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Chlorine in PDB 8rpt: Crystal Structure of Human DNPH1 Mutant- D80A

Protein crystallography data

The structure of Crystal Structure of Human DNPH1 Mutant- D80A, PDB code: 8rpt was solved by S.Devi, R.G.Da Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.60 / 1.95
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.481, 65.584, 69.209, 90, 90, 90
R / Rfree (%) 17.8 / 22

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human DNPH1 Mutant- D80A (pdb code 8rpt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Human DNPH1 Mutant- D80A, PDB code: 8rpt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8rpt

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Chlorine binding site 1 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:28.0
occ:1.00
 O A:HOH347 3.0 26.6 1.0
N B:LEU99 3.2 18.7 1.0
O B:HOH360 3.3 27.0 1.0
CB A:PRO97 3.7 27.0 1.0
CA B:SER98 3.8 24.5 1.0
CB B:LEU99 3.9 21.4 1.0
CG A:PRO97 4.0 29.0 1.0
CA A:PRO97 4.0 24.8 1.0
C B:SER98 4.0 23.2 1.0
CG B:LEU99 4.1 22.1 1.0
CA B:LEU99 4.1 20.9 1.0
CD1 B:LEU99 4.1 20.3 1.0
CB A:SER128 4.3 26.1 1.0
OG B:SER98 4.3 20.8 1.0
O B:HOH352 4.4 30.3 1.0
N B:GLY100 4.6 16.7 1.0
CB B:SER98 4.6 25.9 1.0
O B:PRO97 4.7 29.0 1.0
O A:HOH319 4.8 28.9 1.0
N A:PRO97 4.8 22.3 1.0
N B:SER98 4.9 23.3 1.0
C B:LEU99 4.9 20.0 1.0

Chlorine binding site 2 out of 8 in 8rpt

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Chlorine binding site 2 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:53.6
occ:1.00
 CG B:GLU34 3.0 45.7 1.0
N B:GLU34 3.2 40.7 1.0
CB B:GLU34 3.5 44.4 1.0
N B:ARG33 3.7 44.4 1.0
CD B:GLU34 3.7 47.6 1.0
O B:GLY31 3.8 54.6 1.0
O B:HOH367 3.9 49.1 1.0
CA B:GLU34 4.0 41.3 1.0
OE1 B:GLU34 4.1 46.9 1.0
C B:GLY32 4.1 44.1 1.0
C B:ARG33 4.2 45.2 1.0
CA B:ARG33 4.2 39.9 1.0
CB B:ARG33 4.2 30.0 1.0
CA B:GLY32 4.4 39.3 1.0
OE2 B:GLU34 4.5 41.2 1.0
C B:GLY31 4.7 47.0 1.0
O B:GLY32 4.8 39.6 1.0
N B:ASP35 5.0 40.8 1.0

Chlorine binding site 3 out of 8 in 8rpt

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Chlorine binding site 3 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:35.7
occ:1.00
 O B:HOH351 3.1 25.0 1.0
N A:LEU99 3.1 17.2 1.0
O B:HOH357 3.4 35.6 1.0
CB B:PRO97 3.6 27.1 1.0
CA A:SER98 3.8 20.3 1.0
CB A:LEU99 3.8 20.9 1.0
CG A:LEU99 3.8 20.6 1.0
C A:SER98 3.9 22.1 1.0
CA B:PRO97 3.9 27.3 1.0
CD1 A:LEU99 3.9 22.5 1.0
CG B:PRO97 4.0 30.7 1.0
CA A:LEU99 4.1 20.1 1.0
OG A:SER98 4.4 23.7 1.0
CB B:SER128 4.4 29.3 1.0
CB A:SER98 4.5 21.6 1.0
N A:GLY100 4.6 21.3 1.0
O A:PRO97 4.7 23.9 1.0
N A:SER98 4.8 23.8 1.0
N B:PRO97 4.9 33.7 1.0
C A:LEU99 4.9 23.0 1.0
C B:PRO97 5.0 27.4 1.0
O B:HOH330 5.0 31.2 1.0
N B:SER98 5.0 23.3 1.0

Chlorine binding site 4 out of 8 in 8rpt

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Chlorine binding site 4 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:63.8
occ:1.00
 O A:HOH318 3.0 46.3 1.0
N A:ARG74 3.1 32.2 1.0
CA A:GLY71 3.2 46.4 1.0
C A:GLY71 3.3 42.9 1.0
N A:ASP73 3.3 33.8 1.0
N A:GLY71 3.4 44.0 1.0
N A:GLY72 3.5 44.0 1.0
CB A:ASP73 3.6 33.8 1.0
CB A:ARG74 3.8 30.9 1.0
CA A:ASP73 3.8 34.6 1.0
O A:GLY71 3.8 38.3 1.0
C A:ASP73 3.9 30.9 1.0
CA A:ARG74 4.0 29.3 1.0
C A:GLY72 4.1 38.2 1.0
CA A:GLY72 4.4 36.0 1.0
C A:ALA70 4.6 51.6 1.0
CG A:ASP73 4.7 40.4 1.0

