0
C A:ARG306 3.7 9.3 1.0
CA A:GLY217 3.7 14.9 1.0
OE1 A:GLU219 3.9 29.6 1.0
O A:HOH496 4.1 19.7 1.0
N A:ARG306 4.2 8.2 1.0
O A:HOH511 4.3 12.8 1.0
CB A:THR305 4.3 10.6 0.5
OG1 A:THR305 4.4 17.7 0.5
CB A:THR305 4.4 11.2 0.5
CA A:ARG306 4.4 9.2 1.0
C A:THR305 4.6 9.8 0.5
O A:HOH495 4.6 16.9 1.0
CG A:GLU219 4.6 27.3 1.0
CD A:GLU219 4.6 39.0 1.0
N A:LEU307 4.7 8.0 1.0
CB A:ARG306 4.7 7.6 1.0
C A:THR305 4.7 9.3 0.5
N A:ALA308 4.7 7.5 1.0
CA A:LEU307 4.8 10.6 1.0
N A:ASP218 4.8 15.9 1.0
C A:LEU307 5.0 9.2 1.0
CA A:THR305 5.0 9.0 0.5
CA A:THR305 5.0 9.8 0.5

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: Tue Dec 15 06:13:08 2020

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