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Chlorine in PDB 5gwf: Frac with Glcnac(6S) Bound

Protein crystallography data

The structure of Frac with Glcnac(6S) Bound, PDB code: 5gwf was solved by J.M.M.Caaveiro, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.06 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.160, 44.400, 114.360, 90.00, 92.76, 90.00
R / Rfree (%) 11.8 / 16.3

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Chlorine atom in the Frac with Glcnac(6S) Bound (pdb code 5gwf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 15 binding sites of Chlorine where determined in the Frac with Glcnac(6S) Bound, PDB code: 5gwf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 15 in 5gwf

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Chlorine binding site 1 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:15.6
occ:1.00
 O A:HOH330 3.0 20.6 1.0
O A:HOH314 3.1 13.6 1.0
NE1 A:TRP116 3.2 13.6 1.0
N A:SER114 3.2 10.2 1.0
CA A:TYR113 3.6 11.3 1.0
CD1 A:TYR113 3.9 11.4 1.0
C A:TYR113 3.9 10.1 1.0
CB A:TYR113 3.9 11.7 1.0
O A:SER114 4.0 11.3 1.0
CD1 A:TRP116 4.1 11.6 1.0
CE2 A:TRP116 4.1 11.5 1.0
CA A:SER114 4.1 11.2 1.0
O A:HOH321 4.2 32.9 1.0
CB A:SER114 4.2 15.9 1.0
CG A:TYR113 4.4 11.6 1.0
CZ2 A:TRP116 4.4 12.2 1.0
OH A:TYR137 4.5 14.0 1.0
C A:SER114 4.5 10.4 1.0
O A:TRP112 4.6 16.9 1.0
OG A:SER114 4.7 21.2 1.0
O A:HOH317 4.8 13.5 1.0
N A:TYR113 4.8 12.1 1.0
CE1 A:TYR113 4.9 11.6 1.0

Chlorine binding site 2 out of 15 in 5gwf

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Chlorine binding site 2 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:20.9
occ:1.00
 O B:HOH346 2.7 30.0 1.0
O B:HOH307 3.1 17.0 1.0
NE1 B:TRP116 3.2 11.6 1.0
N B:SER114 3.2 11.1 1.0
CA B:TYR113 3.6 10.3 1.0
CB B:TYR113 3.9 11.6 1.0
OG B:SER114 3.9 13.7 0.4
C B:TYR113 3.9 10.5 1.0
CD1 B:TYR113 3.9 11.9 1.0
CD1 B:TRP116 4.0 10.0 1.0
O B:SER114 4.0 10.6 1.0
CE2 B:TRP116 4.2 11.3 1.0
CA B:SER114 4.2 11.0 0.6
CA B:SER114 4.3 10.9 0.4
CB B:SER114 4.3 12.6 0.6
OH B:TYR137 4.3 14.1 1.0
CG B:TYR113 4.4 10.1 1.0
CZ2 B:TRP116 4.5 12.0 1.0
O B:TRP112 4.5 18.3 1.0
C B:SER114 4.6 10.0 1.0
CB B:SER114 4.6 11.7 0.4
OG B:SER114 4.7 16.7 0.6
N B:TYR113 4.8 11.9 1.0
O B:HOH319 4.8 14.2 1.0

Chlorine binding site 3 out of 15 in 5gwf

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Chlorine binding site 3 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:18.9
occ:1.00
 O B:HOH438 3.0 15.0 1.0
O B:HOH326 3.1 14.2 1.0
N B:LEU61 3.3 12.4 1.0
O A:HOH458 3.3 18.8 0.5
O B:HOH453 3.6 29.8 0.6
CA B:VAL60 3.8 12.3 1.0
CG1 B:VAL60 3.8 15.1 1.0
C B:VAL60 4.0 12.4 1.0
CG B:LEU61 4.0 12.9 1.0
CB B:LEU61 4.1 13.1 1.0
CD A:LYS20 4.1 14.8 1.0
CA B:LEU61 4.3 12.4 1.0
CB B:VAL60 4.3 12.9 1.0
CG A:LYS20 4.4 12.3 1.0
O B:HOH453 4.4 28.5 0.4
CE A:LYS20 4.4 15.6 1.0
CD1 B:LEU61 4.5 13.1 1.0
O B:HOH373 4.5 14.9 1.0
O B:ILE59 4.5 12.1 1.0
N B:THR50 4.7 10.8 1.0
CB A:LYS20 4.8 10.9 1.0
CG2 B:VAL60 4.9 15.3 1.0
NZ A:LYS20 4.9 15.4 1.0
CA B:ASN49 4.9 10.6 1.0
OG1 B:THR50 5.0 13.3 1.0
N B:VAL60 5.0 11.1 1.0
O A:HOH349 5.0 21.7 1.0

