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Calcium in PDB 1hv5: Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor

Protein crystallography data

The structure of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor, PDB code: 1hv5 was solved by A.L.Gall, M.Ruff, R.Kannan, P.Cuniasse, A.Yiotakis, V.Dive, M.C.Rio, P.Basset, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 140.100, 148.500, 91.400, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.2

Other elements in 1hv5:

The structure of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor (pdb code 1hv5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor, PDB code: 1hv5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1hv5

Go back to Calcium Binding Sites List in 1hv5
Calcium binding site 1 out of 6 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5503

b:18.8
occ:1.00
 O A:GLY178 2.1 22.2 1.0
O A:GLY176 2.1 21.1 1.0
OD1 A:ASP175 2.2 21.7 1.0
OE2 A:GLU201 2.3 21.8 1.0
O A:ILE180 2.4 21.1 1.0
OD2 A:ASP198 2.4 18.8 1.0
C A:GLY178 3.3 22.2 1.0
C A:GLY176 3.3 21.9 1.0
CG A:ASP198 3.5 19.2 1.0
CG A:ASP175 3.5 22.6 1.0
CD A:GLU201 3.5 21.0 1.0
C A:ILE180 3.5 21.6 1.0
N A:ILE180 3.9 21.9 1.0
N A:GLY178 3.9 22.6 1.0
N A:GLY176 3.9 21.7 1.0
C A:PRO177 4.0 23.1 1.0
C A:ASP175 4.0 22.1 1.0
CB A:ASP198 4.1 18.5 1.0
OE1 A:GLU201 4.1 20.0 1.0
OD2 A:ASP175 4.1 23.1 1.0
CA A:GLY176 4.2 21.7 1.0
N A:ASP175 4.2 21.9 1.0
CA A:GLY178 4.2 22.2 1.0
C A:GLY179 4.2 22.2 1.0
CA A:ILE180 4.3 21.5 1.0
N A:PRO177 4.3 23.2 1.0
N A:GLY179 4.3 21.7 1.0
CA A:PRO177 4.4 23.3 1.0
OD1 A:ASP198 4.4 17.8 1.0
O A:PRO177 4.4 24.5 1.0
O A:ASP175 4.4 22.0 1.0
CA A:GLY179 4.5 21.3 1.0
CA A:ASP175 4.5 21.9 1.0
N A:LEU181 4.6 20.9 1.0
CB A:ASP175 4.6 22.2 1.0
CG A:GLU201 4.7 20.5 1.0
CA A:LEU181 4.8 19.1 1.0
CB A:ILE180 4.8 22.0 1.0
O A:GLY179 4.9 22.4 1.0

Calcium binding site 2 out of 6 in 1hv5

Go back to Calcium Binding Sites List in 1hv5
Calcium binding site 2 out of 6 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5506

b:26.1
occ:1.00
 O B:GLY176 2.2 33.4 1.0
OE2 B:GLU201 2.3 26.9 1.0
O B:GLY178 2.3 33.2 1.0
O B:ILE180 2.4 27.5 1.0
OD1 B:ASP175 2.4 29.9 1.0
OD2 B:ASP198 2.6 22.0 1.0
C B:GLY176 3.4 33.0 1.0
CD B:GLU201 3.4 25.9 1.0
CG B:ASP198 3.5 22.8 1.0
C B:GLY178 3.5 33.2 1.0
C B:ILE180 3.6 28.0 1.0
CG B:ASP175 3.7 30.9 1.0
OE1 B:GLU201 3.9 25.6 1.0
N B:ILE180 4.0 31.2 1.0
N B:GLY176 4.0 31.2 1.0
C B:PRO177 4.0 34.1 1.0
CB B:ASP198 4.0 21.9 1.0
N B:GLY178 4.0 33.7 1.0
C B:ASP175 4.1 30.5 1.0
N B:ASP175 4.2 29.1 1.0
CA B:GLY176 4.3 31.7 1.0
O B:PRO177 4.3 35.1 1.0
C B:GLY179 4.3 31.6 1.0
N B:PRO177 4.3 33.6 1.0
CA B:ILE180 4.4 29.8 1.0
OD1 B:ASP198 4.4 22.4 1.0
CA B:GLY178 4.4 33.2 1.0
O B:ASP175 4.4 30.1 1.0
OD2 B:ASP175 4.4 32.6 1.0
CA B:PRO177 4.4 34.0 1.0
N B:GLY179 4.5 32.9 1.0
CA B:ASP175 4.5 29.9 1.0
CA B:GLY179 4.6 32.0 1.0
N B:LEU181 4.6 26.5 1.0
CB B:ASP175 4.7 29.9 1.0
CG B:GLU201 4.7 26.3 1.0
CA B:LEU181 4.8 24.9 1.0
CB B:ILE180 4.8 31.0 1.0
O B:HOH6028 4.9 21.1 1.0
O B:GLY179 4.9 32.0 1.0

