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Chlorine in PDB 4jde: Crystal Structure of Pud-1/Pud-2 Heterodimer

Protein crystallography data

The structure of Crystal Structure of Pud-1/Pud-2 Heterodimer, PDB code: 4jde was solved by S.Luo, K.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.991, 89.775, 102.503, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Pud-1/Pud-2 Heterodimer (pdb code 4jde). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Pud-1/Pud-2 Heterodimer, PDB code: 4jde:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 4jde

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Chlorine binding site 1 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:23.7
occ:1.00
 O A:HOH323 3.0 24.3 1.0
NE A:ARG110 3.2 17.5 1.0
O A:HOH443 3.3 37.2 1.0
CD A:ARG110 3.6 17.0 1.0
CA A:SER109 3.8 17.4 1.0
CB A:SER109 3.9 17.8 1.0
CG A:ARG110 3.9 16.8 1.0
C A:SER109 4.1 16.9 1.0
O A:SER109 4.2 17.0 1.0
O A:HOH421 4.2 38.2 1.0
CZ A:ARG110 4.3 18.8 1.0
OG1 A:THR149 4.5 20.2 1.0
OG A:SER109 4.5 19.8 1.0
NH2 A:ARG110 4.6 19.2 1.0
N A:ARG110 4.7 15.6 1.0
O A:HOH428 4.9 41.7 1.0
CB A:ARG110 5.0 16.2 1.0

Chlorine binding site 2 out of 10 in 4jde

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Chlorine binding site 2 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:37.7
occ:1.00
 N A:TYR99 3.4 30.3 1.0
NZ A:LYS96 3.7 44.8 1.0
CA A:SER98 3.7 32.0 1.0
CD2 A:TYR99 3.8 28.6 1.0
C A:SER98 4.0 31.2 1.0
CB A:TYR99 4.0 28.4 1.0
CB A:SER98 4.2 33.5 1.0
CA A:TYR99 4.2 29.1 1.0
CG A:TYR99 4.4 28.8 1.0
O A:TYR99 4.5 29.3 1.0
O A:LYS97 4.6 35.5 1.0
CE2 A:TYR99 4.8 28.9 1.0
C A:TYR99 4.9 29.0 1.0
N A:SER98 5.0 33.4 1.0

Chlorine binding site 3 out of 10 in 4jde

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Chlorine binding site 3 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:18.6
occ:1.00
 OH A:TYR35 3.1 16.9 1.0
N A:THR69 3.4 21.6 1.0
N A:GLY70 3.5 19.2 1.0
CB A:THR68 3.6 24.1 1.0
ND2 A:ASN63 3.6 14.4 1.0
CA A:THR68 3.6 22.9 1.0
CE2 A:TYR35 3.8 16.9 1.0
CZ A:TYR35 3.9 17.4 1.0
CG2 A:THR68 3.9 23.5 1.0
C A:THR68 4.0 22.4 1.0
CA A:GLY70 4.2 19.4 1.0
CB A:ASN63 4.3 15.4 1.0
OG1 A:THR69 4.3 20.2 1.0
CA A:THR69 4.4 20.3 1.0
C A:THR69 4.4 20.5 1.0
CG A:ASN63 4.5 15.1 1.0
N A:THR68 4.9 22.4 1.0
OG1 A:THR68 4.9 26.1 1.0

Chlorine binding site 4 out of 10 in 4jde

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Chlorine binding site 4 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:23.6
occ:1.00
 O A:HOH363 3.0 40.2 1.0
NZ A:LYS113 3.3 16.3 1.0
N A:THR145 3.3 17.7 1.0
O A:HOH319 3.6 31.8 1.0
CA A:SER144 3.6 18.4 1.0
O A:THR145 3.7 16.4 1.0
CB A:SER144 3.7 18.5 1.0
O A:HOH360 3.8 49.0 1.0
CE A:LYS113 4.0 15.8 1.0
C A:SER144 4.0 18.0 1.0
OG A:SER144 4.2 18.2 1.0
OG1 A:THR145 4.2 22.5 1.0
CA A:THR145 4.4 18.5 1.0
O A:HOH475 4.4 40.2 1.0
C A:THR145 4.4 17.8 1.0
O A:GLU143 4.8 22.9 1.0
CB A:THR145 4.9 20.5 1.0
N A:SER144 5.0 19.4 1.0

