Chlorine in PDB 6rlo: Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop

Protein crystallography data

The structure of Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop, PDB code: 6rlo was solved by V.Neviani, N.M.Pearce, W.Pos, R.Schotte, H.Spits, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.80 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.776, 89.858, 91.533, 71.12, 89.59, 85.96
R / Rfree (%) 25.4 / 28.7

Other elements in 6rlo:

The structure of Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop also contains other interesting chemical elements:

Sodium (Na) 7 atoms
Potassium (K) 1 atom

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop (pdb code 6rlo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop, PDB code: 6rlo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 6rlo

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Chlorine binding site 1 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:27.6
occ:1.00
 O A:HOH407 3.2 20.9 1.0
N A:TRP52 3.3 21.1 1.0
O A:HOH415 3.5 19.5 1.0
N B:PHE114 3.6 19.7 1.0
CA B:THR113 3.7 21.8 1.0
CA A:GLU51 3.8 20.9 1.0
CB A:TRP52 3.9 21.7 1.0
CD2 B:PHE114 3.9 18.1 1.0
CB B:THR113 3.9 22.8 1.0
CG2 B:THR113 4.0 22.0 1.0
C A:GLU51 4.1 20.1 1.0
C B:THR113 4.2 20.9 1.0
CG A:GLU51 4.2 23.0 1.0
CA A:TRP52 4.2 21.2 1.0
CB B:PHE114 4.4 18.2 1.0
O A:LEU50 4.5 18.9 1.0
CB A:GLU51 4.6 21.8 1.0
CA B:PHE114 4.6 18.4 1.0
O A:TRP52 4.6 22.4 1.0
CG B:PHE114 4.7 17.8 1.0
O B:PHE114 4.8 18.0 1.0
N B:THR113 4.8 23.0 1.0
CE2 B:PHE114 4.9 18.3 1.0
N A:GLU51 4.9 19.8 1.0
O B:SER112 4.9 22.0 1.0
C A:TRP52 5.0 22.1 1.0

Chlorine binding site 2 out of 11 in 6rlo

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Chlorine binding site 2 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:40.9
occ:1.00
 O B:PRO135 2.8 22.7 1.0
O A:PRO138 3.2 27.1 1.0
N A:ALA140 3.3 29.9 1.0
C B:PRO135 3.8 24.4 1.0
CB A:ALA140 3.9 34.4 1.0
CA A:LEU139 3.9 26.5 1.0
N B:SER137 4.0 29.4 1.0
C A:PRO138 4.0 26.5 1.0
C A:LEU139 4.1 26.0 1.0
C B:PRO136 4.2 27.4 1.0
CA A:ALA140 4.2 33.3 1.0
CA B:SER137 4.3 30.4 1.0
N B:PRO135 4.3 23.9 1.0
N A:LEU139 4.4 26.2 1.0
O B:PRO136 4.4 25.2 1.0
CD B:PRO135 4.5 24.9 1.0
O B:HOH423 4.5 40.9 1.0
CA B:PRO135 4.5 24.6 1.0
CB B:SER137 4.6 31.5 1.0
CB B:PHE134 4.6 22.3 1.0
CB B:PRO135 4.7 24.4 1.0
C B:PHE134 4.7 22.2 1.0
N B:PRO136 4.7 25.5 1.0
CA B:PRO136 4.7 25.9 1.0
O A:ALA140 4.8 36.1 1.0
CA B:PHE134 4.9 22.5 1.0
CD2 A:LEU139 5.0 25.2 1.0

