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Calcium in PDB 3uvc: MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin

Enzymatic activity of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin

All present enzymatic activity of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin:
3.4.24.65;

Protein crystallography data

The structure of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin, PDB code: 3uvc was solved by D.J.Derbyshire, H.Danielson, S.Nystrum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.49 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.746, 60.625, 58.403, 90.00, 103.10, 90.00
R / Rfree (%) 13 / 17.4

Other elements in 3uvc:

The structure of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin (pdb code 3uvc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin, PDB code: 3uvc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3uvc

Go back to Calcium Binding Sites List in 3uvc
Calcium binding site 1 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.6
occ:1.00
 O A:HOH431 2.3 17.1 1.0
O A:GLU199 2.4 12.0 1.0
OE2 A:GLU199 2.4 13.2 1.0
OD1 A:ASP124 2.4 12.4 1.0
O A:GLU201 2.4 12.2 1.0
O A:HOH414 2.4 16.5 1.0
OD2 A:ASP124 2.6 13.1 1.0
CG A:ASP124 2.8 12.4 1.0
CD A:GLU199 3.4 13.7 1.0
C A:GLU199 3.5 12.2 1.0
C A:GLU201 3.6 12.1 1.0
CG A:GLU199 3.9 13.4 1.0
CA A:GLU199 4.1 11.3 1.0
OG1 A:THR122 4.1 14.0 1.0
O A:HOH468 4.1 37.1 1.0
CA A:PHE202 4.3 12.4 0.5
CA A:PHE202 4.3 12.5 0.5
CD1 A:TRP203 4.3 11.2 1.0
CB A:ASP124 4.3 12.8 1.0
N A:PHE202 4.4 12.4 1.0
N A:GLU201 4.4 11.9 1.0
C A:ASP200 4.5 12.9 1.0
N A:ASP200 4.5 12.0 1.0
OE1 A:GLU199 4.6 15.1 1.0
O A:HOH458 4.6 22.3 1.0
CB A:GLU199 4.6 12.6 1.0
CA A:ASP200 4.7 12.7 1.0
CA A:GLU201 4.7 12.1 1.0
NH2 A:ARG165 4.7 19.3 0.4
N A:TRP203 4.8 11.3 1.0
NE1 A:TRP203 4.8 11.6 1.0
CD1 A:PHE202 4.9 14.7 0.5
O A:HOH483 4.9 26.2 1.0
O A:ASP200 4.9 13.3 1.0

Calcium binding site 2 out of 7 in 3uvc

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Calcium binding site 2 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.4
occ:1.00
 O A:HOH444 2.3 18.8 1.0
O A:ASP158 2.3 12.9 1.0
O A:GLY190 2.3 13.1 1.0
O A:GLY192 2.3 12.9 1.0
O A:HOH402 2.4 12.7 1.0
OD2 A:ASP194 2.5 12.4 1.0
C A:ASP158 3.4 12.0 1.0
CG A:ASP194 3.5 12.1 1.0
C A:GLY190 3.5 14.2 1.0
C A:GLY192 3.5 11.9 1.0
OD1 A:ASP194 3.9 12.8 1.0
O A:HOH441 3.9 19.9 1.0
C A:ILE191 4.0 13.4 1.0
N A:GLY192 4.1 13.3 1.0
O A:HOH614 4.1 35.6 1.0
O A:ALA157 4.1 14.9 1.0
O A:ILE191 4.2 12.7 1.0
N A:ASP194 4.3 11.4 1.0
CA A:ASP158 4.3 12.4 1.0
CA A:ILE191 4.3 15.1 1.0
CA A:GLY192 4.4 12.3 1.0
N A:ILE191 4.4 14.8 1.0
O A:GLY188 4.4 15.8 1.0
N A:ILE159 4.4 12.5 1.0
N A:GLY190 4.4 15.1 1.0
CA A:GLY190 4.5 14.2 1.0
N A:GLY193 4.5 11.1 1.0
CA A:ILE159 4.5 12.1 1.0
CA A:GLY193 4.6 11.3 1.0
N A:LEU160 4.6 11.4 1.0
CB A:ASP194 4.7 12.1 1.0
C A:GLY193 4.7 10.8 1.0
O A:HOH411 4.8 17.6 1.0
C A:SER189 4.8 15.8 1.0
CA A:ASP194 4.8 10.7 1.0
CH2 A:TRP109 5.0 14.3 1.0

