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Chlorine in PDB 4wgf: Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide

Protein crystallography data

The structure of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide, PDB code: 4wgf was solved by M.K.Groftehauge, D.Truan, A.Vasil, P.W.Denny, M.L.Vasil, E.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.72 / 2.34
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.360, 74.480, 141.060, 90.00, 92.29, 90.00
R / Rfree (%) 17.2 / 20.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide (pdb code 4wgf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide, PDB code: 4wgf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4wgf

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Chlorine binding site 1 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:23.1
occ:1.00
 ND2 A:ASN87 3.0 16.1 1.0
N A:ASN87 3.1 13.5 1.0
ND2 A:ASN93 3.3 12.8 1.0
CD A:PRO85 3.3 18.2 1.0
CB A:ASN87 3.4 15.1 1.0
N A:GLY86 3.4 21.5 1.0
CB A:ARG84 3.6 9.9 1.0
CG A:ASN87 3.6 17.2 1.0
N A:PRO85 3.7 18.7 1.0
CA A:ARG84 3.7 15.0 1.0
CA A:ASN87 3.8 13.1 1.0
CG A:PRO85 3.9 17.9 1.0
C A:ARG84 3.9 17.9 1.0
NH2 B:ARG177 4.0 21.2 1.0
C A:GLY86 4.0 15.5 1.0
CA A:GLY86 4.1 20.5 1.0
CG A:ASN93 4.3 12.6 1.0
CB A:ASN93 4.4 13.5 1.0
C A:PRO85 4.5 23.3 1.0
CG A:ARG84 4.5 9.6 1.0
CA A:PRO85 4.6 20.1 1.0
O A:ASN87 4.6 11.9 1.0
CZ B:ARG177 4.6 20.7 1.0
C A:ASN87 4.7 12.0 1.0
O A:ARG84 4.7 21.2 1.0
OD1 A:ASN87 4.8 18.1 1.0
CB A:PRO85 4.9 18.1 1.0
CD A:ARG84 4.9 9.3 1.0
O A:HOH495 5.0 24.5 1.0

Chlorine binding site 2 out of 8 in 4wgf

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Chlorine binding site 2 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:36.4
occ:1.00
 ND2 B:ASN87 2.8 24.0 1.0
ND2 B:ASN93 2.9 10.9 1.0
N B:ASN87 3.2 16.9 1.0
CB B:ASN87 3.3 19.5 1.0
CD B:PRO85 3.3 22.6 1.0
CG B:ASN87 3.5 21.7 1.0
N B:GLY86 3.7 23.2 1.0
CB B:ARG84 3.8 15.0 1.0
CG B:PRO85 3.8 24.0 1.0
CA B:ASN87 3.8 17.2 1.0
N B:PRO85 3.9 22.5 1.0
CG B:ASN93 3.9 11.3 1.0
CA B:ARG84 4.0 16.8 1.0
CB B:ASN93 4.0 10.3 1.0
C B:ARG84 4.1 20.4 1.0
NH2 C:ARG177 4.1 18.3 1.0
C B:GLY86 4.2 18.4 1.0
CA B:GLY86 4.3 22.4 1.0
O B:ASN87 4.6 9.5 1.0
CA B:ASN93 4.6 13.0 1.0
CG B:ARG84 4.6 13.3 1.0
OD1 B:ASN87 4.7 20.9 1.0
C B:PRO85 4.7 26.4 1.0
C B:ASN87 4.7 9.7 1.0
CA B:PRO85 4.7 24.5 1.0
O B:HOH407 4.8 35.3 1.0
CZ C:ARG177 4.9 18.5 1.0
CD B:ARG84 4.9 11.1 1.0
CB B:PRO85 4.9 25.3 1.0
O B:HOH406 5.0 20.8 1.0

Chlorine binding site 3 out of 8 in 4wgf

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Chlorine binding site 3 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:24.1
occ:1.00
 N C:ASN87 3.0 16.2 1.0
CD C:PRO85 3.3 20.7 1.0
ND2 C:ASN93 3.3 11.8 1.0
N C:GLY86 3.3 19.8 1.0
CB C:ASN87 3.5 17.9 1.0
ND2 C:ASN87 3.5 21.2 1.0
N C:PRO85 3.6 20.0 1.0
CB C:ARG84 3.7 14.0 1.0
CG C:ASN87 3.7 19.3 1.0
CA C:ARG84 3.8 16.1 1.0
CA C:ASN87 3.8 14.7 1.0
CG C:PRO85 3.9 20.8 1.0
C C:ARG84 3.9 19.1 1.0
C C:GLY86 3.9 18.6 1.0
CA C:GLY86 4.0 20.2 1.0
NH2 D:ARG177 4.1 16.7 1.0
CG C:ASN93 4.4 11.5 1.0
C C:PRO85 4.4 20.7 1.0
CB C:ASN93 4.5 20.9 1.0
CA C:PRO85 4.5 19.7 1.0
O C:ASN87 4.6 11.6 1.0
CZ D:ARG177 4.6 19.1 1.0
CG C:ARG84 4.6 13.9 1.0
OD1 C:ASN87 4.6 19.0 1.0
O C:ARG84 4.7 22.1 1.0
C C:ASN87 4.7 13.1 1.0
CB C:PRO85 4.9 19.1 1.0