Chlorine binding site 3 out of 11 in 6rlo

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Chlorine binding site 3 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:42.4
occ:1.00
 OG1 B:THR188 2.7 24.9 1.0
O B:HOH404 2.8 21.7 1.0
OD1 B:ASN154 3.0 21.9 1.0
CE1 A:HIS179 3.2 22.2 1.0
OG B:SER190 3.2 21.1 1.0
NE2 A:HIS179 3.3 22.7 1.0
C B:TYR189 3.4 23.7 1.0
O B:THR188 3.4 21.0 1.0
O B:TYR189 3.5 23.0 1.0
N B:SER190 3.6 23.4 1.0
C B:THR188 3.6 23.3 1.0
CG B:ASN154 3.7 21.2 1.0
CA B:ASN154 3.8 21.2 1.0
CB B:THR188 3.8 24.0 1.0
CA B:TYR189 3.9 23.8 1.0
N B:TYR189 3.9 23.4 1.0
CB B:SER190 4.0 22.3 1.0
N B:ASN154 4.1 20.6 1.0
ND1 A:HIS179 4.1 23.5 1.0
CB B:ASP183 4.1 28.1 1.0
CD2 A:HIS179 4.2 22.7 1.0
CA B:THR188 4.3 23.0 1.0
CA B:SER190 4.3 22.0 1.0
CB B:ASN154 4.3 20.5 1.0
OD1 B:ASP186 4.3 28.6 1.0
OG1 B:THR180 4.5 23.5 1.0
ND2 B:ASN154 4.6 22.4 1.0
CG A:HIS179 4.7 23.6 1.0
CG B:ASP183 4.8 27.6 1.0
OD1 B:ASP183 4.8 28.5 1.0
N B:THR188 4.8 23.1 1.0
C B:ASN154 4.9 21.4 1.0

Chlorine binding site 4 out of 11 in 6rlo

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Chlorine binding site 4 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl301

b:42.4
occ:1.00
 N I:LEU173 3.1 33.9 1.0
OG A:SER64 3.2 35.1 1.0
N I:GLU174 3.4 38.6 1.0
CG I:GLU174 3.4 43.6 1.0
CB A:SER64 3.7 33.4 1.0
CA I:LEU173 3.9 34.2 1.0
CA I:VAL172 3.9 32.1 1.0
CB I:VAL172 4.0 31.2 1.0
CB I:LEU173 4.0 33.9 1.0
C I:VAL172 4.0 33.9 1.0
OE2 I:GLU174 4.1 44.7 1.0
CB I:GLU174 4.1 41.2 1.0
C I:LEU173 4.1 36.1 1.0
CD I:GLU174 4.2 45.2 1.0
CA I:GLU174 4.4 40.2 1.0
CG1 I:VAL172 4.7 30.8 1.0
CG I:LEU173 4.8 34.7 1.0

Chlorine binding site 5 out of 11 in 6rlo

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Chlorine binding site 5 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:34.0
occ:1.00
 O C:HOH403 3.2 25.6 1.0
N C:TRP52 3.2 21.5 1.0
O C:HOH409 3.2 21.4 1.0
N D:PHE114 3.5 19.9 1.0
CA D:THR113 3.6 21.1 1.0
CA C:GLU51 3.7 22.8 1.0
CD2 D:PHE114 3.7 21.0 1.0
CB C:TRP52 3.9 22.4 1.0
C C:GLU51 3.9 21.0 1.0
CB D:THR113 4.0 21.1 1.0
C D:THR113 4.1 20.7 1.0
CA C:TRP52 4.1 21.5 1.0
CG2 D:THR113 4.1 20.8 1.0
CG C:GLU51 4.3 24.8 1.0
CB D:PHE114 4.3 20.9 1.0
O C:LEU50 4.4 24.5 1.0
CA D:PHE114 4.4 20.3 1.0
CG D:PHE114 4.5 20.2 1.0
CB C:GLU51 4.5 23.6 1.0
O C:TRP52 4.6 22.2 1.0
CE2 D:PHE114 4.7 21.1 1.0
N C:GLU51 4.8 23.2 1.0
O D:PHE114 4.8 20.3 1.0
N D:THR113 4.8 22.2 1.0
O D:SER112 4.8 23.8 1.0
C C:TRP52 4.9 22.4 1.0
C C:LEU50 4.9 23.5 1.0