Chlorine binding site 5 out of 8 in 8rpt

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Chlorine binding site 5 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:30.4
occ:1.00
 N A:GLU147 3.2 19.1 1.0
O A:HOH326 3.2 30.0 1.0
O A:HOH304 3.7 38.8 1.0
CA A:GLU146 3.8 23.1 1.0
CB A:GLN122 3.8 27.3 1.0
CB A:GLU147 3.8 30.2 1.0
C A:GLU146 4.0 21.0 1.0
CD A:ARG120 4.0 24.3 1.0
CG A:GLU147 4.0 34.7 1.0
CA A:GLU147 4.1 27.1 1.0
CG A:GLN122 4.2 27.2 1.0
CB A:GLU146 4.3 25.8 1.0
NE A:ARG120 4.4 29.6 1.0
CB A:ARG120 4.4 23.4 1.0
CG A:GLU146 4.6 30.5 1.0
O A:TYR145 4.6 24.9 1.0
CG A:ARG120 4.6 29.1 1.0
CA A:GLN122 4.9 24.2 1.0
N A:GLU146 5.0 24.7 1.0

Chlorine binding site 6 out of 8 in 8rpt

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Chlorine binding site 6 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:39.1
occ:1.00
 NE1 A:TRP83 3.5 33.6 1.0
CZ2 A:TRP83 4.1 35.4 1.0
OE1 A:GLN79 4.2 39.6 1.0
CE2 A:TRP83 4.2 30.4 1.0
NE2 A:GLN79 4.3 39.8 1.0
CD A:GLN79 4.4 39.0 1.0
CD1 A:TRP83 4.7 31.6 1.0
OE2 A:GLU61 4.9 42.8 1.0

Chlorine binding site 7 out of 8 in 8rpt

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Chlorine binding site 7 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:34.6
occ:1.00
 O A:HOH344 2.9 38.0 1.0
N A:VAL142 3.3 20.2 1.0
CA A:GLN141 3.6 22.6 1.0
CB A:ALA135 3.7 25.0 1.0
CA A:GLY137 3.9 32.9 1.0
O A:VAL142 3.9 19.4 1.0
N A:GLY137 4.0 33.7 1.0
C A:GLN141 4.0 23.3 1.0
CB A:GLN141 4.0 20.7 1.0
CG A:GLN141 4.1 22.4 1.0
O A:PHE140 4.2 23.3 1.0
CA A:VAL142 4.4 18.8 1.0
C A:VAL142 4.5 19.9 1.0
O A:HOH317 4.5 34.1 1.0
N A:GLN141 4.7 19.1 1.0
CB A:VAL142 4.7 20.3 1.0
C A:GLY137 4.7 35.9 1.0
CD1 A:TRP143 4.8 29.1 1.0
NE1 A:TRP143 4.9 27.9 1.0
C A:PHE140 4.9 24.4 1.0
CA A:ALA135 4.9 23.6 1.0
OE1 A:GLN141 4.9 36.8 1.0

Chlorine binding site 8 out of 8 in 8rpt

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Chlorine binding site 8 out of 8 in the Crystal Structure of Human DNPH1 Mutant- D80A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human DNPH1 Mutant- D80A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:46.7
occ:1.00
 NE A:ARG107 2.6 23.4 1.0
O A:ARG107 2.9 21.6 1.0
O A:HOH356 3.1 35.1 1.0
CA A:ARG107 3.4 18.2 1.0
O A:HOH327 3.4 34.0 1.0
NH2 A:ARG107 3.4 24.1 1.0
CZ A:ARG107 3.4 26.5 1.0
CZ A:PHE111 3.5 28.4 1.0
CE1 A:PHE111 3.5 28.3 1.0
CB A:ALA110 3.5 22.5 1.0
C A:ARG107 3.5 21.4 1.0
CD A:ARG107 3.6 22.1 1.0
CE2 A:PHE111 3.6 29.5 1.0
CB A:ARG107 3.6 19.3 1.0
CB B:ALA110 3.7 19.6 1.0
CD1 A:PHE111 3.7 29.8 1.0
CD2 A:PHE111 3.8 23.3 1.0
CG A:PHE111 3.8 21.6 1.0
CG A:ARG107 4.2 21.7 1.0
N A:PHE111 4.2 22.7 1.0
C A:ALA110 4.4 23.3 1.0
CA A:ALA110 4.5 24.4 1.0
CA B:ALA110 4.7 21.0 1.0
NH1 A:ARG107 4.7 20.6 1.0
N A:ARG107 4.7 17.6 1.0
CB A:PHE111 4.8 21.7 1.0
N A:ALA108 4.8 19.9 1.0
N A:ALA110 4.9 20.8 1.0
CA A:PHE111 4.9 25.8 1.0
O A:GLY106 5.0 16.9 1.0

Reference:

A.E.Carberry, S.Devi, D.J.Harrison, R.G.Da Silva. Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: the Catalytic Roles of TYR24 and ASP80. Chembiochem V. 25 00047 2024.
ISSN: ESSN 1439-7633
PubMed: 38350003
DOI: 10.1002/CBIC.202400047
Page generated: Sun Jul 13 13:59:07 2025

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