Chlorine binding site 5 out of 10 in 4jde

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Chlorine binding site 5 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:48.0
occ:1.00
 NZ A:LYS34 3.0 34.3 1.0
N A:GLY37 3.2 19.1 1.0
CE A:LYS34 3.7 34.1 1.0
CA A:THR36 3.8 18.8 1.0
CD A:LYS34 4.0 28.7 1.0
C A:THR36 4.0 19.6 1.0
O A:HOH446 4.2 52.8 1.0
CA A:GLY37 4.2 20.2 1.0
CG2 A:THR36 4.3 18.9 1.0
O A:HOH431 4.3 51.2 1.0
O A:HOH399 4.5 30.7 1.0
CG A:LYS34 4.5 26.1 1.0
O A:HOH351 4.6 28.9 1.0
O A:TYR35 4.6 16.4 1.0
CB A:THR36 4.6 18.4 1.0
N A:THR36 4.7 18.0 1.0
C A:GLY37 5.0 20.1 1.0
C A:TYR35 5.0 17.8 1.0

Chlorine binding site 6 out of 10 in 4jde

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Chlorine binding site 6 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:30.4
occ:1.00
 OG1 A:THR64 2.9 21.1 1.0
O A:HOH374 3.2 36.7 1.0
O A:HOH380 3.3 38.8 1.0
NH2 A:ARG13 3.3 23.4 1.0
OG1 A:THR11 3.6 21.8 1.0
N A:GLY65 3.8 19.7 1.0
CA A:GLY65 3.8 21.4 1.0
CB A:THR64 3.8 19.3 1.0
C A:THR64 3.9 19.4 1.0
CB A:THR11 3.9 21.3 1.0
O A:THR64 4.1 19.1 1.0
CB A:SER8 4.1 30.1 1.0
CZ A:ARG13 4.3 24.2 1.0
NE A:ARG13 4.3 23.4 1.0
OG A:SER8 4.5 32.2 1.0
CA A:THR64 4.5 18.3 1.0
O A:SER8 4.5 23.5 1.0
N A:THR11 4.8 18.7 1.0
CG2 A:THR11 4.9 22.1 1.0
CA A:THR11 5.0 19.4 1.0
CA A:SER8 5.0 26.9 1.0

Chlorine binding site 7 out of 10 in 4jde

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Chlorine binding site 7 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:32.9
occ:1.00
 N A:GLN114 3.1 15.2 1.0
O A:HOH402 3.2 35.1 1.0
O A:HOH483 3.6 26.1 1.0
CB A:GLN114 3.7 20.0 1.0
CD A:LYS113 3.8 15.9 1.0
CA A:LYS113 3.9 14.8 1.0
CA A:GLN114 3.9 17.1 1.0
C A:LYS113 4.0 15.1 1.0
O A:TRP112 4.2 16.4 1.0
O A:HOH479 4.3 12.9 1.0
OD2 A:ASP108 4.4 20.1 1.0
O A:GLN114 4.5 15.6 1.0
CE A:LYS113 4.5 15.8 1.0
NZ A:LYS113 4.5 16.3 1.0
CG A:LYS113 4.6 15.5 1.0
C A:GLN114 4.7 16.5 1.0
O A:HOH396 4.7 47.2 1.0
CB A:LYS113 4.8 15.6 1.0
O A:HOH484 4.8 46.1 1.0
N A:LYS113 4.9 14.9 1.0
C A:TRP112 5.0 16.0 1.0

Chlorine binding site 8 out of 10 in 4jde

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Chlorine binding site 8 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


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 Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:31.6
occ:1.00
 N B:THR68 3.3 30.6 1.0
OH B:TYR34 3.3 32.7 1.0
ND2 B:ASN62 3.4 30.0 1.0
O B:HOH326 3.4 36.2 1.0
O B:HOH410 3.4 45.8 1.0
CA B:THR67 3.6 29.4 1.0
N B:GLY69 3.6 31.5 1.0
CE2 B:TYR34 3.6 29.4 1.0
CB B:THR67 3.7 29.7 1.0
C B:THR67 3.9 30.7 1.0
CZ B:TYR34 4.0 29.3 1.0
OG1 B:THR68 4.0 33.5 1.0
CG2 B:THR67 4.0 27.4 1.0
CB B:ASN62 4.1 27.8 1.0
CG B:ASN62 4.2 29.6 1.0
CA B:THR68 4.3 32.4 1.0
CA B:GLY69 4.4 34.4 1.0
C B:THR68 4.4 32.6 1.0
O B:HOH316 4.5 29.0 1.0
CB B:THR68 4.7 33.8 1.0
CG2 B:VAL9 4.8 33.5 1.0
CD2 B:TYR34 4.8 27.6 1.0
CG1 B:VAL9 4.9 36.3 1.0
N B:THR67 4.9 28.8 1.0

Chlorine binding site 9 out of 10 in 4jde

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Chlorine binding site 9 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:43.6
occ:1.00
 OG1 B:THR10 3.0 38.7 1.0
O B:HOH409 3.3 36.7 1.0
O B:HOH428 3.3 54.3 1.0
N B:GLY8 3.3 47.5 1.0
C B:GLY8 3.6 37.5 1.0
N B:VAL9 3.7 36.2 1.0
CA B:GLY64 3.7 30.1 1.0
O B:GLY8 3.8 35.6 1.0
N B:THR10 3.9 34.5 1.0
C B:VAL9 3.9 35.1 1.0
O B:THR63 3.9 27.6 1.0
CB B:THR10 4.0 36.4 1.0
CA B:VAL9 4.0 34.8 1.0
CA B:GLY8 4.0 40.8 1.0
CD B:PRO65 4.1 31.4 1.0
CA B:SER7 4.3 56.8 1.0
C B:SER7 4.3 54.6 1.0
O B:HOH406 4.3 51.4 1.0
O B:VAL9 4.4 35.0 1.0
CA B:THR10 4.5 35.3 1.0
OG B:SER7 4.5 62.0 1.0
C B:THR63 4.6 28.9 1.0
N B:GLY64 4.6 29.2 1.0
O B:HOH335 4.8 53.7 1.0
C B:GLY64 4.9 30.1 1.0
N B:PRO65 5.0 30.2 1.0

Chlorine binding site 10 out of 10 in 4jde

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Chlorine binding site 10 out of 10 in the Crystal Structure of Pud-1/Pud-2 Heterodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Pud-1/Pud-2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:37.0
occ:1.00
 OG1 B:THR147 3.1 32.7 1.0
O B:HOH332 3.2 44.0 1.0
NZ B:LYS114 3.3 30.4 1.0
CB B:THR147 3.6 30.9 1.0
C B:HIS107 3.6 33.3 1.0
CA B:HIS107 3.8 31.1 1.0
CD B:LYS114 3.8 30.1 1.0
N B:HIS107 3.8 29.3 1.0
N B:PRO108 3.9 35.1 1.0
O B:HIS107 4.0 34.2 1.0
CD B:PRO108 4.0 33.8 1.0
CE B:LYS114 4.1 30.3 1.0
O B:THR146 4.2 33.6 1.0
CA B:THR147 4.2 31.0 1.0
C B:GLY106 4.5 27.8 1.0
CA B:PRO108 4.7 36.7 1.0
CG B:PRO108 4.7 35.6 1.0
O B:GLY106 4.8 28.3 1.0
O B:HOH317 4.9 48.0 1.0
CG2 B:THR147 5.0 30.5 1.0

Reference:

Y.H.Ding, Y.G.Du, S.Luo, Y.X.Li, T.M.Li, S.Yoshina, X.Wang, K.Klage, S.Mitani, K.Ye, M.Q.Dong. Characterization of Pud-1 and Pud-2, Two Proteins Up-Regulated in A Long-Lived Daf-2 Mutant. Plos One V. 8 67158 2013.
ISSN: ESSN 1932-6203
PubMed: 23799143
DOI: 10.1371/JOURNAL.PONE.0067158
Page generated: Sun Jul 21 17:22:08 2024

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