Atomistry » Chlorine » PDB 5grn-5h4z » 5gwf
Atomistry »
  Chlorine »
    PDB 5grn-5h4z »
      5gwf »

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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Go back to Chlorine Binding Sites List in 5gwf
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy