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Chlorine in PDB 7zl7: Human Gabarap in Complex with Stapled Peptide PEN8-Ortho

Protein crystallography data

The structure of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho, PDB code: 7zl7 was solved by A.Ueffing, H.Brown, D.Willbold, J.A.Kritzer, O.H.Weiergraeber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.35 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 68.47, 72.42, 49.66, 90, 100.04, 90
R / Rfree (%) 17.4 / 22

Other elements in 7zl7:

The structure of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho (pdb code 7zl7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho, PDB code: 7zl7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7zl7

Go back to Chlorine Binding Sites List in 7zl7
Chlorine binding site 1 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:34.0
occ:1.00
 O A:HOH410 3.2 30.2 1.0
N A:PHE3 3.3 21.2 1.0
NZ A:LYS6 3.3 26.8 1.0
O A:HOH397 3.5 37.9 1.0
CD2 A:PHE3 3.6 26.1 1.0
O A:HOH368 3.6 38.5 1.0
CG A:PHE3 3.6 31.4 1.0
CA A:LYS2 3.7 25.5 1.0
CD A:LYS6 3.9 21.1 1.0
CE2 A:PHE3 3.9 29.1 1.0
CG A:LYS2 3.9 30.0 1.0
CD1 A:PHE3 3.9 35.5 1.0
C A:LYS2 4.0 25.8 1.0
CE A:LYS6 4.0 21.5 1.0
CB A:PHE3 4.1 26.2 1.0
CZ A:PHE3 4.2 24.7 1.0
CE1 A:PHE3 4.2 30.8 1.0
CB A:LYS2 4.2 27.7 1.0
CA A:PHE3 4.3 21.0 1.0
O A:HOH316 4.5 37.1 1.0
O A:MET1 4.7 45.5 1.0
N A:LYS2 4.9 39.0 1.0
OE2 A:GLU100 5.0 22.3 1.0
O A:HOH394 5.0 15.4 0.5

Chlorine binding site 2 out of 8 in 7zl7

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Chlorine binding site 2 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:20.3
occ:1.00
 NZ A:LYS66 3.2 23.2 1.0
NH1 A:ARG67 3.4 21.8 1.0
O A:HOH417 3.4 32.5 1.0
NH2 A:ARG67 3.5 24.4 1.0
CZ A:ARG67 3.8 21.5 1.0
CD A:LYS66 3.9 16.9 1.0
CE A:LYS66 4.0 17.6 1.0
O B:HOH208 4.0 21.4 1.0
CD2 A:LEU63 4.3 15.5 1.0
CG A:LYS66 4.5 22.7 1.0

Chlorine binding site 3 out of 8 in 7zl7

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Chlorine binding site 3 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:30.3
occ:1.00
 O A:HOH311 3.2 28.0 1.0
N A:ALA72 3.3 19.1 1.0
CB A:ALA72 3.8 21.6 1.0
CA A:ARG71 4.0 21.8 1.0
C A:ARG71 4.1 21.9 1.0
CA A:ALA72 4.2 19.8 1.0
CB A:ARG71 4.2 27.1 1.0
CG A:ARG71 4.6 30.4 1.0
OE1 A:GLU73 4.7 19.4 0.7
O A:HOH433 4.9 40.4 1.0

Chlorine binding site 4 out of 8 in 7zl7

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Chlorine binding site 4 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:23.6
occ:1.00
 O A:HOH419 2.9 29.5 1.0
N A:GLU12 3.2 19.7 1.0
N A:PHE11 3.6 14.5 1.0
CG A:GLU12 3.6 21.1 1.0
CB A:GLU12 3.7 17.4 1.0
CB A:PRO10 3.9 19.3 1.0
CB A:PHE11 4.0 15.7 1.0
CA A:GLU12 4.1 19.0 1.0
CA A:PHE11 4.1 14.3 1.0
C A:PHE11 4.1 22.2 1.0
C A:PRO10 4.2 15.7 1.0
O A:HOH382 4.4 23.1 1.0
CA A:PRO10 4.6 18.2 1.0
CG A:PRO10 4.8 20.5 1.0
O A:PRO10 4.8 16.9 1.0
CD2 A:PHE11 5.0 16.4 1.0
N A:LYS13 5.0 16.8 1.0