Chlorine binding site 4 out of 15 in 5gwf

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Chlorine binding site 4 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:25.7
occ:1.00
 O C:HOH466 3.0 22.8 1.0
O C:HOH459 3.1 18.9 0.5
O B:HOH425 3.1 18.1 1.0
N B:ASP17 3.2 13.7 1.0
NZ C:LYS64 3.3 22.8 1.0
N B:PHE16 3.5 13.1 1.0
CG B:ASP17 3.6 21.4 1.0
CB B:ASP17 3.6 18.0 1.0
OD2 B:ASP17 3.7 24.6 1.0
CA B:GLY15 3.8 12.5 1.0
C B:GLY15 3.8 12.4 1.0
OG1 C:THR46 3.9 16.2 1.0
O C:HOH409 3.9 32.7 1.0
CA B:ASP17 4.0 16.6 1.0
OD1 B:ASP17 4.0 24.6 1.0
C B:PHE16 4.2 13.6 1.0
CA B:PHE16 4.3 14.8 1.0
O B:HOH354 4.5 27.7 1.0
O3 B:GOL208 4.5 17.2 1.0
CB B:PHE16 4.6 17.0 1.0
O B:GLY15 4.6 13.2 1.0
O C:HOH338 4.6 17.9 1.0
N B:GLY15 4.7 12.3 1.0
CG2 C:THR46 4.7 16.4 1.0
O B:HOH356 4.7 18.2 1.0
CB C:THR46 4.7 15.6 1.0
CE C:LYS64 4.8 23.5 1.0
O B:HOH359 4.8 19.4 1.0
N B:VAL18 4.9 12.7 1.0
C3 B:GOL208 4.9 19.0 1.0

Chlorine binding site 5 out of 15 in 5gwf

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Chlorine binding site 5 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:27.0
occ:1.00
 O B:HOH313 3.2 26.3 1.0
N B:LYS123 3.2 17.0 1.0
O B:HOH309 3.7 25.3 0.5
CA B:TYR122 3.9 12.7 1.0
CD2 B:TYR122 3.9 17.7 1.0
CB B:LYS123 3.9 18.3 1.0
C B:TYR122 4.1 15.2 1.0
CA B:LYS123 4.1 17.5 1.0
CB B:TYR122 4.3 13.2 1.0
CG B:TYR122 4.5 14.5 1.0
OH B:TYR156 4.6 27.9 1.0
O B:LYS123 4.7 19.6 1.0
CE2 B:TYR122 4.8 18.8 1.0
O B:VAL121 4.8 17.6 1.0
C B:LYS123 5.0 16.4 1.0

Chlorine binding site 6 out of 15 in 5gwf

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Chlorine binding site 6 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl206

b:29.3
occ:1.00
 O C:HOH363 2.9 18.6 0.5
O B:HOH395 2.9 26.9 1.0
NH2 B:ARG161 3.2 16.0 1.0
ND1 B:HIS175 3.6 13.3 1.0
CB B:HIS175 3.7 11.2 1.0
CG2 B:THR177 3.8 15.8 1.0
CG B:HIS175 3.8 11.1 1.0
NE B:ARG161 4.0 14.2 1.0
CZ B:ARG161 4.1 14.8 1.0
OD2 B:ASP38 4.2 15.5 1.0
CE1 B:HIS175 4.5 10.7 1.0
O C:HOH357 4.7 23.0 1.0
O B:HOH375 4.7 24.7 1.0
CA C:ASP96 4.8 14.2 1.0
O C:HOH407 4.8 27.5 1.0
CD2 B:HIS175 4.8 11.6 1.0
CG B:GLU40 4.9 14.8 1.0
NZ C:LYS43 5.0 33.2 1.0
O B:HOH487 5.0 36.4 1.0

Chlorine binding site 7 out of 15 in 5gwf

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Chlorine binding site 7 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl207

b:26.7
occ:1.00
 N B:GLY85 3.3 10.4 1.0
N B:TYR108 3.3 10.1 1.0
O B:HOH417 3.5 13.9 1.0
CA B:PRO107 3.8 9.9 1.0
O B:HOH385 3.9 22.8 0.5
CA B:THR84 3.9 11.1 1.0
C B:PRO107 4.0 9.8 1.0
CA B:GLY85 4.0 10.7 1.0
C B:THR84 4.0 10.2 1.0
CB B:TYR108 4.1 11.4 1.0
CA B:TYR108 4.3 11.7 1.0
CB B:PRO107 4.4 11.7 1.0
CB B:THR84 4.4 12.4 1.0
OG B:SER54 4.5 18.0 0.5
OG B:SER54 4.6 14.4 0.5
O B:ALA83 4.8 12.6 1.0
O B:VAL106 4.8 12.1 1.0
CG2 B:VAL87 4.8 10.0 1.0
CG2 B:THR84 4.9 14.4 1.0
O B:HOH472 5.0 38.3 1.0
C B:GLY85 5.0 10.7 1.0

