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Chlorine 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
Sodium (Na) 3 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 3h7k

Go back to Chlorine Binding Sites List in 3h7k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl388

b:24.7
occ:1.00
CG2 A:THR305 2.7 2.0 0.5
O A:HOH495 3.0 16.9 1.0
OG1 A:THR305 3.4 6.0 0.5
N A:LEU302 3.4 9.6 1.0
O A:HOH582 3.5 19.3 1.0
CB A:THR305 3.5 11.2 0.5
CB A:THR305 3.6 10.6 0.5
O A:PRO300 3.7 13.2 1.0
CG2 A:THR305 3.8 15.2 0.5
CB A:LEU302 4.0 9.5 1.0
CA A:ARG301 4.0 9.0 1.0
CG A:LEU302 4.0 11.0 1.0
OG1 A:THR305 4.0 17.7 0.5
C A:ARG301 4.2 10.1 1.0
CA A:LEU302 4.3 10.5 1.0
CD1 A:LEU302 4.4 14.0 1.0
O A:LEU302 4.4 10.6 1.0
C A:PRO300 4.5 12.3 1.0
N A:ARG301 4.7 10.2 1.0
C A:LEU302 4.8 9.7 1.0
CA A:THR305 4.9 9.8 0.5
O A:HOH490 4.9 25.4 1.0
CA A:THR305 5.0 9.0 0.5
O A:HOH540 5.0 21.6 1.0
CD A:ARG301 5.0 10.7 1.0

Chlorine binding site 2 out of 3 in 3h7k

Go back to Chlorine Binding Sites List in 3h7k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl389

b:48.1
occ:1.00
NE A:ARG269 3.4 18.9 1.0
NH1 A:ARG269 3.5 16.6 1.0
O A:HOH462 3.8 21.9 1.0
CZ A:ARG269 3.9 14.1 1.0
CD A:ARG269 4.5 19.1 1.0
O A:PRO234 5.0 12.2 1.0

Chlorine binding site 3 out of 3 in 3h7k

Go back to Chlorine Binding Sites List in 3h7k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl390

b:16.5
occ:1.00
CE A:LYS52 3.3 19.8 1.0
NZ A:LYS52 3.5 16.3 1.0
NZ A:LYS56 3.9 41.3 1.0
O A:HOH543 4.7 29.0 1.0
CD A:LYS52 4.8 16.3 1.0
CB A:PRO77 4.8 18.0 1.0
CE A:LYS56 4.9 35.4 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: Fri Jul 11 05:52:33 2025

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