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Chlorine in PDB 7d5r: Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)

Enzymatic activity of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)

All present enzymatic activity of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3):
3.5.3.15;

Protein crystallography data

The structure of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3), PDB code: 7d5r was solved by R.Mashimo, M.Akimoto, M.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.07 / 3.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 114.536, 114.536, 326.766, 90, 90, 120
R / Rfree (%) 23.3 / 28.1

Other elements in 7d5r:

The structure of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) (pdb code 7d5r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3), PDB code: 7d5r:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7d5r

Go back to Chlorine Binding Sites List in 7d5r
Chlorine binding site 1 out of 4 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:88.5
occ:1.00
 NZ A:LYS498 3.2 91.0 1.0
NH1 B:ARG8 3.5 77.8 1.0
NH2 B:ARG8 3.7 73.5 1.0
OG A:SER492 3.9 77.7 1.0
CZ B:ARG8 4.0 71.0 1.0
CE A:LYS498 4.2 93.8 1.0
C A:GLY494 4.3 64.8 1.0
OD2 A:ASP568 4.3 63.8 1.0
N A:ALA495 4.3 60.4 1.0
CA A:GLY494 4.5 55.3 1.0
O A:GLY494 4.6 64.2 1.0
CD A:LYS498 4.7 83.1 1.0
CG A:ASP568 4.8 56.6 1.0
OE1 A:GLN545 4.9 59.6 1.0
CA A:ALA495 4.9 61.9 1.0
O B:ILE29 4.9 72.2 1.0

Chlorine binding site 2 out of 4 in 7d5r

Go back to Chlorine Binding Sites List in 7d5r
Chlorine binding site 2 out of 4 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl901

b:83.3
occ:1.00
 CB B:SER32 4.2 120.2 1.0
CA B:PRO34 4.3 64.6 1.0
NZ A:LYS505 4.4 92.8 1.0
O B:SER32 4.5 137.1 1.0
CE A:LYS505 4.5 102.3 1.0
OG B:SER32 4.6 115.6 1.0
C B:SER32 4.6 123.2 1.0
N B:PRO34 4.6 69.1 1.0
CA B:SER32 4.6 121.7 1.0
CB B:PRO34 4.8 41.6 1.0
CG B:PRO34 4.8 41.1 1.0
CD1 B:LEU11 4.8 58.5 1.0

Chlorine binding site 3 out of 4 in 7d5r

Go back to Chlorine Binding Sites List in 7d5r
Chlorine binding site 3 out of 4 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl908

b:74.5
occ:1.00
 NZ B:LYS505 3.4 109.1 1.0
CE B:LYS505 3.7 106.0 1.0
CA A:PRO34 4.0 49.8 1.0
O A:VAL33 4.1 70.4 1.0
N A:PRO34 4.4 43.8 1.0
C A:VAL33 4.5 56.2 1.0
O A:SER32 4.5 49.7 1.0
N A:GLU35 4.7 78.0 1.0
C A:PRO34 4.8 57.5 1.0
OG A:SER32 4.9 79.9 1.0
CD1 A:LEU11 5.0 64.2 1.0
CB A:PRO34 5.0 51.6 1.0

Chlorine binding site 4 out of 4 in 7d5r

Go back to Chlorine Binding Sites List in 7d5r
Chlorine binding site 4 out of 4 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl909

b:101.1
occ:1.00
 NZ B:LYS498 2.5 73.2 1.0
CG1 A:VAL33 3.5 49.5 1.0
CZ A:PHE70 3.6 47.3 1.0
CE B:LYS498 3.8 73.4 1.0
N A:VAL33 3.8 56.5 1.0
CG2 A:VAL33 3.9 53.9 1.0
CB A:VAL33 4.2 57.6 1.0
CA A:SER32 4.2 54.0 1.0
CE2 A:PHE70 4.3 55.4 1.0
C A:SER32 4.5 54.7 1.0
CD B:LYS498 4.6 67.3 1.0
CE1 A:PHE70 4.6 44.3 1.0
CA A:VAL33 4.6 60.0 1.0
CD1 A:ILE29 4.7 64.0 1.0
O A:GLY31 4.9 53.8 1.0
CB A:SER32 5.0 52.2 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: Mon Jul 29 19:59:59 2024

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