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Chlorine in PDB 5c1b: P97-DELTA709-728 in Complex with A UFD1-Shp Peptide

Enzymatic activity of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide

All present enzymatic activity of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide:
3.6.4.6;

Protein crystallography data

The structure of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide, PDB code: 5c1b was solved by P.Haenzelmann, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 3.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 140.715, 180.664, 254.958, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24

Other elements in 5c1b:

The structure of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide (pdb code 5c1b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide, PDB code: 5c1b:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5c1b

Go back to Chlorine Binding Sites List in 5c1b
Chlorine binding site 1 out of 6 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:98.4
occ:1.00
H A:ASP630 2.7 92.3 1.0
HH11 A:ARG586 2.7 0.6 1.0
HD13 A:ILE601 2.8 0.7 1.0
HB2 A:ASP630 2.9 86.8 1.0
HD12 A:ILE601 3.1 0.7 1.0
CD1 A:ILE601 3.2 0.1 1.0
HD11 A:ILE601 3.3 0.7 1.0
HA A:ALA583 3.3 0.7 1.0
N A:ASP630 3.4 76.9 1.0
HD3 A:ARG586 3.4 0.5 1.0
NH1 A:ARG586 3.5 0.5 1.0
HA A:ILE629 3.5 0.1 1.0
HB2 A:ALA583 3.5 0.8 1.0
HD11 A:ILE633 3.5 91.9 1.0
CB A:ASP630 3.6 72.3 1.0
HB3 A:ASP630 3.6 86.8 1.0
HH12 A:ARG586 3.7 0.6 1.0
HD12 A:ILE633 3.8 91.9 1.0
HG13 A:ILE629 3.9 0.2 1.0
HD2 A:ARG586 4.0 0.5 1.0
CA A:ALA583 4.0 87.2 1.0
CD1 A:ILE633 4.1 76.6 1.0
HG21 A:ILE601 4.1 84.4 1.0
CA A:ASP630 4.1 68.7 1.0
CB A:ALA583 4.1 84.0 1.0
CD A:ARG586 4.1 0.8 1.0
N A:ALA583 4.3 78.3 1.0
O A:ILE628 4.3 85.4 1.0
C A:ILE629 4.3 79.2 1.0
CA A:ILE629 4.3 85.9 1.0
HB1 A:ALA583 4.4 0.8 1.0
H A:ALA583 4.4 93.9 1.0
HB A:ILE582 4.4 0.1 1.0
HG22 A:ILE582 4.4 91.5 1.0
HA A:ASP630 4.6 82.5 1.0
CZ A:ARG586 4.6 0.1 1.0
HD13 A:ILE633 4.6 91.9 1.0
CG1 A:ILE629 4.7 84.4 1.0
CG1 A:ILE601 4.7 91.8 1.0
HG12 A:ILE629 4.7 0.2 1.0
C A:ILE582 4.8 89.2 1.0
NE A:ARG586 4.8 0.5 1.0
CG A:ASP630 4.9 88.4 1.0
CG2 A:ILE601 5.0 70.4 1.0
HB3 A:ALA583 5.0 0.8 1.0

Chlorine binding site 2 out of 6 in 5c1b

Go back to Chlorine Binding Sites List in 5c1b
Chlorine binding site 2 out of 6 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl905