Calcium binding site 3 out of 6 in 1hv5

Go back to Calcium Binding Sites List in 1hv5
Calcium binding site 3 out of 6 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5509

b:24.1
occ:1.00
 O C:GLY176 2.1 25.2 1.0
OE2 C:GLU201 2.2 26.9 1.0
OD1 C:ASP175 2.3 26.5 1.0
O C:GLY178 2.3 25.2 1.0
OD2 C:ASP198 2.3 21.9 1.0
O C:ILE180 2.5 25.5 1.0
C C:GLY176 3.3 25.4 1.0
CG C:ASP198 3.4 21.6 1.0
CD C:GLU201 3.4 26.0 1.0
CG C:ASP175 3.5 28.2 1.0
C C:GLY178 3.5 25.9 1.0
C C:ILE180 3.6 24.9 1.0
N C:GLY176 3.7 27.6 1.0
N C:ILE180 3.8 26.6 1.0
N C:GLY178 3.9 24.8 1.0
CB C:ASP198 3.9 21.9 1.0
C C:PRO177 4.0 24.8 1.0
C C:ASP175 4.0 28.1 1.0
OE1 C:GLU201 4.1 25.5 1.0
CA C:GLY176 4.1 26.7 1.0
OD2 C:ASP175 4.1 28.9 1.0
N C:ASP175 4.2 28.1 1.0
C C:GLY179 4.2 26.8 1.0
CA C:ILE180 4.2 25.4 1.0
N C:PRO177 4.2 25.3 1.0
CA C:GLY178 4.3 25.1 1.0
OD1 C:ASP198 4.3 22.8 1.0
O C:PRO177 4.4 24.2 1.0
CA C:PRO177 4.4 25.0 1.0
CA C:ASP175 4.4 27.8 1.0
N C:GLY179 4.4 26.5 1.0
CG C:GLU201 4.5 25.5 1.0
CA C:GLY179 4.5 26.7 1.0
CB C:ASP175 4.5 27.6 1.0
N C:LEU181 4.6 25.1 1.0
O C:ASP175 4.6 27.9 1.0
CB C:ILE180 4.8 25.6 1.0
CA C:LEU181 4.8 24.4 1.0
O C:GLY179 4.8 27.2 1.0
CD2 C:LEU181 5.0 23.5 1.0

Calcium binding site 4 out of 6 in 1hv5

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Calcium binding site 4 out of 6 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca5512

b:15.6
occ:1.00
 O D:GLY176 2.2 23.0 1.0
O D:GLY178 2.3 18.7 1.0
OD2 D:ASP198 2.3 18.9 1.0
OE2 D:GLU201 2.3 18.9 1.0
O D:ILE180 2.5 17.6 1.0
OD1 D:ASP175 2.5 23.1 1.0
CG D:ASP198 3.3 20.7 1.0
C D:GLY176 3.4 23.5 1.0
C D:GLY178 3.5 19.1 1.0
CD D:GLU201 3.5 21.4 1.0
C D:ILE180 3.6 18.7 1.0
CG D:ASP175 3.6 25.4 1.0
CB D:ASP198 3.9 19.9 1.0
N D:GLY178 3.9 20.6 1.0
N D:GLY176 3.9 24.4 1.0
N D:ILE180 3.9 19.3 1.0
C D:ASP175 4.0 24.9 1.0
C D:PRO177 4.1 21.8 1.0
OE1 D:GLU201 4.2 20.8 1.0
N D:ASP175 4.2 27.3 1.0
OD1 D:ASP198 4.2 19.3 1.0
CA D:GLY178 4.3 19.1 1.0
CA D:GLY176 4.3 23.4 1.0
C D:GLY179 4.3 19.6 1.0
CA D:ILE180 4.3 19.3 1.0
OD2 D:ASP175 4.3 26.9 1.0
N D:PRO177 4.4 23.6 1.0
O D:ASP175 4.4 24.3 1.0
CA D:ASP175 4.4 26.1 1.0
N D:GLY179 4.5 18.9 1.0
CA D:PRO177 4.5 22.6 1.0
O D:PRO177 4.5 23.1 1.0
N D:LEU181 4.6 19.0 1.0
CB D:ASP175 4.6 26.1 1.0
CA D:GLY179 4.6 18.9 1.0
CG D:GLU201 4.6 22.1 1.0
CA D:LEU181 4.7 20.0 1.0
CB D:ILE180 4.8 20.0 1.0
O D:GLY179 4.9 20.4 1.0

Calcium binding site 5 out of 6 in 1hv5

Go back to Calcium Binding Sites List in 1hv5
Calcium binding site 5 out of 6 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5515

b:28.3
occ:1.00
 O E:GLY176 2.2 25.3 1.0
O E:GLY178 2.3 25.2 1.0
OE2 E:GLU201 2.3 24.9 1.0
O E:ILE180 2.4 20.7 1.0
OD1 E:ASP175 2.4 25.4 1.0
OD2 E:ASP198 2.4 22.1 1.0
C E:GLY176 3.4 26.0 1.0
CG E:ASP198 3.4 19.8 1.0
CD E:GLU201 3.5 25.1 1.0
CG E:ASP175 3.5 26.7 1.0
C E:GLY178 3.5 26.2 1.0
C E:ILE180 3.5 21.1 1.0
N E:GLY176 3.9 27.6 1.0
N E:ILE180 3.9 22.8 1.0
C E:ASP175 4.0 28.5 1.0
N E:GLY178 4.0 26.4 1.0
CB E:ASP198 4.0 18.2 1.0
C E:PRO177 4.1 27.3 1.0
OE1 E:GLU201 4.1 26.6 1.0
OD2 E:ASP175 4.1 26.5 1.0
N E:ASP175 4.2 29.3 1.0
CA E:GLY176 4.2 26.9 1.0
C E:GLY179 4.2 23.9 1.0
OD1 E:ASP198 4.3 19.9 1.0
N E:PRO177 4.3 26.4 1.0
CA E:ILE180 4.3 21.6 1.0
O E:ASP175 4.4 29.6 1.0
CA E:GLY178 4.4 25.9 1.0
CA E:PRO177 4.4 27.0 1.0
CA E:ASP175 4.4 28.4 1.0
O E:PRO177 4.5 28.5 1.0
N E:GLY179 4.5 25.5 1.0
N E:LEU181 4.5 20.5 1.0
CA E:GLY179 4.5 24.3 1.0
CB E:ASP175 4.6 27.5 1.0
CA E:LEU181 4.6 20.1 1.0
CG E:GLU201 4.6 24.1 1.0
O E:GLY179 4.8 24.4 1.0
CB E:ILE180 4.9 22.1 1.0

Calcium binding site 6 out of 6 in 1hv5

Go back to Calcium Binding Sites List in 1hv5
Calcium binding site 6 out of 6 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca5518

b:18.8
occ:1.00
 OE2 F:GLU201 2.2 22.4 1.0
O F:GLY178 2.2 22.9 1.0
O F:GLY176 2.2 23.9 1.0
OD2 F:ASP198 2.3 21.6 1.0
O F:ILE180 2.5 23.3 1.0
OD1 F:ASP175 2.5 27.9 1.0
CG F:ASP198 3.3 20.0 1.0
C F:GLY178 3.4 23.7 1.0
CD F:GLU201 3.4 20.7 1.0
C F:GLY176 3.4 25.0 1.0
CG F:ASP175 3.6 28.3 1.0
C F:ILE180 3.6 23.0 1.0
N F:GLY176 3.9 25.6 1.0
N F:GLY178 3.9 25.1 1.0
N F:ILE180 3.9 23.1 1.0
CB F:ASP198 4.0 18.6 1.0
OE1 F:GLU201 4.0 21.1 1.0
C F:PRO177 4.1 25.7 1.0
C F:ASP175 4.1 26.0 1.0
OD2 F:ASP175 4.2 29.9 1.0
CA F:GLY178 4.2 23.4 1.0
OD1 F:ASP198 4.2 19.6 1.0
CA F:GLY176 4.2 24.3 1.0
N F:ASP175 4.3 27.7 1.0
C F:GLY179 4.3 23.3 1.0
CA F:ILE180 4.3 23.2 1.0
N F:PRO177 4.4 25.9 1.0
N F:GLY179 4.4 23.9 1.0
O F:PRO177 4.4 25.7 1.0
CA F:PRO177 4.5 25.4 1.0
CA F:ASP175 4.5 26.5 1.0
CG F:GLU201 4.6 20.2 1.0
N F:LEU181 4.6 21.6 1.0
O F:ASP175 4.6 26.0 1.0
CA F:GLY179 4.6 23.1 1.0
CB F:ASP175 4.6 27.3 1.0
CA F:LEU181 4.7 20.5 1.0
CB F:ILE180 4.8 23.5 1.0
O F:GLY179 4.9 23.2 1.0
CD2 F:LEU181 4.9 17.9 1.0

Reference:

A.L.Gall, M.Ruff, R.Kannan, P.Cuniasse, A.Yiotakis, V.Dive, M.C.Rio, P.Basset, D.Moras. Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor Mimicking the Transition-State. J.Mol.Biol. V. 307 577 2001.
ISSN: ISSN 0022-2836
PubMed: 11254383
DOI: 10.1006/JMBI.2001.4493
Page generated: Thu Jul 11 10:09:58 2024

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