Chlorine binding site 8 out of 15 in 5gwf

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Chlorine binding site 8 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:16.4
occ:1.00
 O C:HOH329 3.0 22.1 1.0
O C:HOH308 3.1 15.4 1.0
NE1 C:TRP116 3.2 12.3 1.0
N C:SER114 3.2 10.8 1.0
CA C:TYR113 3.5 10.5 1.0
OG C:SER114 3.7 17.2 0.4
CB C:TYR113 3.9 11.1 1.0
C C:TYR113 3.9 10.7 1.0
CD1 C:TYR113 3.9 10.9 1.0
O C:HOH332 4.0 33.3 1.0
O C:SER114 4.0 10.4 1.0
CD1 C:TRP116 4.1 11.1 1.0
CE2 C:TRP116 4.1 12.0 1.0
CA C:SER114 4.2 11.4 0.6
CA C:SER114 4.2 11.5 0.4
CB C:SER114 4.3 13.2 0.6
CG C:TYR113 4.3 10.9 1.0
OH C:TYR137 4.4 16.5 1.0
CZ2 C:TRP116 4.4 12.5 1.0
CB C:SER114 4.5 13.4 0.4
O C:TRP112 4.5 17.6 1.0
C C:SER114 4.5 10.2 1.0
OG C:SER114 4.7 15.3 0.6
O C:HOH316 4.8 13.8 1.0
N C:TYR113 4.8 11.7 1.0
CE1 C:TYR113 5.0 11.6 1.0

Chlorine binding site 9 out of 15 in 5gwf

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Chlorine binding site 9 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:30.3
occ:1.00
 O C:HOH319 3.1 22.5 1.0
O C:HOH334 3.2 28.0 1.0
N C:LYS123 3.3 16.0 1.0
NH1 C:ARG120 3.5 52.7 1.0
CA C:TYR122 3.8 12.5 1.0
CD2 C:TYR122 3.9 16.2 1.0
CB C:LYS123 4.0 20.3 1.0
C C:TYR122 4.0 14.7 1.0
NH2 C:ARG120 4.1 44.6 1.0
CA C:LYS123 4.2 17.2 1.0
CZ C:ARG120 4.2 38.5 1.0
CB C:TYR122 4.2 13.8 1.0
CG C:TYR122 4.5 13.3 1.0
OH C:TYR156 4.5 21.7 1.0
O C:VAL121 4.7 15.4 1.0
O C:LYS123 4.7 16.6 1.0
CE2 C:TYR122 4.8 15.6 1.0
C C:LYS123 5.0 14.0 1.0

Chlorine binding site 10 out of 15 in 5gwf

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Chlorine binding site 10 out of 15 in the Frac with Glcnac(6S) Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Frac with Glcnac(6S) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:20.6
occ:0.60
 CL C:CL203 0.0 20.6 0.6
CL C:CL203 1.8 23.0 0.4
N C:GLY85 3.3 11.4 1.0
N C:TYR108 3.3 11.9 1.0
O C:HOH393 3.5 21.0 1.0
O C:HOH446 3.6 41.4 1.0
CA C:PRO107 3.7 11.3 1.0
CA C:THR84 3.9 11.4 1.0
C C:PRO107 4.0 11.8 1.0
CA C:GLY85 4.0 11.8 1.0
C C:THR84 4.0 13.6 1.0
CB C:TYR108 4.2 11.8 1.0
CB C:PRO107 4.3 10.8 1.0
O C:HOH455 4.3 36.5 1.0
CA C:TYR108 4.4 12.1 1.0
CB C:THR84 4.5 13.1 1.0
O C:VAL106 4.6 12.6 1.0
OG C:SER54 4.7 19.3 0.5
NH1 C:ARG53 4.8 22.2 0.5
CG2 C:VAL87 4.8 13.2 1.0
C C:GLY85 4.9 11.2 1.0
O C:ALA83 4.9 13.8 1.0
CG2 C:THR84 4.9 15.0 1.0
N C:PRO107 4.9 10.4 1.0

Reference:

K.Tanaka, J.M.M.Caaveiro, K.Morante, K.Tsumoto. Haemolytic Actinoporins Interact with Carbohydrates Using Their Lipid-Binding Module Philos. Trans. R. Soc. V. 372 2017LOND., B, Biol. Sci..
ISSN: ESSN 1471-2970
PubMed: 28630155
DOI: 10.1098/RSTB.2016.0216
Page generated: Fri Jul 26 08:37:09 2024

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