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Chlorine in PDB 6kok: Crystal Structure of SNX11/SNX10-Pxe Chimera

Protein crystallography data

The structure of Crystal Structure of SNX11/SNX10-Pxe Chimera, PDB code: 6kok was solved by T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.53 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.103, 47.910, 87.309, 90.00, 94.39, 90.00
R / Rfree (%) 20.4 / 25

Other elements in 6kok:

The structure of Crystal Structure of SNX11/SNX10-Pxe Chimera also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of SNX11/SNX10-Pxe Chimera (pdb code 6kok). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 13 binding sites of Chlorine where determined in the Crystal Structure of SNX11/SNX10-Pxe Chimera, PDB code: 6kok:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 6kok

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Chlorine binding site 1 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:12.1
occ:1.00
 OG A:SER34 3.1 5.0 0.6
N A:GLY30 3.2 4.7 1.0
OG A:SER34 3.3 6.4 0.4
O A:HOH327 3.4 14.1 1.0
CB A:SER34 3.6 5.1 0.4
CB A:SER34 3.6 4.8 0.6
CE2 A:PHE89 3.8 2.9 1.0
CA A:GLY30 3.9 14.7 1.0
CA A:GLU29 4.1 5.5 1.0
C A:GLU29 4.1 7.0 1.0
CG1 A:VAL26 4.2 7.2 1.0
CG A:GLU29 4.2 11.3 1.0
CD2 A:PHE89 4.6 4.6 1.0
CG2 A:THR91 4.6 6.1 1.0
CB A:GLU29 4.7 9.6 1.0
CZ A:PHE89 4.7 2.1 1.0
C A:GLY30 4.8 13.8 1.0

Chlorine binding site 2 out of 13 in 6kok

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Chlorine binding site 2 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:7.5
occ:1.00
 OG A:SER131 2.9 0.8 1.0
CB A:SER131 3.9 1.1 1.0
CB A:PRO133 4.1 3.8 1.0
CG A:GLU134 4.2 4.5 1.0
CG A:PRO133 4.3 5.0 1.0
CD A:GLU134 4.4 5.8 1.0
CD A:PRO133 4.5 3.7 1.0
N A:GLU134 4.7 1.2 1.0
OE1 A:GLU134 4.7 11.5 1.0
OE2 A:GLU134 4.8 2.7 1.0

Chlorine binding site 3 out of 13 in 6kok

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Chlorine binding site 3 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:18.4
occ:1.00
 O A:HOH342 2.8 3.1 1.0
O A:HOH365 2.8 7.9 1.0
O A:HOH382 2.9 11.4 1.0
O A:THR53 3.0 5.0 1.0
CA A:ALA155 3.4 6.5 1.0
CB A:ALA155 3.5 3.0 1.0
CA A:SER54 3.6 3.2 1.0
CB A:SER54 3.7 6.6 1.0
C A:THR53 4.0 5.0 1.0
CB A:ALA51 4.0 7.1 1.0
N A:ALA155 4.0 3.0 1.0
CD2 A:PHE154 4.1 4.2 1.0
N A:SER54 4.3 5.2 1.0
CE2 A:PHE154 4.4 9.8 1.0
C A:ALA155 4.5 5.0 1.0
N A:CYS55 4.6 4.8 1.0
C A:PHE154 4.6 5.3 1.0
O A:ALA155 4.6 9.0 1.0
O A:PHE154 4.6 3.8 1.0
C A:SER54 4.7 9.6 1.0
O A:GLN127 4.9 3.4 1.0

Chlorine binding site 4 out of 13 in 6kok

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Chlorine binding site 4 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:13.3
occ:1.00
 N A:ARG61 3.0 1.2 1.0
NH2 A:ARG59 3.0 11.7 1.0
NE A:ARG59 3.2 21.6 1.0
CL A:CL208 3.3 14.1 1.0
CB A:ARG61 3.4 8.6 1.0
O A:HOH391 3.4 11.6 1.0
CZ A:ARG59 3.5 19.2 1.0
N A:TYR60 3.6 5.5 1.0
CA A:ARG61 3.8 3.2 1.0
CB A:TYR60 3.8 8.9 1.0
C A:TYR60 3.9 4.7 1.0
CA A:TYR60 4.0 7.3 1.0
CB A:ARG59 4.0 4.9 1.0
C A:ARG59 4.3 1.3 1.0
CD A:ARG59 4.4 14.7 1.0
CG A:ARG59 4.4 11.8 1.0
CD2 A:TYR60 4.6 6.4 1.0
CG A:TYR60 4.7 9.2 1.0
CA A:ARG59 4.8 2.5 1.0
NH1 A:ARG59 4.8 15.4 1.0
CG A:ARG61 4.8 8.6 1.0

