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Iodine in PDB 4na4: Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd

Enzymatic activity of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd

All present enzymatic activity of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd:
3.2.1.143;

Protein crystallography data

The structure of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd, PDB code: 4na4 was solved by Z.Wang, Z.Cheng, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 188.949, 55.569, 165.993, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.2

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd (pdb code 4na4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd, PDB code: 4na4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 4na4

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Iodine binding site 1 out of 5 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:88.2
occ:1.00
 C A:TYR514 3.7 70.8 1.0
N A:PRO515 3.7 74.6 1.0
O A:TYR514 3.8 69.6 1.0
CA A:PRO515 4.0 79.1 1.0
CB A:LEU513 4.2 60.0 1.0
CA A:TYR514 4.2 65.9 1.0
CA A:ALA525 4.2 74.4 1.0
CB A:ALA525 4.2 72.9 1.0
N A:TYR514 4.3 63.4 1.0
CG A:PRO515 4.3 76.8 1.0
CD A:PRO515 4.4 74.0 1.0
CB A:PRO515 4.4 80.7 1.0
C A:LEU513 4.5 60.6 1.0
O A:THR524 4.6 78.8 1.0
O A:LEU513 4.9 60.3 1.0
CD1 A:LEU513 5.0 63.6 1.0

Iodine binding site 2 out of 5 in 4na4

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Iodine binding site 2 out of 5 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:66.5
occ:1.00
 NZ A:LYS668 3.7 48.1 1.0
OG A:SER662 3.7 73.2 1.0
O A:HOH1145 3.8 97.3 1.0
CE A:LYS665 3.9 77.3 1.0
O A:GLY742 3.9 61.4 1.0
CE A:LYS668 3.9 49.5 1.0
CD A:LYS668 4.0 52.3 1.0
CD A:LYS665 4.1 76.6 1.0
CB A:ARG664 4.1 75.5 1.0
NZ A:LYS665 4.2 72.4 1.0
N A:LYS665 4.3 76.5 1.0
CB A:SER662 4.3 77.0 1.0
C A:ARG664 4.3 75.6 1.0
CA A:ALA743 4.3 62.7 1.0
CG A:LYS665 4.4 78.3 1.0
O A:ARG664 4.6 72.5 1.0
N A:GLY744 4.6 58.7 1.0
CA A:LYS665 4.6 75.0 1.0
CA A:ARG664 4.8 78.1 1.0
CG A:LYS668 4.8 54.3 1.0
CD2 A:LEU745 4.9 60.0 1.0
C A:GLY742 4.9 61.6 1.0
CB A:ALA743 5.0 63.8 1.0

Iodine binding site 3 out of 5 in 4na4

Go back to Iodine Binding Sites List in 4na4
Iodine binding site 3 out of 5 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1002

b:0.9
occ:1.00
 CB B:ARG664 3.6 0.2 1.0
OG B:SER662 3.8 0.6 1.0
C B:ARG664 3.8 0.4 1.0
CE B:LYS668 3.8 0.7 1.0
O B:ARG664 4.0 1.0 1.0
CE B:LYS665 4.0 0.4 1.0
N B:LYS665 4.0 0.8 1.0
NZ B:LYS668 4.0 0.1 1.0
CD B:LYS668 4.1 0.0 1.0
CA B:ARG664 4.3 0.8 1.0
CG B:LYS665 4.3 0.2 1.0
CD2 B:LEU745 4.3 0.8 1.0
CA B:LYS665 4.4 0.6 1.0
CD B:LYS665 4.4 0.7 1.0
CG B:LYS668 4.6 0.2 1.0
O B:GLY742 4.6 0.2 1.0
CB B:SER662 4.7 0.5 1.0
NZ B:LYS665 4.8 0.9 1.0
CG B:ARG664 4.8 0.8 1.0
CB B:LEU745 4.8 0.6 1.0
N B:ARG664 4.9 0.6 1.0
CB B:LYS665 5.0 1.0 1.0

Iodine binding site 4 out of 5 in 4na4

Go back to Iodine Binding Sites List in 4na4
Iodine binding site 4 out of 5 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1002

b:68.1
occ:1.00
 NZ C:LYS668 3.6 45.2 1.0
CE C:LYS668 3.7 46.1 1.0
OG C:SER662 3.7 66.8 1.0
CB C:ARG664 3.9 64.4 1.0
CE C:LYS665 4.0 60.5 1.0
N C:GLY744 4.1 51.1 1.0
O C:GLY742 4.1 49.3 1.0
CG C:LYS665 4.2 66.3 1.0
CA C:ALA743 4.4 53.4 1.0
CB C:SER662 4.4 71.2 1.0
CD C:LYS668 4.5 47.0 1.0
N C:LYS665 4.5 64.1 1.0
C C:ARG664 4.7 64.2 1.0
CB C:LEU745 4.7 47.3 1.0
CD C:LYS665 4.7 62.5 1.0
CD2 C:LEU745 4.7 51.6 1.0
O C:GLY744 4.8 41.8 1.0
C C:ALA743 4.8 52.0 1.0
CG C:ARG664 4.8 64.0 1.0
C C:GLY744 4.8 44.1 1.0
CA C:ARG664 4.9 66.9 1.0
CA C:LYS665 4.9 63.8 1.0

Iodine binding site 5 out of 5 in 4na4

Go back to Iodine Binding Sites List in 4na4
Iodine binding site 5 out of 5 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adp-Hpd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1003

b:0.1
occ:1.00
 C C:TYR514 3.7 59.1 1.0
N C:PRO515 3.8 63.8 1.0
O C:TYR514 3.8 57.3 1.0
CA C:TYR514 4.1 57.2 1.0
N C:TYR514 4.1 55.2 1.0
CA C:PRO515 4.2 68.1 1.0
C C:LEU513 4.3 51.8 1.0
CB C:LEU513 4.3 48.6 1.0
CD C:PRO515 4.3 64.3 1.0
CB C:ALA525 4.4 61.1 1.0
O C:LEU513 4.4 52.8 1.0
CA C:ALA525 4.5 61.7 1.0
O C:THR524 4.7 68.0 1.0

Reference:

Z.Wang, J.P.Gagne, G.G.Poirier, W.Xu. Crystallographic and Biochemical Analysis of the Mouse Poly(Adp-Ribose) Glycohydrolase. Plos One V. 9 86010 2014.
ISSN: ESSN 1932-6203
PubMed: 24465839
DOI: 10.1371/JOURNAL.PONE.0086010
Page generated: Sun Dec 13 19:35:15 2020

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