Chlorine binding site 4 out of 8 in 4wgf

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Chlorine binding site 4 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:18.4
occ:1.00
 ND2 D:ASN87 2.9 20.6 1.0
N D:ASN87 3.0 17.1 1.0
ND2 D:ASN93 3.2 11.5 1.0
CD D:PRO85 3.3 15.3 1.0
CB D:ASN87 3.4 16.7 1.0
N D:GLY86 3.4 17.5 1.0
CG D:ASN87 3.6 19.5 1.0
N D:PRO85 3.7 16.6 1.0
CB D:ARG84 3.7 12.6 1.0
CA D:ASN87 3.8 17.5 1.0
CA D:ARG84 3.8 15.4 1.0
CG D:PRO85 3.8 17.9 1.0
NH2 A:ARG177 4.0 14.1 1.0
C D:ARG84 4.0 18.1 1.0
C D:GLY86 4.0 17.1 1.0
CA D:GLY86 4.1 16.8 1.0
CG D:ASN93 4.2 11.3 1.0
CB D:ASN93 4.4 11.0 1.0
C D:PRO85 4.5 19.1 1.0
CZ A:ARG177 4.5 14.9 1.0
O D:ASN87 4.6 18.8 1.0
CA D:PRO85 4.6 18.1 1.0
CG D:ARG84 4.6 10.5 1.0
C D:ASN87 4.7 18.8 1.0
OD1 D:ASN87 4.8 20.9 1.0
O D:ARG84 4.8 22.4 1.0
O D:HOH455 4.8 19.0 1.0
CB D:PRO85 4.9 18.8 1.0
O D:HOH479 4.9 22.0 1.0
NH1 A:ARG177 4.9 17.3 1.0
CD D:ARG84 5.0 9.9 1.0
CA D:ASN93 5.0 11.4 1.0

Chlorine binding site 5 out of 8 in 4wgf

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Chlorine binding site 5 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:18.8
occ:1.00
 ND2 E:ASN87 3.1 20.8 1.0
ND2 E:ASN93 3.1 12.1 1.0
N E:ASN87 3.2 19.4 1.0
CD E:PRO85 3.4 18.6 1.0
N E:GLY86 3.5 19.8 1.0
CB E:ASN87 3.5 16.6 1.0
CB E:ARG84 3.6 15.3 1.0
N E:PRO85 3.7 19.7 1.0
CA E:ARG84 3.7 16.9 1.0
CG E:ASN87 3.7 19.4 1.0
CA E:ASN87 3.9 15.8 1.0
C E:ARG84 3.9 18.4 1.0
CG E:PRO85 3.9 19.2 1.0
NH2 F:ARG177 4.0 13.6 1.0
C E:GLY86 4.1 19.8 1.0
CA E:GLY86 4.1 18.6 1.0
CG E:ASN93 4.2 14.6 1.0
CB E:ASN93 4.3 13.4 1.0
C E:PRO85 4.5 23.5 1.0
CG E:ARG84 4.5 13.9 1.0
CZ F:ARG177 4.6 17.4 1.0
O E:ASN87 4.6 12.3 1.0
CA E:PRO85 4.6 20.8 1.0
O E:ARG84 4.8 19.0 1.0
C E:ASN87 4.8 12.4 1.0
OD1 E:ASN87 4.9 20.2 1.0
CA E:ASN93 4.9 14.1 1.0
CD E:ARG84 4.9 10.6 1.0
CB E:PRO85 5.0 19.7 1.0
NH1 F:ARG177 5.0 19.2 1.0

Chlorine binding site 6 out of 8 in 4wgf

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Chlorine binding site 6 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl303