b:0.2
occ:1.00
H B:ASP630 2.6 0.7 1.0
HD13 B:ILE601 2.7 0.4 1.0
HB2 B:ASP630 2.9 0.6 1.0
HD12 B:ILE601 3.2 0.4 1.0
CD1 B:ILE601 3.2 0.3 1.0
HD11 B:ILE601 3.2 0.4 1.0
HD11 B:ILE633 3.3 0.7 1.0
N B:ASP630 3.4 87.2 1.0
HA B:ILE629 3.4 0.2 1.0
HH11 B:ARG586 3.4 0.0 1.0
HB2 B:ALA583 3.4 97.4 1.0
HD12 B:ILE633 3.5 0.7 1.0
HA B:ALA583 3.5 95.5 1.0
HB3 B:ASP630 3.6 0.6 1.0
CB B:ASP630 3.6 94.7 1.0
HG13 B:ILE629 3.7 0.3 1.0
CD1 B:ILE633 3.9 86.5 1.0
HD3 B:ARG586 3.9 0.5 1.0
HG21 B:ILE601 4.1 0.3 1.0
NH1 B:ARG586 4.1 0.2 1.0
CA B:ASP630 4.1 93.1 1.0
CB B:ALA583 4.1 81.2 1.0
CA B:ALA583 4.2 79.6 1.0
CA B:ILE629 4.2 86.8 1.0
C B:ILE629 4.2 77.7 1.0
HH12 B:ARG586 4.3 0.0 1.0
O B:ILE628 4.3 91.4 1.0
HD13 B:ILE633 4.3 0.7 1.0
HB1 B:ALA583 4.4 97.4 1.0
N B:ALA583 4.4 68.3 1.0
H B:ALA583 4.4 81.9 1.0
HB B:ILE582 4.5 89.8 1.0
CG1 B:ILE629 4.5 0.1 1.0
HG12 B:ILE629 4.5 0.3 1.0
HD2 B:ARG586 4.6 0.5 1.0
HA B:ASP630 4.6 0.7 1.0
CG1 B:ILE601 4.7 99.7 1.0
HG22 B:ILE582 4.7 75.5 1.0
CD B:ARG586 4.7 0.6 1.0
HB3 B:LEU579 4.8 81.5 1.0
CG2 B:ILE601 4.9 98.6 1.0
CG B:ASP630 4.9 98.1 1.0
HG12 B:ILE601 5.0 0.7 1.0
HB3 B:ALA583 5.0 97.4 1.0
HG13 B:ILE633 5.0 1.0 1.0
O B:LEU579 5.0 0.2 1.0

Chlorine binding site 3 out of 6 in 5c1b

Go back to Chlorine Binding Sites List in 5c1b
Chlorine binding site 3 out of 6 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl901

b:0.9
occ:1.00
H C:ASP630 2.5 0.2 1.0
HD13 C:ILE601 2.9 0.8 1.0
HB2 C:ASP630 2.9 0.1 1.0
HH11 C:ARG586 3.1 0.3 1.0
HD11 C:ILE601 3.2 0.8 1.0
HD12 C:ILE601 3.2 0.8 1.0
HA C:ILE629 3.3 0.6 1.0
N C:ASP630 3.3 83.5 1.0
CD1 C:ILE601 3.3 0.5 1.0
HB2 C:ALA583 3.3 0.1 1.0
HA C:ALA583 3.3 0.8 1.0
HB3 C:ASP630 3.6 0.1 1.0
CB C:ASP630 3.6 0.1 1.0
HD11 C:ILE633 3.7 0.8 1.0
HG13 C:ILE629 3.7 0.2 1.0
HD3 C:ARG586 3.8 0.3 1.0
HD12 C:ILE633 3.8 0.8 1.0
NH1 C:ARG586 3.9 0.4 1.0
CA C:ALA583 4.0 93.2 1.0
CB C:ALA583 4.0 94.2 1.0
HH12 C:ARG586 4.0 0.3 1.0
CA C:ASP630 4.0 89.9 1.0
CA C:ILE629 4.1 95.5 1.0
C C:ILE629 4.1 89.2 1.0
HB1 C:ALA583 4.2 0.1 1.0
O C:ILE628 4.2 95.7 1.0
CD1 C:ILE633 4.2 0.5 1.0
HD2 C:ARG586 4.2 0.3 1.0
N C:ALA583 4.3 90.1 1.0
HG21 C:ILE601 4.3 0.6 1.0
H C:ALA583 4.3 0.1 1.0
CG1 C:ILE629 4.5 91.0 1.0
HG12 C:ILE629 4.5 0.2 1.0
CD C:ARG586 4.5 0.1 1.0
HG22 C:ILE582 4.5 81.8 1.0
HB C:ILE582 4.5 0.4 1.0
HA C:ASP630 4.5 0.8 1.0
HD13 C:ILE633 4.7 0.8 1.0
CG1 C:ILE601 4.8 0.0 1.0
HB3 C:ALA583 4.8 0.1 1.0
C C:ILE582 4.9 93.3 1.0
CB C:ILE629 4.9 95.2 1.0
CG C:ASP630 4.9 0.1 1.0
HB3 C:LEU579 4.9 92.6 1.0
CZ C:ARG586 5.0 0.2 1.0

Chlorine binding site 4 out of 6 in 5c1b

Go back to Chlorine Binding Sites List in 5c1b
Chlorine binding site 4 out of 6 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl901

b:0.0
occ:1.00
H D:ASP630 2.7 0.2 1.0
HD13 D:ILE601 2.8 0.5 1.0
HB2 D:ASP630 3.0 0.0 1.0
HD12 D:ILE601 3.2 0.5 1.0
HH11 D:ARG586 3.2 0.9 1.0
HD11 D:ILE601 3.2 0.5 1.0
CD1 D:ILE601 3.2 0.1 1.0
HB2 D:ALA583 3.4 0.9 1.0
HA D:ALA583 3.4 0.6 1.0
N D:ASP630 3.4 96.0 1.0
HA D:ILE629 3.5 0.1 1.0
HD11 D:ILE633 3.5 0.5 1.0
HB3 D:ASP630 3.6 0.0 1.0
CB D:ASP630 3.7 0.2 1.0
HD12 D:ILE633 3.7 0.5 1.0
HD3 D:ARG586 3.7 0.2 1.0
HG13 D:ILE629 3.8 0.7 1.0
NH1 D:ARG586 3.9 0.6 1.0
CA D:ALA583 4.0 99.7 1.0
CD1 D:ILE633 4.0 97.1 1.0
CB D:ALA583 4.1 88.2 1.0
HG21 D:ILE601 4.1 0.6 1.0
HH12 D:ARG586 4.1 0.9 1.0
CA D:ASP630 4.2 0.8 1.0
N D:ALA583 4.3 0.7 1.0
HB1 D:ALA583 4.3 0.9 1.0
CA D:ILE629 4.3 0.6 1.0
C D:ILE629 4.3 0.6 1.0
H D:ALA583 4.3 0.1 1.0
HD2 D:ARG586 4.4 0.2 1.0
HB D:ILE582 4.4 0.9 1.0
O D:ILE628 4.4 0.5 1.0
CD D:ARG586 4.5 0.0 1.0
HD13 D:ILE633 4.5 0.5 1.0
CG1 D:ILE629 4.6 93.9 1.0
HG22 D:ILE582 4.6 0.7 1.0
HG12 D:ILE629 4.6 0.7 1.0
HA D:ASP630 4.6 0.5 1.0
CG1 D:ILE601 4.7 0.7 1.0
HB3 D:LEU579 4.9 86.9 1.0
HB3 D:ALA583 4.9 0.9 1.0
C D:ILE582 4.9 0.1 1.0
O D:LEU579 4.9 92.3 1.0
CG D:ASP630 5.0 0.3 1.0
CG2 D:ILE601 5.0 85.5 1.0
CZ D:ARG586 5.0 0.9 1.0

Chlorine binding site 5 out of 6 in 5c1b

Go back to Chlorine Binding Sites List in 5c1b
Chlorine binding site 5 out of 6 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl905

b:0.8
occ:1.00
H E:ASP630 2.5 0.7 1.0
HD13 E:ILE601 2.8 0.4 1.0
HB2 E:ASP630 2.9 0.7 1.0
HH11 E:ARG586 3.2 0.8 1.0
HD12 E:ILE601 3.2 0.4 1.0
CD1 E:ILE601 3.3 0.8 1.0
HD11 E:ILE601 3.3 0.4 1.0
N E:ASP630 3.3 85.5 1.0
HA E:ILE629 3.4 0.9 1.0
HD11 E:ILE633 3.4 0.2 1.0
HB2 E:ALA583 3.5 92.9 1.0
HA E:ALA583 3.5 0.8 1.0
HB3 E:ASP630 3.5 0.7 1.0
CB E:ASP630 3.5 90.6 1.0
HD12 E:ILE633 3.6 0.2 1.0
HG13 E:ILE629 3.6 0.6 1.0
HD3 E:ARG586 3.9 0.6 1.0
NH1 E:ARG586 3.9 0.1 1.0
CD1 E:ILE633 4.0 0.7 1.0
HG21 E:ILE601 4.0 92.8 1.0
CA E:ASP630 4.0 80.9 1.0
HH12 E:ARG586 4.1 0.8 1.0
CB E:ALA583 4.1 77.4 1.0
CA E:ALA583 4.1 94.0 1.0
CA E:ILE629 4.2 90.7 1.0
C E:ILE629 4.2 93.3 1.0
HB1 E:ALA583 4.3 92.9 1.0
HD2 E:ARG586 4.4 0.6 1.0
O E:ILE628 4.4 95.5 1.0
CG1 E:ILE629 4.4 0.6 1.0
HG12 E:ILE629 4.4 0.6 1.0
N E:ALA583 4.4 1.0 1.0
HD13 E:ILE633 4.5 0.2 1.0
H E:ALA583 4.5 0.4 1.0
HA E:ASP630 4.5 97.0 1.0
CD E:ARG586 4.6 0.1 1.0
HB E:ILE582 4.7 88.4 1.0
CG1 E:ILE601 4.7 0.5 1.0
HG22 E:ILE582 4.8 88.6 1.0
CG E:ASP630 4.8 90.9 1.0
CG2 E:ILE601 4.9 77.4 1.0
HB3 E:ALA583 5.0 92.9 1.0
HG13 E:ILE633 5.0 0.8 1.0
CB E:ILE629 5.0 95.7 1.0