Calcium binding site 3 out of 7 in 3uvc

Go back to Calcium Binding Sites List in 3uvc
Calcium binding site 3 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:12.9
occ:1.00
 O A:GLY176 2.2 13.8 1.0
OD1 A:ASP198 2.3 13.9 1.0
OE2 A:GLU201 2.3 16.9 1.0
O A:ILE180 2.3 12.7 1.0
OD2 A:ASP175 2.4 13.7 1.0
O A:GLY178 2.4 16.2 1.0
CG A:ASP198 3.4 11.6 1.0
C A:ILE180 3.5 12.8 1.0
C A:GLY176 3.5 14.4 1.0
CG A:ASP175 3.5 14.5 1.0
C A:GLY178 3.5 15.9 1.0
CD A:GLU201 3.5 15.0 1.0
N A:GLY178 3.8 16.6 1.0
N A:ILE180 3.9 13.9 1.0
OD1 A:ASP175 4.0 16.2 1.0
C A:LYS177 4.1 16.4 1.0
CB A:ASP198 4.1 10.9 1.0
N A:GLY176 4.1 15.1 1.0
CA A:ILE180 4.1 14.2 1.0
CA A:GLY178 4.2 17.0 1.0
CA A:LYS177 4.3 16.1 0.7
CA A:LYS177 4.3 16.2 0.3
C A:ASP175 4.3 15.3 1.0
N A:ASP175 4.3 13.9 1.0
N A:LYS177 4.3 15.1 1.0
CG A:GLU201 4.4 14.4 1.0
OE1 A:GLU201 4.4 14.8 1.0
OD2 A:ASP198 4.4 11.4 1.0
CA A:GLY176 4.4 14.6 1.0
CB A:ILE180 4.4 14.8 1.0
C A:GLY179 4.4 14.7 1.0
N A:LEU181 4.5 11.9 1.0
N A:GLY179 4.5 16.1 1.0
CA A:ASP175 4.7 14.9 1.0
CB A:ASP175 4.7 14.5 1.0
O A:LYS177 4.7 18.3 1.0
CA A:LEU181 4.7 12.1 1.0
O A:ASP175 4.8 16.8 1.0
CA A:GLY179 4.8 15.3 1.0
O A:HOH666 4.9 49.3 1.0

Calcium binding site 4 out of 7 in 3uvc

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Calcium binding site 4 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:16.9
occ:1.00
 O A:HOH410 2.3 18.0 1.0
O A:THR145 2.3 15.9 1.0
O A:HOH427 2.3 23.4 1.0
O A:HOH446 2.4 21.5 1.0
O A:SER142 2.4 14.7 1.0
O A:HOH401 2.4 26.5 1.0
O A:HOH428 2.5 22.6 1.0
C A:THR145 3.5 15.6 1.0
C A:SER142 3.6 14.6 1.0
CA A:PRO146 4.2 16.0 1.0
N A:THR145 4.2 15.8 1.0
N A:PRO146 4.2 15.5 1.0
CA A:SER142 4.4 14.2 0.5
CA A:SER142 4.4 14.0 0.5
O A:HOH534 4.4 30.3 1.0
C A:ASN143 4.5 16.6 1.0
CA A:THR145 4.5 16.1 1.0
O A:HOH533 4.5 20.3 0.5
O A:HOH536 4.5 67.5 1.0
N A:ASN143 4.6 14.2 1.0
O A:LEU147 4.6 15.6 1.0
CA A:ASN143 4.6 15.7 1.0
C A:PRO146 4.7 16.1 1.0
O A:ASN143 4.7 17.3 1.0
CB A:SER142 4.7 13.8 0.5
CB A:SER142 4.7 13.2 0.5
N A:VAL144 4.8 15.7 1.0
N A:LEU147 4.9 15.9 1.0

