Atomistry » Calcium » PDB 1hov-1i6t » 1hv5
Atomistry »
  Calcium »
    PDB 1hov-1i6t »
      1hv5 »

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

Go back to Calcium Binding Sites List in 1hv5
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy