Chlorine in PDB 7zbv: Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor

Enzymatic activity of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor

All present enzymatic activity of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor:
3.4.24.3;

Protein crystallography data

The structure of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor, PDB code: 7zbv was solved by E.Schoenauer, H.Brandstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.76 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.267, 77.787, 97.319, 90, 90, 90
R / Rfree (%) 18.7 / 22.9

Other elements in 7zbv:

The structure of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor (pdb code 7zbv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor, PDB code: 7zbv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7zbv

Go back to Chlorine Binding Sites List in 7zbv
Chlorine binding site 1 out of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:52.9
occ:1.00
 CL A:ITO802 0.0 52.9 1.0
C3 A:ITO802 1.7 62.0 1.0
C2 A:ITO802 2.7 56.4 1.0
C4 A:ITO802 2.7 70.1 1.0
H2 A:ITO802 2.8 67.8 1.0
CL1 A:ITO802 3.2 56.1 1.0
C1 A:ITO802 4.0 63.3 1.0
C5 A:ITO802 4.0 57.0 1.0
C6 A:ITO802 4.5 60.9 1.0
H3 A:ITO802 4.9 68.5 1.0

Chlorine binding site 2 out of 4 in 7zbv

Go back to Chlorine Binding Sites List in 7zbv
Chlorine binding site 2 out of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:56.1
occ:1.00
 CL1 A:ITO802 0.0 56.1 1.0
C4 A:ITO802 1.7 70.1 1.0
C5 A:ITO802 2.7 57.0 1.0
C3 A:ITO802 2.7 62.0 1.0
H3 A:ITO802 2.8 68.5 1.0
CL A:ITO802 3.2 52.9 1.0
C6 A:ITO802 4.0 60.9 1.0
C2 A:ITO802 4.0 56.4 1.0
C1 A:ITO802 4.5 63.3 1.0
H2 A:ITO802 4.9 67.8 1.0

Chlorine binding site 3 out of 4 in 7zbv

Go back to Chlorine Binding Sites List in 7zbv
Chlorine binding site 3 out of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor


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 the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:83.1
occ:0.70
 CL A:ITO804 0.0 83.1 0.7
C3 A:ITO804 1.7 72.3 0.7
C2 A:ITO804 2.7 74.4 0.7
C4 A:ITO804 2.7 66.9 0.7
H2 A:ITO804 2.8 89.3 0.7
HH22 A:ARG573 3.0 41.8 1.0
CG A:PHE515 3.1 62.1 1.0
HA A:LEU520 3.2 30.7 1.0
CL1 A:ITO804 3.2 79.8 0.7
HB3 A:PHE515 3.2 55.7 1.0
CD2 A:PHE515 3.2 55.6 1.0
CD1 A:PHE515 3.4 68.9 1.0
HD2 A:PHE515 3.6 66.8 1.0
NH2 A:ARG573 3.6 34.8 1.0
HG2 A:GLU519 3.6 45.6 1.0
HH21 A:ARG573 3.6 41.8 1.0
CE2 A:PHE515 3.7 69.7 1.0
CB A:PHE515 3.7 46.4 1.0
HD12 A:LEU520 3.8 53.9 1.0
CE1 A:PHE515 3.8 63.2 1.0
HD1 A:PHE515 3.9 82.7 1.0
HB2 A:LEU520 3.9 33.7 1.0
CZ A:PHE515 3.9 73.4 1.0
C5 A:ITO804 4.0 60.7 0.7
C1 A:ITO804 4.0 71.7 0.7
HB2 A:PHE515 4.0 55.7 1.0
CA A:LEU520 4.0 25.5 1.0
HD13 A:LEU520 4.0 53.9 1.0
HE2 A:PHE515 4.2 83.7 1.0
HB2 A:HIS523 4.2 32.6 1.0
N A:LEU520 4.3 24.3 1.0
HB3 A:HIS523 4.3 32.6 1.0
O A:GLU519 4.3 26.7 1.0
CD1 A:LEU520 4.3 44.9 1.0
C A:GLU519 4.4 26.0 1.0
HE1 A:PHE515 4.4 75.9 1.0
CB A:LEU520 4.5 28.1 1.0
C6 A:ITO804 4.5 65.6 0.7
CG A:GLU519 4.5 38.0 1.0
HZ A:PHE515 4.6 88.1 1.0
HB3 A:GLU519 4.6 31.6 1.0
H A:LEU520 4.6 29.2 1.0
CB A:HIS523 4.7 27.1 1.0
CZ A:ARG573 4.7 31.0 1.0
HD1 A:HIS523 4.7 37.4 1.0
HH12 A:ARG573 4.7 33.3 1.0
OE1 A:GLU559 4.8 39.5 1.0
H3 A:ITO804 4.8 73.0 0.7

