Atomistry » Chlorine » PDB 7cwa-7dan » 7d5r
Atomistry »
  Chlorine »
    PDB 7cwa-7dan »
      7d5r »

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: Sat Jul 12 23:58:01 2025

Last articles

Mg in 1KW1
Mg in 1KP8
Mg in 1KVK
Mg in 1KV8
Mg in 1KUV
Mg in 1KSZ
Mg in 1KSJ
Mg in 1KSH
Mg in 1KSG
Mg in 1KQP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy