Chlorine in PDB 8ff9: Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)

Protein crystallography data

The structure of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form), PDB code: 8ff9 was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.43 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 129.541, 129.82, 156.598, 90, 90, 90
R / Rfree (%) 14.6 / 17

Other elements in 8ff9:

The structure of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) also contains other interesting chemical elements:

Sodium (Na) 12 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) (pdb code 8ff9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 24 binding sites of Chlorine where determined in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form), PDB code: 8ff9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 24 in 8ff9

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Chlorine binding site 1 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:35.6
occ:1.00
OG1 A:THR26 2.8 18.7 1.0
NE A:ARG139 2.8 18.9 1.0
NE2 A:HIS143 2.8 21.0 1.0
NH2 A:ARG139 3.5 20.0 1.0
CG2 A:THR26 3.5 17.6 1.0
CG1 A:VAL113 3.5 20.0 1.0
CD2 A:HIS143 3.5 18.6 1.0
CZ A:ARG139 3.6 19.5 1.0
CG A:ARG139 3.7 18.7 1.0
CD A:ARG139 3.7 19.9 1.0
CB A:THR26 3.7 18.5 1.0
CB A:ARG139 3.8 17.4 1.0
CE1 A:HIS143 3.9 20.1 1.0
CD1 A:ILE66 4.0 18.8 1.0
CB A:ALA62 4.6 17.6 1.0
CA A:THR26 4.6 17.3 1.0
CD1 A:LEU22 4.7 21.4 1.0
CA A:ARG139 4.7 20.0 1.0
CB A:VAL113 4.8 20.4 1.0
CG A:HIS143 4.8 18.7 1.0
NH1 A:ARG139 4.8 19.5 1.0
CG A:LEU22 4.9 20.0 1.0
CD2 A:LEU59 4.9 23.9 1.0
ND1 A:HIS143 4.9 19.1 1.0

Chlorine binding site 2 out of 24 in 8ff9

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Chlorine binding site 2 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:26.0
occ:1.00
O A:HOH460 2.8 36.1 1.0
O A:HOH344 3.1 22.3 1.0
O A:HOH405 3.2 28.8 1.0
N A:LYS91 3.3 24.8 1.0
CG A:LYS91 3.9 33.6 1.0
O A:HOH374 4.0 35.8 1.0
CB A:LYS91 4.0 27.2 1.0
CA A:ILE90 4.0 23.0 1.0
N A:GLY109 4.0 18.8 1.0
C A:GLN108 4.0 20.5 1.0
CG2 A:ILE90 4.0 25.1 1.0
O A:GLN108 4.0 19.4 1.0
CA A:GLY109 4.0 19.0 1.0
C A:ILE90 4.2 23.7 1.0
CB A:GLN108 4.2 21.0 1.0
CA A:LYS91 4.3 25.6 1.0
CD1 A:ILE90 4.3 25.0 1.0
CB A:ALA112 4.4 23.6 1.0
CB A:ILE90 4.5 20.9 1.0
NZ A:LYS32 4.6 20.8 1.0
O A:LYS91 4.7 23.9 1.0
O A:GLN105 4.7 19.2 1.0
CA A:GLN108 4.8 20.1 1.0
O A:HOH361 4.8 25.0 1.0
O A:SER89 4.8 28.3 1.0

Chlorine binding site 3 out of 24 in 8ff9

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Chlorine binding site 3 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:31.0
occ:1.00
NE2 B:HIS143 2.8 17.4 1.0
NE B:ARG139 2.8 15.5 1.0
OG1 B:THR26 2.8 15.4 1.0
CG1 B:VAL113 3.5 16.6 1.0
NH2 B:ARG139 3.5 17.8 1.0
CG2 B:THR26 3.6 14.2 1.0
CD2 B:HIS143 3.6 18.3 1.0
CZ B:ARG139 3.6 17.0 1.0
CG B:ARG139 3.7 16.0 1.0
CD B:ARG139 3.7 16.7 1.0
CB B:THR26 3.8 14.7 1.0
CB B:ARG139 3.8 14.7 1.0
CE1 B:HIS143 3.9 16.9 1.0
CD1 B:ILE66 4.1 18.9 1.0
CB B:ALA62 4.5 17.1 1.0
CA B:THR26 4.6 15.0 1.0
CB B:VAL113 4.7 15.6 1.0
CA B:ARG139 4.7 16.9 1.0
CG B:HIS143 4.8 15.8 1.0
CD2 B:LEU59 4.8 18.8 1.0
NH1 B:ARG139 4.9 19.4 1.0
ND1 B:HIS143 4.9 15.3 1.0
CD1 B:LEU22 4.9 19.8 1.0
CG2 B:VAL113 5.0 15.8 1.0

