Chlorine in PDB 7d8n: Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+

Enzymatic activity of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+

All present enzymatic activity of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+:
3.5.3.15;

Protein crystallography data

The structure of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+, PDB code: 7d8n was solved by K.Funabashi, M.Sawata, M.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.72 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.874, 108.11, 93.56, 90, 118.51, 90
R / Rfree (%) 20.5 / 25.2

Other elements in 7d8n:

The structure of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ (pdb code 7d8n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+, PDB code: 7d8n:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7d8n

Go back to Chlorine Binding Sites List in 7d8n
Chlorine binding site 1 out of 2 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl908

b:74.6
occ:1.00
NZ A:LYS333 3.2 63.5 1.0
OE1 A:GLU307 3.7 83.6 1.0
CE A:LYS333 3.9 59.9 1.0
SG A:CYS651 4.7 46.9 1.0
NH2 A:ARG383 4.7 124.3 1.0
CB A:LEU306 4.8 49.4 1.0
CD A:GLU307 4.9 78.4 1.0
CB A:GLU307 4.9 56.7 1.0
CE2 A:PHE389 5.0 44.3 1.0

Chlorine binding site 2 out of 2 in 7d8n

Go back to Chlorine Binding Sites List in 7d8n
Chlorine binding site 2 out of 2 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl710

b:78.3
occ:1.00
NZ B:LYS333 3.4 64.2 1.0
OE1 B:GLU307 3.8 67.1 1.0
CE B:LYS333 4.0 63.9 1.0
SG B:CYS651 4.4 47.6 1.0
CB B:LEU306 4.6 49.5 1.0
CD1 B:LEU306 4.8 47.6 1.0
CB B:GLU307 4.9 43.1 1.0
CD B:GLU307 4.9 62.9 1.0

Reference:

K.Funabashi, M.Sawata, A.Nagai, M.Akimoto, R.Mashimo, H.Takahara, K.Kizawa, P.R.Thompson, K.Ite, K.Kitanishi, M.Unno. Structures of Human Peptidylarginine Deiminase Type III Provide Insights Into Substrate Recognition and Inhibitor Design. Arch.Biochem.Biophys. 08911 2021.
ISSN: ESSN 1096-0384
PubMed: 33971157
DOI: 10.1016/J.ABB.2021.108911
Page generated: Sat Jul 10 12:43:38 2021

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