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Sodium 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:

Potassium (K) 1 atom
Chlorine (Cl) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of AT1412DM Fab Fragment in Complex with CD9 Large Extracellular Loop, PDB code: 6rlo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6rlo

Go back to Sodium Binding Sites List in 6rlo
Sodium binding site 1 out of 7 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 Sodium with other atoms in the Na 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
B:Na303

b:30.6
occ:1.00
OG B:SER187 2.6 20.6 1.0
O B:ASP183 2.7 29.1 1.0
O B:ALA96 2.7 26.5 1.0
CB B:SER187 3.2 21.5 1.0
CA B:SER187 3.2 22.5 1.0
C B:ALA96 3.5 27.2 1.0
CA B:ALA96 3.6 27.6 1.0
CD1 B:ILE122 3.7 32.5 1.0
N B:SER187 3.7 23.8 1.0
C B:ASP183 3.8 28.1 1.0
CB B:ALA96 3.8 27.0 1.0
CG1 B:VAL99 3.9 26.1 1.0
CB B:VAL99 3.9 25.8 1.0
CG1 B:ILE122 4.0 32.2 1.0
CG B:GLN182 4.2 28.0 1.0
CA B:SER184 4.3 27.1 1.0
CB B:ILE122 4.3 31.6 1.0
C B:SER184 4.3 28.0 1.0
O B:SER184 4.5 28.0 1.0
N B:SER184 4.5 27.4 1.0
C B:SER187 4.6 22.9 1.0
CG2 B:VAL99 4.6 27.4 1.0
CD B:GLN182 4.6 27.9 1.0
N B:GLU97 4.7 29.1 1.0
CG2 B:ILE122 4.8 32.5 1.0
C B:GLN182 4.8 25.8 1.0
N B:LYS185 4.8 28.5 1.0
N B:ASP183 4.8 25.9 1.0
O B:GLN182 4.8 24.8 1.0
NE2 B:GLN182 4.8 27.4 1.0
CB B:GLN182 4.9 27.0 1.0
C B:ASP186 4.9 25.6 1.0
CA B:ASP183 4.9 26.9 1.0
O B:HOH428 5.0 20.9 1.0
N B:ALA96 5.0 27.4 1.0
O B:SER187 5.0 22.1 1.0

Sodium binding site 2 out of 7 in 6rlo

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Sodium binding site 2 out of 7 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 Sodium with other atoms in the Na 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
C:Na303

b:32.8
occ:1.00
N C:TYR67 3.3 28.3 1.0
NZ C:LYS72 3.4 47.6 1.0
CE C:LYS72 3.5 45.3 1.0
CA C:VAL66 3.8 30.3 1.0
O C:TYR67 3.8 24.1 1.0
CD2 C:TYR67 4.0 24.0 1.0
C C:VAL66 4.0 29.4 1.0
CD C:LYS72 4.0 42.8 1.0
CA C:TYR67 4.2 26.6 1.0
CB C:TYR67 4.2 25.5 1.0
CG1 C:VAL66 4.2 31.9 1.0
CG C:LYS72 4.3 40.8 1.0
O C:ILE65 4.4 31.5 1.0
C C:TYR67 4.5 26.9 1.0
CG C:TYR67 4.5 23.9 1.0
CB C:VAL66 4.6 31.8 1.0
N C:VAL66 4.8 32.4 1.0
CE2 C:TYR67 4.9 23.8 1.0
C C:ILE65 5.0 31.9 1.0

Sodium binding site 3 out of 7 in 6rlo

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Sodium binding site 3 out of 7 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 Sodium with other atoms in the Na 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
C:Na304

b:32.2
occ:1.00
OD1 D:ASP183 2.7 22.3 1.0
ND1 C:HIS179 3.4 22.1 1.0
CE1 C:HIS179 3.5 21.3 1.0
CG D:ASP183 3.8 21.4 1.0
O D:HOH401 4.0 23.3 1.0
CB D:ASP183 4.1 22.7 1.0
CA D:ASP183 4.2 22.1 1.0
O C:VAL178 4.3 29.4 1.0
CG C:HIS179 4.7 23.1 1.0
NE2 C:HIS179 4.8 21.7 1.0
OD2 D:ASP183 4.8 21.0 1.0
O D:GLU181 5.0 28.0 1.0

Sodium binding site 4 out of 7 in 6rlo

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Sodium binding site 4 out of 7 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 Sodium with other atoms in the Na 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
D:Na303

b:28.7
occ:1.00
OE1 B:GLN215 2.7 23.9 1.0
O D:ARG18 3.2 28.8 1.0
OE2 D:GLU17 3.3 34.7 1.0
CD B:GLN215 3.7 23.9 1.0
CG2 B:VAL126 3.7 23.7 1.0
CB D:ALA19 3.7 28.7 1.0
CG1 D:VAL13 3.8 26.6 1.0
CB B:VAL126 3.8 23.3 1.0
CA D:ALA19 4.0 27.9 1.0
CG B:GLN215 4.0 23.3 1.0
CG2 D:VAL13 4.1 26.7 1.0
C D:ARG18 4.1 27.4 1.0
CD D:GLU17 4.2 36.0 1.0
CB D:VAL13 4.3 27.5 1.0
O D:SER12 4.3 24.2 1.0
CB B:GLN215 4.4 23.8 1.0
CA D:VAL13 4.4 27.0 1.0
N D:ALA19 4.4 29.2 1.0
CG D:GLU17 4.5 36.6 1.0
CG1 B:VAL126 4.5 22.8 1.0
O B:GLN215 4.8 23.5 1.0
NE2 B:GLN215 4.9 25.4 1.0
CB D:GLU17 4.9 34.5 1.0
C B:GLN215 4.9 23.2 1.0
CA B:VAL126 5.0 23.4 1.0

Sodium binding site 5 out of 7 in 6rlo

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Sodium binding site 5 out of 7 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 Sodium with other atoms in the Na 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
D:Na304

b:39.1
occ:1.00
OE1 D:GLN140 2.4 29.8 1.0
N D:SER137 3.2 29.0 1.0
OG D:SER137 3.4 27.9 1.0
CD D:GLN140 3.4 28.6 1.0
CB D:GLN140 3.5 29.3 1.0
CB C:PHE137 3.5 24.7 1.0
CA D:PRO136 3.6 26.0 1.0
O D:HOH418 3.9 23.7 1.0
CG C:PHE137 3.9 24.2 1.0
C D:PRO136 3.9 27.4 1.0
CB D:SER137 4.0 29.4 1.0
CD2 C:PHE137 4.0 24.2 1.0
CG D:GLN140 4.0 28.4 1.0
O D:SER147 4.1 21.1 1.0
CD2 C:LEU156 4.1 25.9 1.0
CA D:SER137 4.1 29.4 1.0
CB D:PRO136 4.2 26.1 1.0
NE2 D:GLN140 4.4 30.1 1.0
O D:SER137 4.6 32.5 1.0
CB D:SER147 4.6 22.9 1.0
O C:PRO138 4.6 25.8 1.0
O D:PRO135 4.8 24.6 1.0
CD1 C:PHE137 4.8 24.7 1.0
N D:SER147 4.8 25.7 1.0
CA D:GLN140 4.9 30.5 1.0
C D:SER137 4.9 30.7 1.0
N D:PRO136 4.9 25.7 1.0
CE2 C:PHE137 4.9 24.3 1.0
CA C:PHE137 4.9 25.8 1.0
C D:SER147 5.0 22.7 1.0

Sodium binding site 6 out of 7 in 6rlo

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Sodium binding site 6 out of 7 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 Sodium with other atoms in the Na 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
D:Na305

b:33.4
occ:1.00
O D:ASP183 2.5 21.2 1.0
O D:ALA96 2.6 25.3 1.0
OG D:SER187 2.9 26.1 1.0
C D:ALA96 3.4 27.1 1.0
CA D:SER187 3.4 25.4 1.0
CB D:SER187 3.5 25.3 1.0
CG1 D:VAL99 3.5 23.9 1.0
C D:ASP183 3.5 22.2 1.0
CA D:ALA96 3.6 27.1 1.0
CB D:VAL99 3.7 22.9 1.0
CB D:ALA96 3.9 26.7 1.0
N D:SER187 3.9 25.6 1.0
CA D:SER184 3.9 23.1 1.0
CD1 D:ILE122 3.9 33.7 1.0
C D:SER184 4.0 24.4 1.0
N D:SER184 4.1 22.6 1.0
CG1 D:ILE122 4.2 33.0 1.0
O D:SER184 4.2 24.3 1.0
CG D:GLN182 4.3 24.4 1.0
CG2 D:VAL99 4.4 23.5 1.0
N D:GLU97 4.5 28.0 1.0
O D:GLN182 4.5 22.1 1.0
N D:LYS185 4.6 25.7 1.0
C D:GLN182 4.6 23.0 1.0
N D:ASP183 4.6 21.7 1.0
CB D:ILE122 4.6 32.4 1.0
CA D:ASP183 4.7 22.1 1.0
C D:SER187 4.8 24.4 1.0
CD D:GLN182 4.8 24.5 1.0
CB D:GLN182 4.8 23.6 1.0
O D:HOH402 4.9 17.7 1.0
N D:VAL99 4.9 23.2 1.0
CA D:VAL99 4.9 22.6 1.0

Sodium binding site 7 out of 7 in 6rlo

Go back to Sodium Binding Sites List in 6rlo
Sodium binding site 7 out of 7 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 Sodium with other atoms in the Na 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
F:Na302

b:29.8
occ:1.00
OE1 F:GLN140 2.7 30.0 1.0
N F:SER137 3.1 28.9 1.0
OG F:SER137 3.1 30.1 1.0
CB E:PHE137 3.4 25.0 1.0
CB F:GLN140 3.5 29.9 1.0
CD F:GLN140 3.6 29.5 1.0
CA F:PRO136 3.7 26.1 1.0
CB F:SER137 3.7 30.8 1.0
CG E:PHE137 3.8 24.9 1.0
C F:PRO136 3.9 27.1 1.0
CA F:SER137 4.0 29.7 1.0
CD2 E:PHE137 4.0 23.7 1.0
CG F:GLN140 4.2 29.3 1.0
CB F:PRO136 4.3 24.8 1.0
CD2 E:LEU156 4.3 24.9 1.0
O F:HOH422 4.3 16.5 1.0
O E:PRO138 4.3 25.3 1.0
O F:SER147 4.3 25.3 1.0
O F:SER137 4.5 30.1 1.0
NE2 F:GLN140 4.7 28.8 1.0
CD1 E:PHE137 4.7 24.5 1.0
CA E:PHE137 4.7 25.9 1.0
O F:PRO135 4.8 25.6 1.0
C F:SER137 4.8 31.6 1.0
CA F:GLN140 4.9 31.7 1.0
CB F:SER147 4.9 27.4 1.0
N F:PRO136 4.9 24.9 1.0
CE2 E:PHE137 5.0 24.6 1.0
N F:GLN140 5.0 34.9 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: Tue Oct 8 13:15:30 2024

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