Chlorine binding site 4 out of 24 in 8ff9

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Chlorine binding site 4 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:28.8
occ:1.00
O B:HOH438 2.5 30.0 1.0
O B:HOH446 2.9 32.2 1.0
O B:HOH383 3.1 18.1 1.0
O B:HOH319 3.3 40.9 1.0
C B:GLN108 3.7 16.5 1.0
O B:GLN108 3.7 18.0 1.0
N B:GLY109 3.8 14.1 1.0
CA B:GLY109 3.9 15.4 1.0
CB B:GLN108 3.9 19.6 1.0
CG2 B:ILE90 4.0 17.9 1.0
CB B:ALA112 4.1 17.1 1.0
O B:HOH379 4.1 20.9 1.0
O B:HOH445 4.2 27.7 1.0
CG1 B:ILE90 4.3 18.9 1.0
CA B:GLN108 4.5 16.8 1.0
CB B:ILE90 4.5 17.0 1.0
CA B:ILE90 4.6 14.7 1.0
O B:GLN105 4.7 15.3 1.0
N B:LYS91 4.9 19.4 1.0

Chlorine binding site 5 out of 24 in 8ff9

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Chlorine binding site 5 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:33.2
occ:1.00
NE C:ARG139 2.7 16.9 1.0
NE2 C:HIS143 2.8 19.4 1.0
OG1 C:THR26 2.8 16.2 1.0
NH2 C:ARG139 3.5 18.7 1.0
CG1 C:VAL113 3.5 20.0 1.0
CZ C:ARG139 3.5 17.0 1.0
CD2 C:HIS143 3.5 18.3 1.0
CG2 C:THR26 3.5 18.9 1.0
CG C:ARG139 3.6 16.2 1.0
CD C:ARG139 3.6 19.8 1.0
CB C:ARG139 3.6 15.7 1.0
CB C:THR26 3.8 15.9 1.0
CE1 C:HIS143 3.9 18.6 1.0
CD1 C:ILE66 4.0 19.3 1.0
CB C:ALA62 4.6 18.9 1.0
CA C:ARG139 4.7 16.8 1.0
CA C:THR26 4.7 15.9 1.0
CB C:VAL113 4.8 18.7 1.0
CD1 C:LEU22 4.8 23.5 1.0
CG C:HIS143 4.8 16.2 1.0
NH1 C:ARG139 4.8 18.9 1.0
CG C:LEU22 4.9 19.6 1.0
ND1 C:HIS143 5.0 17.6 1.0

Chlorine binding site 6 out of 24 in 8ff9

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Chlorine binding site 6 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl204

b:30.9
occ:1.00
O C:HOH418 2.8 30.2 1.0
O C:HOH359 3.2 22.3 1.0
O C:HOH398 3.6 30.5 1.0
O C:GLN108 3.6 17.8 1.0
C C:GLN108 3.7 17.2 1.0
N C:GLY109 3.8 16.5 1.0
CA C:GLY109 3.8 17.7 1.0
CB C:ALA112 3.9 20.6 1.0
CG1 C:ILE90 3.9 22.7 1.0
CB C:GLN108 4.0 18.7 1.0
CG2 C:ILE90 4.1 19.5 1.0
O C:HOH366 4.3 23.5 1.0
CB C:ILE90 4.3 18.5 1.0
CA C:ILE90 4.4 18.4 1.0
CA C:GLN108 4.5 19.3 1.0
CD1 C:ILE90 4.6 23.0 1.0
O C:HOH428 4.7 30.2 1.0
O C:GLN105 4.8 17.2 1.0
O C:HOH436 4.8 34.0 1.0
N C:LYS91 5.0 18.9 1.0
C C:GLY109 5.0 16.4 1.0

Chlorine binding site 7 out of 24 in 8ff9

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Chlorine binding site 7 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:32.7
occ:1.00
NE D:ARG139 2.7 16.3 1.0
NE2 D:HIS143 2.8 20.1 1.0
OG1 D:THR26 2.8 16.7 1.0
NH2 D:ARG139 3.4 18.1 1.0
CG2 D:THR26 3.5 17.4 1.0
CZ D:ARG139 3.5 18.5 1.0
CD2 D:HIS143 3.6 18.3 1.0
CG1 D:VAL113 3.6 20.1 1.0
CD D:ARG139 3.7 19.8 1.0
CG D:ARG139 3.7 20.3 1.0
CB D:THR26 3.7 16.4 1.0
CB D:ARG139 3.8 18.4 1.0
CE1 D:HIS143 3.9 16.4 1.0
CD1 D:ILE66 4.0 17.9 1.0
CB D:ALA62 4.5 19.3 1.0
CA D:THR26 4.7 15.9 1.0
CB D:VAL113 4.7 17.7 1.0
CA D:ARG139 4.8 19.2 1.0
NH1 D:ARG139 4.8 21.2 1.0
CG D:HIS143 4.8 14.7 1.0
CG2 D:VAL113 4.9 17.9 1.0
CD2 D:LEU59 4.9 21.0 1.0
ND1 D:HIS143 4.9 16.4 1.0

Chlorine binding site 8 out of 24 in 8ff9

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Chlorine binding site 8 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl204

b:29.1
occ:1.00
O D:HOH344 2.7 34.8 1.0
O D:HOH380 3.1 20.6 1.0
O D:HOH390 3.3 38.3 1.0
O D:HOH333 3.4 29.4 1.0
O D:GLN108 3.8 19.0 1.0
C D:GLN108 3.8 20.2 1.0
N D:GLY109 3.8 18.9 1.0
CA D:GLY109 3.9 18.9 1.0
CB D:GLN108 4.0 21.4 1.0
CG2 D:ILE90 4.0 20.6 1.0
O D:HOH446 4.1 31.1 1.0
CG1 D:ILE90 4.1 26.4 1.0
CB D:ALA112 4.2 19.4 1.0
CA D:ILE90 4.4 17.2 1.0
O D:HOH341 4.4 21.4 1.0
CB D:ILE90 4.4 21.4 1.0
CA D:GLN108 4.5 20.6 1.0
N D:LYS91 4.6 23.9 1.0
O D:GLN105 4.7 18.1 1.0
CD1 D:ILE90 4.9 22.0 1.0
NZ D:LYS32 5.0 21.1 1.0

Chlorine binding site 9 out of 24 in 8ff9

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Chlorine binding site 9 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl203

b:34.7
occ:1.00
OG1 E:THR26 2.8 17.9 1.0
NE E:ARG139 2.8 16.7 1.0
NE2 E:HIS143 2.9 18.1 1.0
CG2 E:THR26 3.5 18.4 1.0
NH2 E:ARG139 3.5 19.1 1.0
CG1 E:VAL113 3.6 19.7 1.0
CZ E:ARG139 3.6 16.5 1.0
CD2 E:HIS143 3.6 19.6 1.0
CB E:THR26 3.7 16.5 1.0
CG E:ARG139 3.7 18.6 1.0
CD E:ARG139 3.7 17.7 1.0
CB E:ARG139 3.8 16.3 1.0
CE1 E:HIS143 4.0 16.8 1.0
CD1 E:ILE66 4.1 17.2 1.0
CA E:THR26 4.6 16.6 1.0
CB E:ALA62 4.6 19.5 1.0
CB E:VAL113 4.7 19.7 1.0
CD1 E:LEU22 4.8 23.0 1.0
CA E:ARG139 4.8 17.6 1.0
CG E:HIS143 4.8 16.5 1.0
CD2 E:LEU59 4.9 23.5 1.0
NH1 E:ARG139 4.9 19.7 1.0
CG2 E:VAL113 4.9 18.9 1.0
CG E:LEU22 4.9 19.6 1.0

Chlorine binding site 10 out of 24 in 8ff9

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Chlorine binding site 10 out of 24 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl204

b:28.9
occ:1.00
O E:HOH356 3.0 21.7 1.0
O E:HOH320 3.1 39.9 1.0
N E:LYS91 3.6 30.4 1.0
O E:HOH397 3.7 38.2 1.0
CG2 E:ILE90 3.8 25.3 1.0
CA E:GLY109 4.0 18.0 1.0
N E:GLY109 4.0 18.5 1.0
CA E:ILE90 4.0 21.9 1.0
C E:GLN108 4.1 18.6 1.0
O E:GLN108 4.1 18.6 1.0
CB E:GLN108 4.2 20.5 1.0
CB E:ALA112 4.2 19.6 1.0
CD1 E:ILE90 4.3 27.2 1.0
C E:ILE90 4.3 25.5 1.0
CB E:LYS91 4.4 32.9 1.0
CB E:ILE90 4.4 25.4 1.0
CA E:LYS91 4.6 34.6 1.0
O E:LYS91 4.7 26.4 1.0
O E:HOH335 4.7 25.4 1.0
NZ E:LYS32 4.7 24.4 1.0
O E:GLN105 4.7 18.6 1.0
CA E:GLN108 4.8 18.0 1.0
CG1 E:ILE90 5.0 29.8 1.0
O E:HOH386 5.0 42.9 1.0
O E:SER89 5.0 28.9 1.0

Reference:

N.Rajapaksha, A.Soldano, H.Yao, F.Donnarumma, M.M.Kashipathy, S.Seibold, K.P.Battaile, S.Lovell, M.Rivera. Pseudomonas Aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits in Vitro Dna Cleaving Activity Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24054669
Page generated: Tue Apr 4 22:55:12 2023

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