Chlorine in PDB 7nbb: Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3

Protein crystallography data

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3, PDB code: 7nbb was solved by S.M.Lange, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.95 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.389, 97.615, 74.967, 90, 109.96, 90
R / Rfree (%) 17.5 / 21.2

Other elements in 7nbb:

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 (pdb code 7nbb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3, PDB code: 7nbb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7nbb

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Chlorine binding site 1 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl101

b:28.4
occ:1.00
 O D:HOH393 3.2 16.8 1.0
N C:ARG74 3.2 19.3 1.0
NE2 C:GLN40 3.3 19.3 1.0
CA C:LEU73 3.8 16.9 1.0
CZ3 D:TRP106 3.9 27.6 1.0
CB C:ARG74 3.9 27.1 1.0
CD2 C:LEU73 3.9 15.9 1.0
C C:LEU73 4.0 19.5 1.0
CG C:GLN40 4.1 20.2 1.0
CA C:ARG74 4.2 23.4 1.0
CD C:GLN40 4.2 21.3 1.0
O D:HOH360 4.2 34.0 1.0
CB C:LEU73 4.3 17.4 1.0
O C:ARG72 4.4 18.2 1.0
CH2 D:TRP106 4.4 27.6 1.0
O D:ARG47 4.4 17.4 1.0
CG C:LEU73 4.8 18.3 1.0
CE3 D:TRP106 4.8 25.2 1.0
N C:LEU73 4.9 17.8 1.0
O C:ARG74 5.0 24.6 1.0

Chlorine binding site 2 out of 7 in 7nbb

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Chlorine binding site 2 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:21.2
occ:1.00
 O D:HOH436 2.9 22.5 1.0
N D:ARG21 3.2 15.6 1.0
O D:HOH399 3.3 24.4 1.0
CA D:LEU20 3.7 15.4 1.0
C D:LEU20 3.9 13.8 1.0
CB D:ARG21 4.1 13.8 1.0
CA D:ARG21 4.2 14.9 1.0
CD1 D:LEU20 4.2 21.9 1.0
O D:SER19 4.3 18.4 1.0
O D:ARG21 4.5 15.8 1.0
N D:LEU20 4.6 14.7 1.0
O D:HOH410 4.6 22.7 1.0
O D:HOH384 4.7 29.4 1.0
CB D:LEU20 4.8 17.3 1.0
C D:SER19 4.8 18.8 1.0
CG D:LEU20 4.8 21.0 1.0
O D:HOH349 4.8 20.4 1.0
C D:ARG21 4.9 14.6 1.0

Chlorine binding site 3 out of 7 in 7nbb

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Chlorine binding site 3 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl102

b:27.7
occ:1.00
 O E:HOH238 2.9 38.1 1.0
O E:HOH248 2.9 26.8 1.0
N E:GLU16 3.2 18.9 1.0
O E:HOH213 3.6 39.2 1.0
NZ E:LYS33 3.6 41.3 1.0
O E:GLU16 3.8 18.5 1.0
CA E:LEU15 3.8 20.0 1.0
CD2 E:LEU15 3.8 19.9 1.0
CE E:LYS33 4.0 37.5 1.0
C E:LEU15 4.0 19.9 1.0
CB E:LEU15 4.1 17.6 1.0
CB E:LYS29 4.1 16.8 1.0
CA E:GLU16 4.1 17.3 1.0
CD E:LYS29 4.2 17.9 1.0
CB E:GLU16 4.2 20.4 1.0
CG E:LYS29 4.3 19.0 1.0
C E:GLU16 4.4 17.3 1.0
NZ E:LYS29 4.5 27.6 1.0
CG E:LEU15 4.6 22.1 1.0
O E:THR14 4.6 22.1 1.0
O E:HOH221 4.6 26.0 1.0
O E:HOH288 4.8 33.0 1.0
N E:LEU15 5.0 18.8 1.0
CD E:LYS33 5.0 36.6 1.0

Chlorine binding site 4 out of 7 in 7nbb

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Chlorine binding site 4 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl202

b:20.9
occ:1.00
 N F:THR14 3.3 20.4 1.0
CA F:ILE13 3.6 19.0 1.0
NZ F:LYS33 3.7 31.7 1.0
CB F:ILE13 3.7 24.6 1.0
CG2 F:THR14 3.8 22.8 1.0
C F:ILE13 4.0 18.9 1.0
CG2 F:ILE13 4.1 24.0 1.0
O F:THR14 4.1 23.3 1.0
CE F:LYS33 4.2 35.8 1.0
CA F:THR14 4.3 18.4 1.0
CD F:LYS33 4.5 33.4 1.0
CB F:THR14 4.5 20.1 1.0
C F:THR14 4.7 21.7 1.0
O F:THR12 4.8 22.6 1.0
N F:ILE13 4.9 20.8 1.0