Chlorine binding site 6 out of 6 in 5c1b

Go back to Chlorine Binding Sites List in 5c1b
Chlorine binding site 6 out of 6 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl905

b:0.7
occ:1.00
H F:ASP630 2.7 0.2 1.0
HD13 F:ILE601 2.8 0.1 1.0
HD11 F:ILE601 3.1 0.1 1.0
HB2 F:ASP630 3.1 0.3 1.0
CD1 F:ILE601 3.2 0.7 1.0
HD12 F:ILE601 3.2 0.1 1.0
HB2 F:ALA583 3.3 77.4 1.0
HA F:ALA583 3.3 80.2 1.0
HH11 F:ARG586 3.3 0.5 1.0
HA F:ILE629 3.4 0.0 1.0
N F:ASP630 3.5 88.5 1.0
HD11 F:ILE633 3.6 0.0 1.0
HG13 F:ILE629 3.7 0.7 1.0
HB3 F:ASP630 3.7 0.3 1.0
HD12 F:ILE633 3.7 0.0 1.0
CB F:ASP630 3.8 0.4 1.0
HD3 F:ARG586 3.8 0.7 1.0
CA F:ALA583 3.9 66.8 1.0
CB F:ALA583 3.9 64.5 1.0
CD1 F:ILE633 4.1 0.5 1.0
NH1 F:ARG586 4.1 0.9 1.0
N F:ALA583 4.2 68.7 1.0
HB1 F:ALA583 4.2 77.4 1.0
HG21 F:ILE601 4.2 92.3 1.0
HD2 F:ARG586 4.2 0.7 1.0
H F:ALA583 4.2 82.4 1.0
CA F:ASP630 4.2 94.7 1.0
CA F:ILE629 4.3 88.4 1.0
HB F:ILE582 4.3 94.1 1.0
HH12 F:ARG586 4.4 0.5 1.0
C F:ILE629 4.4 89.1 1.0
O F:ILE628 4.4 87.5 1.0
CD F:ARG586 4.5 0.4 1.0
HG22 F:ILE582 4.5 86.9 1.0
CG1 F:ILE629 4.5 86.4 1.0
HD13 F:ILE633 4.6 0.0 1.0
HG12 F:ILE629 4.6 0.7 1.0
CG1 F:ILE601 4.7 0.5 1.0
HA F:ASP630 4.7 0.6 1.0
HB3 F:LEU579 4.7 69.9 1.0
HB3 F:ALA583 4.8 77.4 1.0
C F:ILE582 4.8 81.2 1.0
O F:LEU579 4.8 93.5 1.0
HG12 F:ILE601 4.9 0.4 1.0

Reference:

P.Hanzelmann, H.Schindelin. Characterization of An Additional Binding Surface on the P97 N-Terminal Domain Involved in Bipartite Cofactor Interactions. Structure V. 24 140 2016.
ISSN: ISSN 0969-2126
PubMed: 26712280
DOI: 10.1016/J.STR.2015.10.027
Page generated: Fri Jul 26 05:50:16 2024

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