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Chlorine in PDB 4nyo: The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3

Protein crystallography data

The structure of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3, PDB code: 4nyo was solved by B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.085, 124.250, 50.458, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.5

Other elements in 4nyo:

The structure of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 (pdb code 4nyo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3, PDB code: 4nyo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4nyo

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Chlorine binding site 1 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:41.3
occ:1.00
 NE B:ARG33 3.5 27.1 1.0
NE A:ARG33 3.5 19.9 1.0
NH2 A:ARG33 3.6 18.8 1.0
NE C:ARG33 3.7 22.0 1.0
NH2 C:ARG33 3.7 20.2 1.0
NH1 B:ARG33 3.7 21.6 1.0
CZ A:ARG33 4.0 20.1 1.0
CZ B:ARG33 4.1 25.4 1.0
CD1 B:ILE54 4.2 24.7 1.0
CZ C:ARG33 4.2 19.6 1.0
CD1 A:ILE54 4.4 26.2 1.0
CD1 C:ILE54 4.4 26.2 1.0
CD B:ARG33 4.5 26.6 1.0
CD A:ARG33 4.6 21.5 1.0
O A:HOH387 4.6 58.6 1.0
CD C:ARG33 4.8 21.2 1.0

Chlorine binding site 2 out of 8 in 4nyo

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Chlorine binding site 2 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:36.0
occ:1.00
 O B:HOH336 2.9 42.2 1.0
CE B:LYS70 3.1 35.5 1.0
N C:GLU90 3.2 17.8 1.0
CA C:ASN89 3.6 18.2 1.0
NZ B:LYS70 3.6 34.4 1.0
CB C:ASN89 3.8 17.3 1.0
C C:ASN89 3.9 19.6 1.0
OD1 C:ASP91 4.0 23.5 1.0
CD B:LYS66 4.1 27.0 1.0
CA C:GLU90 4.2 18.5 1.0
CB C:GLU90 4.2 19.5 1.0
CG C:GLU90 4.3 20.9 1.0
CD B:LYS70 4.4 31.9 1.0
N C:ASP91 4.5 19.5 1.0
O B:HOH391 4.7 37.2 1.0
C C:GLU90 4.8 18.8 1.0
NZ B:LYS66 4.9 35.2 1.0
OE2 B:GLU67 5.0 39.2 1.0

Chlorine binding site 3 out of 8 in 4nyo

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Chlorine binding site 3 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:36.4
occ:1.00
 O B:HOH312 3.2 32.2 1.0
N B:MET1 3.3 22.2 1.0
N B:GLU59 3.4 22.7 1.0
CA B:MET1 3.5 20.7 1.0
CA B:ARG58 3.7 22.4 1.0
CB B:ARG58 4.0 23.4 1.0
CB B:GLU59 4.1 29.0 1.0
C B:ARG58 4.1 22.1 1.0
CB B:MET1 4.2 20.4 1.0
O B:HOH346 4.3 28.5 1.0
CA B:GLU59 4.3 25.5 1.0
CG B:ARG58 4.4 24.1 1.0
CD1 B:LEU93 4.5 23.4 1.0
C B:MET1 4.7 19.4 1.0
O B:HOH368 4.7 76.0 1.0
CD B:ARG58 4.8 26.9 1.0
O B:THR57 5.0 18.9 1.0
OD1 B:ASP60 5.0 28.6 1.0
N B:ARG58 5.0 22.5 1.0

Chlorine binding site 4 out of 8 in 4nyo

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Chlorine binding site 4 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:31.8
occ:1.00
 NZ C:LYS70 2.8 38.4 1.0
N A:GLU90 3.2 22.7 1.0
O A:HOH328 3.3 46.2 1.0
NZ C:LYS66 3.5 26.7 1.0
O A:HOH338 3.6 34.5 1.0
CE C:LYS70 3.6 34.6 1.0
CA A:ASN89 3.6 20.3 1.0
CB A:GLU90 3.9 30.5 1.0
C A:ASN89 3.9 22.4 1.0
CD C:LYS66 4.0 25.3 1.0
CE C:LYS66 4.0 27.9 1.0
CB A:ASN89 4.1 19.7 1.0
CA A:GLU90 4.1 26.6 1.0
O A:VAL88 4.6 21.2 1.0
OE1 C:GLU67 4.7 38.6 1.0
CG C:LYS66 4.8 23.9 1.0
N A:ASN89 4.8 20.7 1.0
OD1 A:ASP91 5.0 39.1 1.0