Chlorine binding site 5 out of 13 in 6kok

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Chlorine binding site 5 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:16.9
occ:1.00
 OG A:SER54 2.8 6.1 1.0
O A:LEU126 2.8 3.9 1.0
O A:ILE40 2.8 3.2 1.0
O A:SER54 3.2 8.2 1.0
C A:SER54 3.5 9.6 1.0
N A:LEU42 3.5 3.5 1.0
C A:ILE40 3.6 7.4 1.0
CB A:LEU42 3.6 4.2 1.0
CB A:SER54 3.7 6.6 1.0
CG2 A:ILE40 3.7 0.7 1.0
N A:CYS55 3.9 4.8 1.0
C A:LEU126 3.9 4.2 1.0
C A:PHE41 4.0 5.6 1.0
CA A:PHE41 4.0 3.1 1.0
CA A:CYS55 4.1 9.4 0.3
CA A:CYS55 4.1 11.3 0.7
N A:PHE41 4.1 3.8 1.0
N A:VAL56 4.2 2.3 1.0
CA A:SER54 4.2 3.2 1.0
CG2 A:VAL56 4.2 5.4 1.0
CB A:ILE40 4.2 3.6 1.0
CA A:LEU42 4.2 7.7 1.0
CA A:LEU126 4.5 2.2 1.0
C A:CYS55 4.5 6.8 1.0
CA A:ILE40 4.5 3.5 1.0
CB A:LEU126 4.6 1.7 1.0
CG1 A:VAL56 4.7 2.9 1.0
O A:PHE41 4.8 7.3 1.0
CD2 A:LEU126 4.8 0.8 1.0
CG A:LEU42 4.9 9.0 1.0
N A:SER54 4.9 5.2 1.0
CB A:VAL56 4.9 3.8 1.0
CD1 A:LEU42 4.9 7.9 1.0
N A:GLN127 5.0 1.2 1.0

Chlorine binding site 6 out of 13 in 6kok

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Chlorine binding site 6 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:17.2
occ:1.00
 O A:HOH337 3.0 10.1 1.0
N A:GLN129 3.2 3.2 1.0
CD1 A:PHE154 3.3 6.0 1.0
CD1 A:LEU130 3.3 3.7 0.4
O A:HOH398 3.5 9.5 1.0
CD2 A:LEU130 3.7 4.0 0.6
CB A:SER128 3.8 4.5 1.0
N A:LEU130 3.8 3.5 1.0
CA A:GLN129 3.9 5.5 1.0
C A:GLN129 3.9 4.2 1.0
CG A:PHE154 4.0 3.7 1.0
CB A:PHE154 4.0 2.7 1.0
CE1 A:PHE154 4.1 7.6 1.0
CB A:GLN129 4.1 5.3 1.0
CA A:SER128 4.1 2.4 1.0
C A:SER128 4.1 4.1 1.0
CG A:LEU130 4.2 2.9 0.6
OG A:SER128 4.4 2.6 1.0
O A:GLN129 4.6 4.2 1.0
CA A:LEU130 4.6 4.0 0.4
CA A:LEU130 4.6 3.9 0.6
CG A:LEU130 4.7 3.8 0.4
CA A:PHE154 4.9 2.2 1.0
CB A:LEU130 5.0 4.3 0.4
CB A:LEU130 5.0 4.5 0.6
O A:ALA150 5.0 5.9 1.0

Chlorine binding site 7 out of 13 in 6kok

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Chlorine binding site 7 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:13.5
occ:1.00
 O A:HOH367 3.0 12.7 1.0
N A:HIS162 3.3 9.4 1.0
N A:GLU160 3.3 14.5 1.0
N A:HIS161 3.3 16.6 1.0
CG A:GLU160 3.7 24.5 1.0
C A:GLU160 3.8 15.4 1.0
CD1 A:LEU159 3.9 17.4 1.0
CD2 A:HIS163 3.9 11.9 1.0
CB A:HIS162 3.9 13.1 1.0
CA A:GLU160 4.0 7.5 1.0
CA A:HIS162 4.1 15.6 1.0
CA A:HIS161 4.1 14.8 1.0
C A:HIS161 4.2 14.9 1.0
CG A:HIS162 4.3 12.4 1.0
C A:LEU159 4.3 9.3 1.0
CA A:LEU159 4.4 5.4 1.0
N A:HIS163 4.4 11.1 1.0
CB A:GLU160 4.5 12.7 1.0
CD2 A:HIS162 4.5 23.8 1.0
C A:HIS162 4.6 9.5 1.0
O A:ASN158 4.6 10.7 1.0
O A:GLU160 4.7 8.0 1.0
NE2 A:HIS163 4.8 12.4 1.0
CG A:HIS163 4.8 18.4 1.0
CD A:GLU160 4.8 34.6 1.0
CG A:LEU159 5.0 6.2 1.0
OE1 A:GLU160 5.0 41.0 1.0