Chlorine binding site 5 out of 8 in 7zl7

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Chlorine binding site 5 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:27.9
occ:1.00
 O C:HOH383 3.1 35.8 1.0
NZ C:LYS6 3.2 37.0 1.0
O C:HOH324 3.4 33.8 1.0
N C:PHE3 3.4 21.1 1.0
CA C:LYS2 3.6 28.5 1.0
CD1 C:PHE3 3.7 20.0 1.0
CD C:LYS6 3.7 24.2 1.0
CD C:LYS2 3.8 34.4 1.0
CE C:LYS6 3.9 30.4 1.0
CB C:LYS2 3.9 26.0 1.0
C C:LYS2 4.0 28.9 1.0
CB C:PHE3 4.4 18.1 1.0
CG C:LYS2 4.5 21.4 1.0
CE1 C:PHE3 4.5 25.2 1.0
CG C:PHE3 4.5 24.9 1.0
CA C:PHE3 4.5 16.2 1.0
OE2 C:GLU100 4.6 27.7 1.0
O C:MET1 4.7 26.7 1.0
N C:LYS2 4.8 26.1 1.0
N C:GLY-1 4.9 32.2 1.0
O C:GLY-1 4.9 37.7 1.0

Chlorine binding site 6 out of 8 in 7zl7

Go back to Chlorine Binding Sites List in 7zl7
Chlorine binding site 6 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:20.2
occ:1.00
 O C:HOH427 3.1 33.6 1.0
NZ C:LYS66 3.2 22.7 1.0
NH1 C:ARG67 3.3 19.4 1.0
NH2 C:ARG67 3.6 25.9 1.0
O C:HOH313 3.7 21.1 0.6
CD C:LYS66 3.7 15.4 1.0
CZ C:ARG67 3.8 25.0 1.0
CE C:LYS66 3.9 20.2 1.0
CG C:LYS66 4.3 18.8 1.0
O C:HOH313 4.4 18.2 0.4
O D:HOH212 4.4 24.7 1.0
CD2 C:LEU63 4.6 16.9 1.0
O C:HOH365 4.9 28.3 1.0
NE C:ARG67 5.0 23.5 1.0

Chlorine binding site 7 out of 8 in 7zl7

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Chlorine binding site 7 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:29.3
occ:1.00
 N C:ALA72 3.3 17.3 1.0
O C:HOH305 3.3 32.4 1.0
CB C:ALA72 3.9 16.8 1.0
CA C:ARG71 3.9 21.4 1.0
C C:ARG71 4.1 20.7 1.0
CB C:ARG71 4.1 27.8 1.0
CA C:ALA72 4.2 17.6 1.0
OE1 C:GLU73 4.5 15.8 0.6
CG C:ARG71 4.8 28.7 1.0

Chlorine binding site 8 out of 8 in 7zl7

Go back to Chlorine Binding Sites List in 7zl7
Chlorine binding site 8 out of 8 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl204

b:38.9
occ:0.50
 N C:GLU101 3.2 17.3 1.0
O C:HOH399 3.5 37.9 1.0
CB C:GLU101 3.7 21.5 1.0
CG C:GLU101 3.7 22.7 1.0
CB C:GLU100 3.8 17.1 1.0
CA C:GLU101 4.1 18.2 1.0
CA C:GLU100 4.1 13.5 1.0
C C:GLU100 4.1 17.0 1.0
CG C:GLU100 4.4 14.6 1.0
OE1 C:GLU100 4.4 25.7 1.0
O C:HOH340 4.6 26.5 1.0
CD C:GLU100 4.7 33.0 1.0
O C:HOH441 4.8 36.5 0.5

Reference:

H.Brown, M.Chung, A.Uffing, N.Batistatou, T.Tsang, S.Doskocil, W.Mao, D.Willbold, R.C.Bast Jr., Z.Lu, O.H.Weiergraber, J.A.Kritzer. Structure-Based Design of Stapled Peptides That Bind Gabarap and Inhibit Autophagy. J.Am.Chem.Soc. V. 144 14687 2022.
ISSN: ESSN 1520-5126
PubMed: 35917476
DOI: 10.1021/JACS.2C04699
Page generated: Tue Jul 30 06:15:44 2024

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