Chlorine binding site 5 out of 8 in 4nyo

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Chlorine binding site 5 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3002

b:30.8
occ:1.00
 NZ D:LYS70 2.9 33.8 1.0
N E:GLU90 3.1 20.0 1.0
NZ D:LYS66 3.3 29.5 1.0
CA E:ASN89 3.5 19.4 1.0
O E:HOH4113 3.6 21.1 1.0
O E:HOH4183 3.6 42.7 1.0
CE D:LYS70 3.7 30.5 1.0
CG E:GLU90 3.7 32.7 1.0
C E:ASN89 3.8 19.8 1.0
CB E:ASN89 3.9 20.7 1.0
CB E:GLU90 4.0 25.5 1.0
CD D:LYS66 4.1 24.9 1.0
CE D:LYS66 4.1 27.0 1.0
CA E:GLU90 4.2 22.1 1.0
CD E:GLU90 4.6 37.0 1.0
OE1 D:GLU67 4.6 32.2 1.0
OE1 E:GLU90 4.7 40.6 1.0
O E:VAL88 4.7 19.7 1.0
CG D:LYS66 4.7 22.9 1.0
N E:ASN89 4.8 19.4 1.0

Chlorine binding site 6 out of 8 in 4nyo

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Chlorine binding site 6 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3003

b:31.5
occ:1.00
 N D:GLU90 3.2 21.5 1.0
CG D:GLU90 3.3 35.0 1.0
NZ F:LYS66 3.3 31.8 1.0
NZ F:LYS70 3.5 36.4 1.0
CA D:ASN89 3.6 20.9 1.0
CE F:LYS66 3.8 28.3 1.0
O D:HOH3192 3.8 44.1 1.0
CD D:GLU90 3.8 37.6 1.0
O D:HOH3193 3.8 51.1 1.0
O D:HOH3120 3.9 28.2 1.0
OE1 D:GLU90 3.9 38.6 1.0
C D:ASN89 3.9 21.2 1.0
CB D:GLU90 4.0 26.6 1.0
CB D:ASN89 4.0 21.4 1.0
CD F:LYS66 4.1 26.7 1.0
CA D:GLU90 4.2 23.5 1.0
CE F:LYS70 4.3 33.4 1.0
OE2 F:GLU67 4.4 34.2 1.0
CD F:LYS70 4.5 32.1 1.0
OE2 D:GLU90 4.7 43.2 1.0
O D:VAL88 4.7 18.8 1.0
N D:ASN89 4.8 19.8 1.0
O D:HOH3200 5.0 68.9 1.0
CG F:LYS66 5.0 23.3 1.0

Chlorine binding site 7 out of 8 in 4nyo

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Chlorine binding site 7 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3004

b:39.2
occ:1.00
 O D:HOH3132 3.0 35.3 1.0
N D:MET1 3.3 19.7 1.0
N D:GLU59 3.6 20.2 1.0
CA D:MET1 3.6 18.9 1.0
CA D:ARG58 3.8 20.6 1.0
CB D:ARG58 3.9 21.7 1.0
OE2 D:GLU59 4.1 29.6 1.0
CG D:ARG58 4.2 24.2 1.0
C D:ARG58 4.2 20.5 1.0
CD D:GLU59 4.3 29.8 1.0
CB D:MET1 4.4 18.7 1.0
CG D:GLU59 4.4 26.9 1.0
CD1 D:LEU93 4.4 17.1 1.0
CB D:GLU59 4.4 23.2 1.0
CD D:ARG58 4.5 24.2 1.0
CA D:GLU59 4.6 22.5 1.0
C D:MET1 4.9 17.9 1.0
OD1 D:ASP60 5.0 28.0 1.0

Chlorine binding site 8 out of 8 in 4nyo

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Chlorine binding site 8 out of 8 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl4001

b:29.8
occ:1.00
 NZ E:LYS70 3.1 32.9 1.0
O F:HOH310 3.2 27.8 1.0
N F:GLU90 3.2 21.1 1.0
NZ E:LYS66 3.3 31.7 1.0
CA F:ASN89 3.6 17.4 1.0
CE E:LYS66 3.6 29.3 1.0
CE E:LYS70 3.8 29.6 1.0
C F:ASN89 3.9 21.6 1.0
CG F:GLU90 3.9 34.7 1.0
CD E:LYS66 3.9 24.6 1.0
CB F:ASN89 4.0 17.6 1.0
CB F:GLU90 4.1 28.1 1.0
CA F:GLU90 4.3 24.0 1.0
OE2 F:GLU90 4.3 42.1 1.0
CD F:GLU90 4.6 39.3 1.0
O F:VAL88 4.7 18.6 1.0
N F:ASN89 4.8 17.9 1.0
CG E:LYS66 4.9 20.2 1.0
O E:HOH4105 5.0 36.6 1.0

Reference:

B.Bagautdinov, B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi). N/A N/A.
ISSN: ISSN 2053-230X
PubMed: 24699729
DOI: 10.1107/S2053230X14003422
Page generated: Thu Jul 25 23:08:03 2024

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