Chlorine binding site 8 out of 13 in 6kok

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Chlorine binding site 8 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:14.1
occ:1.00
 O A:HOH357 2.6 2.9 1.0
O A:VAL36 2.7 5.2 1.0
N A:TYR60 2.9 5.5 1.0
O A:HOH391 3.1 11.6 1.0
CL A:CL204 3.3 13.3 1.0
CB A:TYR60 3.3 8.9 1.0
C A:VAL36 3.6 4.0 1.0
CB A:ARG59 3.7 4.9 1.0
CA A:TYR60 3.7 7.3 1.0
CA A:ARG59 3.8 2.5 1.0
CE1 A:TYR38 3.8 3.9 1.0
C A:ARG59 3.8 1.3 1.0
CB A:VAL36 4.0 6.5 1.0
CA A:VAL36 4.2 4.2 1.0
N A:VAL36 4.3 2.2 1.0
NH1 A:ARG99 4.4 7.0 1.0
O A:HOH326 4.5 3.3 1.0
CD1 A:TYR38 4.6 1.7 1.0
CG1 A:VAL36 4.6 2.5 1.0
OH A:TYR38 4.6 3.6 1.0
NE A:ARG59 4.7 21.6 1.0
N A:ASP37 4.7 2.0 1.0
CZ A:TYR38 4.7 2.4 1.0
N A:ARG61 4.7 1.2 1.0
CG A:TYR60 4.7 9.2 1.0
C A:TYR60 4.8 4.7 1.0
CA A:ASP37 4.9 4.8 1.0
O A:ARG59 5.0 2.3 1.0

Chlorine binding site 9 out of 13 in 6kok

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Chlorine binding site 9 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:5.4
occ:1.00
 NE B:ARG59 3.2 1.9 1.0
O B:HOH328 3.2 8.2 1.0
N B:ARG61 3.3 4.8 1.0
NH2 B:ARG59 3.5 5.0 1.0
N B:TYR60 3.5 4.8 1.0
CZ B:ARG59 3.8 4.5 1.0
CB B:ARG59 3.8 2.8 1.0
CB B:ARG61 3.9 12.6 1.0
CB B:TYR60 3.9 2.2 1.0
O B:HOH363 4.0 6.4 1.0
CA B:TYR60 4.0 3.6 1.0
C B:TYR60 4.1 6.4 1.0
CG B:ARG59 4.1 3.9 1.0
CA B:ARG61 4.2 7.0 1.0
CD B:ARG59 4.2 4.5 1.0
C B:ARG59 4.3 5.0 1.0
CB B:TYR35 4.3 8.5 1.0
CA B:ARG59 4.6 3.4 1.0
CG B:TYR35 5.0 8.8 1.0

Chlorine binding site 10 out of 13 in 6kok

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Chlorine binding site 10 out of 13 in the Crystal Structure of SNX11/SNX10-Pxe Chimera


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 SNX11/SNX10-Pxe Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:12.9
occ:1.00
 NA B:NA206 2.6 15.2 1.0
OG B:SER131 3.0 3.9 1.0
CB B:SER131 3.7 5.1 1.0
CB B:PRO133 4.1 7.8 1.0
CG B:PRO133 4.1 5.2 1.0
CG B:GLU134 4.4 4.4 1.0
O B:HOH322 4.4 12.7 1.0
CD B:PRO133 4.5 3.5 1.0
CD B:GLU134 4.7 12.2 1.0
N B:GLU134 4.9 2.2 1.0
OE2 B:GLU134 4.9 10.2 1.0

Reference:

T.Xu, Q.Gan, B.Wu, M.Yin, J.Xu, X.Shu, J.Liu. Molecular Basis For Pi(3,5)P2RECOGNITION By SNX11, A Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation. J.Mol.Biol. V. 432 4750 2020.
ISSN: ESSN 1089-8638
PubMed: 32561432
DOI: 10.1016/J.JMB.2020.06.010
Page generated: Sun Jul 28 02:31:00 2024

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