Chlorine binding site 6 out of 11 in 6rlo

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Chlorine binding site 6 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:43.6
occ:1.00
 N C:SER70 3.0 30.2 1.0
CB C:SER70 3.3 29.4 1.0
OG C:SER70 3.4 26.7 1.0
N C:ASP69 3.4 30.9 1.0
CB C:ALA68 3.7 29.1 1.0
CA C:SER70 3.7 29.8 1.0
C C:ASP69 3.9 31.0 1.0
CA C:ASP69 3.9 30.5 1.0
C C:ALA68 4.0 30.2 1.0
CB C:ASP69 4.0 31.0 1.0
O C:HOH409 4.1 21.4 1.0
OE2 C:GLU51 4.1 29.6 1.0
CA C:ALA68 4.3 29.1 1.0
O C:ALA68 4.8 31.0 1.0

Chlorine binding site 7 out of 11 in 6rlo

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Chlorine binding site 7 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:44.4
occ:1.00
 OG1 D:THR188 2.8 27.0 1.0
O D:HOH401 2.9 23.3 1.0
OD1 D:ASN154 3.1 16.3 1.0
OG D:SER190 3.2 21.1 1.0
C D:TYR189 3.2 25.4 1.0
CE1 C:HIS179 3.3 21.3 1.0
O D:TYR189 3.4 25.3 1.0
O D:THR188 3.4 22.5 1.0
N D:SER190 3.4 24.2 1.0
C D:THR188 3.5 24.6 1.0
NE2 C:HIS179 3.6 21.7 1.0
CA D:TYR189 3.7 24.7 1.0
N D:TYR189 3.8 23.9 1.0
CG D:ASN154 3.8 18.1 1.0
CA D:ASN154 3.8 19.3 1.0
CB D:THR188 3.8 26.7 1.0
CB D:SER190 3.9 22.2 1.0
ND1 C:HIS179 4.1 22.1 1.0
N D:ASN154 4.1 19.5 1.0
CA D:SER190 4.2 22.6 1.0
CB D:ASP183 4.2 22.7 1.0
CA D:THR188 4.3 25.1 1.0
CB D:ASN154 4.4 17.7 1.0
OG1 D:THR180 4.4 25.8 1.0
OD1 D:ASP186 4.4 28.0 1.0
CD2 C:HIS179 4.5 22.4 1.0
ND2 D:ASN154 4.6 18.4 1.0
CG C:HIS179 4.8 23.1 1.0
OD1 D:ASP183 4.9 22.3 1.0
CG D:ASP183 4.9 21.4 1.0
N D:THR188 4.9 24.8 1.0
C D:ASN154 4.9 19.2 1.0

Chlorine binding site 8 out of 11 in 6rlo

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Chlorine binding site 8 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:42.3
occ:1.00
 ND2 D:ASN22 2.8 19.8 1.0
O D:THR5 2.9 26.1 1.0
CB D:SER7 3.4 25.9 1.0
C D:GLN6 3.5 24.1 1.0
N D:SER7 3.5 24.1 1.0
C D:THR5 3.6 26.4 1.0
CG D:ASN22 3.7 21.5 1.0
CA D:GLN6 3.8 24.1 1.0
O D:GLN6 3.8 23.4 1.0
CD D:LYS24 3.8 35.5 1.0
CB D:ASN22 3.9 22.0 1.0
N D:GLN6 4.0 25.8 1.0
CA D:SER7 4.1 25.5 1.0
O D:ASN22 4.1 22.3 1.0
N D:LYS24 4.1 28.7 1.0
C D:ASN22 4.2 22.1 1.0
CB D:LYS24 4.3 32.5 1.0
CG D:LYS24 4.3 33.8 1.0
CG2 D:THR5 4.4 27.2 1.0
N D:CYS23 4.4 22.7 1.0
CA D:CYS23 4.4 25.0 1.0
C D:CYS23 4.5 25.9 1.0
CB D:THR5 4.6 28.0 1.0
OG D:SER7 4.6 27.3 1.0
NZ B:LYS161 4.6 32.8 1.0
CE D:LYS24 4.7 37.2 1.0
CA D:THR5 4.7 26.6 1.0
CA D:ASN22 4.7 22.2 1.0
CA D:LYS24 4.9 30.2 1.0
OD1 D:ASN22 4.9 22.8 1.0

Chlorine binding site 9 out of 11 in 6rlo

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Chlorine binding site 9 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:30.7
occ:1.00
 N E:TRP52 3.2 31.1 1.0
N F:PHE114 3.3 31.0 1.0
CA F:THR113 3.5 31.3 1.0
CD2 F:PHE114 3.7 28.2 1.0
CB E:TRP52 3.8 32.9 1.0
CA E:GLU51 3.8 31.2 1.0
CB F:THR113 3.8 32.7 1.0
C F:THR113 3.9 31.3 1.0
C E:GLU51 4.0 31.1 1.0
CG2 F:THR113 4.0 32.6 1.0
CA E:TRP52 4.1 32.1 1.0
CB F:PHE114 4.2 29.3 1.0
CA F:PHE114 4.3 30.0 1.0
CG E:GLU51 4.4 33.4 1.0
CG F:PHE114 4.4 29.2 1.0
O E:LEU50 4.4 29.9 1.0
CE2 F:PHE114 4.6 27.1 1.0
N F:THR113 4.6 31.5 1.0
O F:PHE114 4.7 31.8 1.0
CB E:GLU51 4.7 31.2 1.0
O F:SER112 4.7 32.6 1.0
O E:TRP52 4.7 32.2 1.0
N E:GLU51 4.8 30.1 1.0
C E:TRP52 5.0 31.5 1.0
C F:SER112 5.0 31.3 1.0

Chlorine binding site 10 out of 11 in 6rlo

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Chlorine binding site 10 out of 11 in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop


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 AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl301

b:32.9
occ:1.00
 O G:HOH410 3.3 14.0 1.0
N H:PHE114 3.3 28.5 1.0
N G:TRP52 3.4 27.3 1.0
CA H:THR113 3.5 28.5 1.0
CB H:THR113 3.8 29.7 1.0
CD2 H:PHE114 3.8 29.2 1.0
CA G:GLU51 3.9 26.3 1.0
CG2 H:THR113 4.0 28.9 1.0
C H:THR113 4.0 28.6 1.0
CB G:TRP52 4.0 28.6 1.0
C G:GLU51 4.2 25.7 1.0
CB H:PHE114 4.3 28.2 1.0
CA G:TRP52 4.3 27.1 1.0
CA H:PHE114 4.4 27.8 1.0
CG G:GLU51 4.4 24.5 1.0
O G:LEU50 4.5 27.5 1.0
CG H:PHE114 4.5 29.5 1.0
O H:PHE114 4.6 26.2 1.0
N H:THR113 4.7 29.0 1.0
CB G:GLU51 4.7 25.0 1.0
O G:TRP52 4.8 27.9 1.0
CE2 H:PHE114 4.8 28.7 1.0
O H:SER112 4.8 29.1 1.0
N G:GLU51 4.9 26.6 1.0

Reference:

V.Neviani, W.Pos, R.Schotte, K.Wagner, D.M.Go, C.Fatmawati, M.Kedde, Y.B.Claassen, L.Kroon-Batenburg, M.Lutz, E.M.E.Verdegaal, S.H.Van Der Burg, H.Spits, P.Gros. Structural Basis of A Homo-Dimerization Site in Tetraspanin CD9 Targeted By A Melanoma Patient-Derived Antibody To Be Published.
Page generated: Sat Jul 10 12:21:15 2021

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