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Iodine in PDB 4na0: Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose

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

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

Protein crystallography data

The structure of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose, PDB code: 4na0 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) 50.00 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 188.300, 55.665, 166.149, 90.00, 90.00, 90.00
R / Rfree (%) 29.8 / 34.2

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose (pdb code 4na0). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose, PDB code: 4na0:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 4na0

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Iodine binding site 1 out of 6 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose


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 Adpribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:78.5
occ:1.00
 OG A:SER662 3.6 81.9 1.0
NZ A:LYS668 3.7 54.2 1.0
CE A:LYS668 3.7 58.2 1.0
CD A:LYS665 3.8 73.5 1.0
CB A:ARG664 3.8 78.7 1.0
CA A:ALA743 4.0 62.1 1.0
O A:ALA743 4.1 62.7 1.0
O A:GLY742 4.1 59.7 1.0
C A:ALA743 4.2 60.4 1.0
NZ A:LYS665 4.3 61.4 1.0
N A:LYS665 4.3 81.7 1.0
CD A:LYS668 4.4 61.0 1.0
CE A:LYS665 4.4 68.6 1.0
CB A:SER662 4.4 86.2 1.0
C A:ARG664 4.4 80.9 1.0
CA A:LYS665 4.6 79.8 1.0
CA A:ARG664 4.7 83.0 1.0
CB A:ALA743 4.7 63.5 1.0
CG A:ARG664 4.8 78.5 1.0
CG A:LYS665 4.9 76.6 1.0
CD2 A:LEU745 4.9 55.5 1.0
O A:ARG664 4.9 78.7 1.0
CB A:LEU745 4.9 57.9 1.0
C A:GLY742 5.0 59.4 1.0
N A:GLY744 5.0 56.4 1.0
N A:ALA743 5.0 59.1 1.0

Iodine binding site 2 out of 6 in 4na0

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Iodine binding site 2 out of 6 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose


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 Adpribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:0.7
occ:1.00
 C A:TYR514 3.1 71.3 1.0
O A:TYR514 3.3 70.0 1.0
O A:ALA525 3.8 75.0 1.0
CA A:TYR514 3.9 67.5 1.0
N A:TYR514 4.1 62.0 1.0
C A:LEU513 4.5 58.3 1.0
CB A:LEU513 4.7 59.3 1.0
O A:LEU513 4.8 59.4 1.0
C A:ALA525 5.0 73.7 1.0

Iodine binding site 3 out of 6 in 4na0

Go back to Iodine Binding Sites List in 4na0
Iodine binding site 3 out of 6 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose


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 Adpribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1001

b:75.3
occ:1.00
 CD B:LYS668 3.4 58.5 1.0
NZ B:LYS668 3.5 47.2 1.0
O B:GLY742 3.8 63.7 1.0
OG B:SER662 3.8 0.5 1.0
CE B:LYS665 3.9 85.0 1.0
CA B:ALA743 4.0 68.6 1.0
CB B:ARG664 4.0 89.8 1.0
CE B:LYS668 4.1 51.9 1.0
CG B:LYS665 4.2 91.3 1.0
CD B:LYS665 4.3 86.6 1.0
N B:LYS665 4.4 91.5 1.0
CB B:SER662 4.5 0.4 1.0
C B:ALA743 4.5 65.5 1.0
C B:ARG664 4.5 90.8 1.0
CA B:LYS665 4.7 89.1 1.0
C B:GLY742 4.7 63.0 1.0
CG B:LYS668 4.7 61.5 1.0
CB B:ALA743 4.7 71.5 1.0
NZ B:LYS665 4.7 89.2 1.0
O B:ALA743 4.8 68.5 1.0
O B:GLY744 4.8 59.5 1.0
O B:ARG664 4.9 87.6 1.0
N B:ALA743 4.9 64.4 1.0
CA B:ARG664 4.9 94.7 1.0
CD2 B:LEU745 4.9 70.2 1.0

Iodine binding site 4 out of 6 in 4na0

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Iodine binding site 4 out of 6 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose


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 Adpribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1002

b:93.4
occ:1.00
 C B:TYR514 3.5 62.8 1.0
O B:TYR514 3.7 62.9 1.0
CB B:ALA525 3.9 75.5 1.0
CA B:TYR514 4.0 58.5 1.0
CA B:ALA525 4.0 76.2 1.0
N B:TYR514 4.1 55.4 1.0
CB B:LEU513 4.3 53.9 1.0
O B:THR524 4.3 82.0 1.0
C B:LEU513 4.4 53.1 1.0
O B:LEU513 4.6 55.4 1.0
N B:ALA525 4.9 81.0 1.0
C B:THR524 4.9 83.7 1.0

Iodine binding site 5 out of 6 in 4na0

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Iodine binding site 5 out of 6 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose


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 Adpribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1001

b:98.5
occ:1.00
 NZ C:LYS668 3.5 68.8 1.0
CE C:LYS665 3.6 95.2 1.0
OG C:SER662 3.7 0.7 1.0
CE C:LYS668 3.7 73.4 1.0
CA C:ALA743 4.0 83.6 1.0
O C:GLY742 4.1 83.9 1.0
N C:GLY744 4.1 77.6 1.0
CD C:LYS668 4.1 80.2 1.0
CD C:LYS665 4.3 0.3 1.0
CG C:LYS665 4.3 0.3 1.0
CB C:ARG664 4.3 0.9 1.0
CD1 C:LEU745 4.3 80.4 1.0
N C:LYS665 4.4 0.0 1.0
C C:ARG664 4.5 0.9 1.0
C C:ALA743 4.6 77.3 1.0
CB C:SER662 4.6 0.1 1.0
CB C:ALA743 4.7 85.6 1.0
NZ C:LYS665 4.8 87.9 1.0
O C:ARG664 4.8 0.7 1.0
CA C:LYS665 4.8 0.6 1.0
C C:GLY742 4.8 82.3 1.0
N C:ALA743 4.8 82.0 1.0
CG C:LEU745 4.9 82.8 1.0
CG C:LYS668 4.9 85.7 1.0
CA C:ARG664 4.9 0.5 1.0

Iodine binding site 6 out of 6 in 4na0

Go back to Iodine Binding Sites List in 4na0
Iodine binding site 6 out of 6 in the Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Mouse Poly(Adp-Ribose) Glycohydrolase (Parg) Catalytic Domain with Adpribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1002

b:0.8
occ:1.00
 O C:TYR514 3.4 0.2 1.0
C C:TYR514 3.4 0.9 1.0
CB C:ALA525 3.9 0.9 1.0
CA C:TYR514 4.1 0.5 1.0
CA C:ALA525 4.2 0.7 1.0
O C:ALA525 4.3 0.8 1.0
N C:TYR514 4.3 0.6 1.0
CB C:LEU513 4.5 95.2 1.0
C C:ALA525 4.7 0.7 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 19:35:13 2020

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