Chlorine binding site 5 out of 7 in 7nbb

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Chlorine binding site 5 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl101

b:29.8
occ:1.00
 N G:ARG74 3.2 16.6 1.0
O G:HOH277 3.2 35.9 1.0
O G:HOH242 3.3 16.8 1.0
NE2 G:GLN40 3.4 17.3 1.0
CA G:LEU73 3.7 12.1 1.0
CZ3 H:TRP106 3.9 27.5 1.0
CB G:ARG74 3.9 19.8 1.0
CD2 G:LEU73 3.9 13.6 1.0
C G:LEU73 4.0 17.0 1.0
O H:HOH374 4.0 34.6 1.0
CA G:ARG74 4.2 20.5 1.0
CB G:LEU73 4.2 12.8 1.0
CG G:GLN40 4.3 17.1 1.0
CD G:GLN40 4.3 19.0 1.0
CH2 H:TRP106 4.4 31.0 1.0
O H:ARG47 4.4 15.9 1.0
O G:ARG72 4.4 14.6 1.0
CG G:LEU73 4.8 13.0 1.0
CE3 H:TRP106 4.8 25.2 1.0
O G:ARG74 4.9 24.0 1.0
N G:LEU73 4.9 11.5 1.0

Chlorine binding site 6 out of 7 in 7nbb

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Chlorine binding site 6 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl102

b:37.1
occ:1.00
 N G:GLU16 3.1 16.9 1.0
O G:GLU16 3.6 22.4 1.0
CA G:LEU15 3.7 16.9 1.0
CD G:LYS29 3.8 28.1 1.0
C G:LEU15 3.9 16.8 1.0
CA G:GLU16 3.9 22.3 1.0
CB G:GLU16 4.0 23.3 1.0
CE G:LYS29 4.1 31.7 1.0
CB G:LEU15 4.2 19.0 1.0
C G:GLU16 4.2 21.6 1.0
NZ G:LYS29 4.2 33.1 1.0
CD2 G:LEU15 4.3 25.5 1.0
CG G:LYS29 4.5 26.8 1.0
O G:HOH229 4.5 37.9 1.0
O G:THR14 4.7 23.2 1.0
CE G:LYS33 4.7 39.7 1.0
CB G:LYS29 4.8 25.5 1.0
CG G:LEU15 4.8 22.2 1.0
N G:LEU15 5.0 18.8 1.0

Chlorine binding site 7 out of 7 in 7nbb

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Chlorine binding site 7 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl103

b:33.4
occ:1.00
 O G:HOH260 2.7 32.8 1.0
O F:HOH305 2.7 19.3 1.0
N G:THR66 3.1 14.7 1.0
CA G:SER65 3.6 18.1 1.0
O G:HOH221 3.8 19.3 1.0
C G:SER65 3.9 17.3 1.0
CE1 G:PHE45 3.9 19.9 1.0
CZ F:PHE45 3.9 19.2 1.0
O G:THR66 3.9 14.8 1.0
CA G:THR66 4.1 13.1 1.0
CB F:ALA46 4.1 16.0 1.0
CB G:SER65 4.1 17.1 1.0
CE2 F:PHE45 4.1 20.0 1.0
CB G:THR66 4.3 13.8 1.0
CA F:ALA46 4.3 13.7 1.0
C G:THR66 4.5 16.1 1.0
OG G:SER65 4.5 20.8 1.0
CE1 F:PHE45 4.6 20.7 1.0
OG1 G:THR66 4.7 17.7 1.0
O G:GLU64 4.7 18.3 1.0
N F:ALA46 4.7 13.9 1.0
CD1 G:PHE45 4.7 18.8 1.0
CZ G:PHE45 4.7 20.5 1.0
O F:HOH362 4.8 27.0 1.0
N G:SER65 4.9 14.4 1.0
CD2 F:PHE45 4.9 19.5 1.0

Reference:

S.M.Lange, Y.Kulathu. Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 To Be Published.
Page generated: Tue Jul 30 00:49:06 2024

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