Chlorine binding site 4 out of 4 in 7zbv

Go back to Chlorine Binding Sites List in 7zbv
Chlorine binding site 4 out of 4 in the Crystal Structure of the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor


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 the Peptidase Domain of Collagenase G From Clostridium Histolyticum in Complex with A Diphosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:79.8
occ:0.70
 CL1 A:ITO804 0.0 79.8 0.7
C4 A:ITO804 1.7 66.9 0.7
C5 A:ITO804 2.7 60.7 0.7
C3 A:ITO804 2.7 72.3 0.7
HD11 A:ILE576 2.8 45.6 1.0
HH22 A:ARG573 2.8 41.8 1.0
OE1 A:GLU559 2.8 39.5 1.0
OE2 A:GLU559 2.8 47.1 1.0
H3 A:ITO804 2.8 73.0 0.7
CD A:GLU559 3.1 42.2 1.0
CL A:ITO804 3.2 83.1 0.7
HZ A:PHE515 3.3 88.1 1.0
CZ A:PHE515 3.4 73.4 1.0
HH12 A:ARG573 3.5 33.3 1.0
O A:HOH902 3.6 40.1 1.0
CD1 A:ILE576 3.6 38.0 1.0
NH2 A:ARG573 3.6 34.8 1.0
HD13 A:ILE576 3.7 45.6 1.0
CE2 A:PHE515 3.8 69.7 1.0
HD1 A:HIS523 3.9 37.4 1.0
HE2 A:PHE515 3.9 83.7 1.0
HD12 A:ILE576 3.9 45.6 1.0
CE1 A:PHE515 3.9 63.2 1.0
C2 A:ITO804 3.9 74.4 0.7
C6 A:ITO804 4.0 65.6 0.7
HH21 A:ARG573 4.1 41.8 1.0
NH1 A:ARG573 4.2 27.7 1.0
HE1 A:PHE515 4.2 75.9 1.0
ND1 A:HIS523 4.4 31.1 1.0
CZ A:ARG573 4.4 31.0 1.0
C1 A:ITO804 4.5 71.7 0.7
HE2 A:TYR579 4.5 57.7 1.0
CD2 A:PHE515 4.5 55.6 1.0
CG A:GLU559 4.6 27.4 1.0
CD1 A:PHE515 4.7 68.9 1.0
HE1 A:HIS523 4.7 41.8 1.0
CG1 A:ILE576 4.7 27.6 1.0
HD2 A:TYR607 4.7 49.5 1.0
HG12 A:ILE576 4.7 33.2 1.0
H2 A:ITO804 4.8 89.3 0.7
CE1 A:HIS523 4.8 34.8 1.0
HG13 A:ILE576 4.9 33.2 1.0
HH11 A:ARG573 4.9 33.3 1.0
CG A:PHE515 4.9 62.1 1.0
HG3 A:GLU559 5.0 32.9 1.0

Reference:

A.Alhayek, A.S.Abdelsamie, E.Schonauer, V.Camberlein, E.Hutterer, G.Posselt, J.Serwanja, C.Blochl, C.G.Huber, J.Haupenthal, H.Brandstetter, S.Wessler, A.K.H.Hirsch. Discovery and Characterization of Synthesized and Fda-Approved Inhibitors of Clostridial and Bacillary Collagenases. J.Med.Chem. V. 65 12933 2022.
ISSN: ISSN 0022-2623
PubMed: 36154055
DOI: 10.1021/ACS.JMEDCHEM.2C00785
Page generated: Tue Jul 30 06:10:52 2024

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