b:24.4
occ:1.00
 ND2 F:ASN93 3.0 11.1 1.0
ND2 F:ASN87 3.1 24.4 1.0
N F:ASN87 3.2 19.1 1.0
CD F:PRO85 3.4 17.8 1.0
CB F:ASN87 3.5 19.3 1.0
N F:GLY86 3.6 22.0 1.0
CB F:ARG84 3.6 13.0 1.0
CA F:ARG84 3.7 16.2 1.0
CG F:ASN87 3.7 22.2 1.0
N F:PRO85 3.8 18.3 1.0
CG F:PRO85 4.0 18.3 1.0
CA F:ASN87 4.0 17.5 1.0
C F:ARG84 4.0 17.9 1.0
CG F:ASN93 4.1 10.8 1.0
NH2 G:ARG177 4.1 17.8 1.0
C F:GLY86 4.2 18.9 1.0
CA F:GLY86 4.2 19.4 1.0
CB F:ASN93 4.3 12.6 1.0
CG F:ARG84 4.5 9.9 1.0
C F:PRO85 4.6 23.2 1.0
CA F:PRO85 4.7 19.6 1.0
CZ G:ARG177 4.7 17.6 1.0
O F:ASN87 4.7 13.7 1.0
O F:ARG84 4.8 22.1 1.0
C F:ASN87 4.9 14.2 1.0
CD F:ARG84 4.9 12.0 1.0
OD1 F:ASN87 4.9 21.6 1.0
CA F:ASN93 4.9 13.9 1.0

Chlorine binding site 7 out of 8 in 4wgf

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Chlorine binding site 7 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl303

b:31.2
occ:1.00
 ND2 G:ASN87 2.8 23.6 1.0
ND2 G:ASN93 2.9 10.1 1.0
N G:ASN87 3.3 11.2 1.0
CB G:ASN87 3.3 18.8 1.0
CD G:PRO85 3.4 15.1 1.0
CG G:ASN87 3.5 21.8 1.0
CG G:PRO85 3.8 17.7 1.0
N G:GLY86 3.8 25.5 1.0
CB G:ARG84 3.8 15.0 1.0
CA G:ASN87 3.9 12.8 1.0
CG G:ASN93 3.9 10.6 1.0
N G:PRO85 3.9 17.1 1.0
CB G:ASN93 4.0 10.6 1.0
CA G:ARG84 4.0 15.9 1.0
C G:ARG84 4.2 18.7 1.0
C G:GLY86 4.3 13.6 1.0
NH2 H:ARG177 4.4 17.8 1.0
CA G:GLY86 4.5 21.8 1.0
CA G:ASN93 4.5 12.0 1.0
O G:ASN87 4.6 9.2 1.0
CG G:ARG84 4.7 12.0 1.0
OD1 G:ASN87 4.7 20.4 1.0
C G:ASN87 4.8 10.0 1.0
C G:PRO85 4.8 25.8 1.0
CA G:PRO85 4.8 20.5 1.0
O G:HOH415 4.8 26.9 1.0
CB G:PRO85 4.9 20.9 1.0
CD G:ARG84 4.9 8.6 1.0
O G:HOH478 5.0 18.7 1.0

Chlorine binding site 8 out of 8 in 4wgf

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Chlorine binding site 8 out of 8 in the Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ycac From Pseudomonas Aeruginosa with Hexane-2,5-Diol and Covalent Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl303

b:23.8
occ:1.00
 ND2 H:ASN87 3.0 26.7 1.0
N H:ASN87 3.1 15.3 1.0
ND2 H:ASN93 3.1 12.4 1.0
CD H:PRO85 3.4 22.3 1.0
N H:GLY86 3.4 25.6 1.0
CB H:ASN87 3.4 21.3 1.0
CG H:ASN87 3.6 25.0 1.0
N H:PRO85 3.7 22.8 1.0
CB H:ARG84 3.7 11.7 1.0
CA H:ARG84 3.8 15.0 1.0
CA H:ASN87 3.8 12.0 1.0
CG H:PRO85 3.9 22.0 1.0
C H:ARG84 4.0 18.7 1.0
C H:GLY86 4.0 17.6 1.0
CA H:GLY86 4.0 22.7 1.0
NH2 E:ARG177 4.1 22.6 1.0
CG H:ASN93 4.2 19.2 1.0
CB H:ASN93 4.3 11.8 1.0
C H:PRO85 4.5 28.6 1.0
CA H:PRO85 4.6 25.3 1.0
O H:ASN87 4.6 11.3 1.0
CG H:ARG84 4.6 11.3 1.0
CZ E:ARG177 4.7 22.5 1.0
C H:ASN87 4.8 17.4 1.0
OD1 H:ASN87 4.8 24.8 1.0
O H:ARG84 4.8 20.9 1.0
CB H:PRO85 4.9 22.4 1.0
CA H:ASN93 5.0 13.2 1.0

Reference:

M.K.Grftehauge, D.Truan, A.Vasil, P.W.Denny, M.L.Vasil, E.Pohl. Crystal Structure of A Hidden Protein, Ycac, A Putative Cysteine Hydrolase From Pseudomonas Aeruginosa, with and Without An Acrylamide Adduct. Int J Mol Sci V. 16 15971 2015.
ISSN: ESSN 1422-0067
PubMed: 26184183
DOI: 10.3390/IJMS160715971
Page generated: Fri Jul 26 02:53:45 2024

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