Calcium binding site 5 out of 7 in 3uvc

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Calcium binding site 5 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:13.5
occ:1.00
 O B:GLU199 2.4 13.2 1.0
OD1 B:ASP124 2.4 12.7 1.0
O B:HOH417 2.4 18.9 1.0
O B:GLU201 2.4 13.2 1.0
OE2 B:GLU199 2.4 13.3 1.0
O B:HOH423 2.4 19.8 1.0
OD2 B:ASP124 2.6 14.9 1.0
CG B:ASP124 2.8 12.7 1.0
CD B:GLU199 3.5 13.0 1.0
C B:GLU199 3.5 12.2 1.0
C B:GLU201 3.6 12.5 1.0
CG B:GLU199 3.9 13.8 1.0
OG1 B:THR122 4.2 14.2 1.0
CA B:GLU199 4.2 12.3 1.0
CA B:PHE202 4.2 13.4 1.0
CD1 B:TRP203 4.3 11.2 1.0
N B:PHE202 4.3 13.3 1.0
CB B:ASP124 4.4 13.7 1.0
N B:GLU201 4.5 12.8 1.0
C B:ASP200 4.5 13.6 1.0
N B:ASP200 4.5 12.8 1.0
OE1 B:GLU199 4.6 15.2 1.0
O B:HOH506 4.6 37.7 1.0
CB B:GLU199 4.6 13.2 1.0
O B:HOH428 4.6 23.7 1.0
CA B:GLU201 4.7 13.2 1.0
CA B:ASP200 4.7 13.9 1.0
N B:TRP203 4.7 12.3 1.0
NE1 B:TRP203 4.8 11.3 1.0
O B:HOH443 4.9 40.6 1.0
O B:ASP200 4.9 14.4 1.0

Calcium binding site 6 out of 7 in 3uvc

Go back to Calcium Binding Sites List in 3uvc
Calcium binding site 6 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:16.1
occ:1.00
 O B:HOH412 2.3 20.2 1.0
O B:GLY190 2.3 18.5 1.0
O B:ASP158 2.3 14.0 1.0
O B:GLY192 2.3 14.5 1.0
O B:HOH408 2.4 17.5 1.0
OD2 B:ASP194 2.4 14.4 1.0
CG B:ASP194 3.4 12.5 1.0
C B:ASP158 3.5 14.1 1.0
C B:GLY190 3.5 18.6 1.0
C B:GLY192 3.5 14.1 1.0
OD1 B:ASP194 3.9 13.7 1.0
C B:ILE191 4.0 15.4 1.0
N B:GLY192 4.0 15.2 1.0
O B:ILE191 4.2 14.9 1.0
O B:ALA157 4.2 18.1 1.0
CA B:ASP158 4.2 15.0 1.0
O B:HOH445 4.2 39.3 1.0
N B:ASP194 4.3 12.2 1.0
CA B:ILE191 4.3 17.1 1.0
CA B:GLY192 4.4 14.6 1.0
N B:ILE191 4.4 17.4 1.0
CA B:GLY190 4.4 19.7 1.0
O B:GLY188 4.4 19.5 1.0
N B:ILE159 4.4 13.1 1.0
N B:GLY193 4.5 13.2 1.0
N B:GLY190 4.5 21.6 1.0
CA B:GLY193 4.6 13.0 1.0
CA B:ILE159 4.6 13.4 1.0
CB B:ASP194 4.7 13.1 1.0
N B:LEU160 4.7 14.0 1.0
C B:GLY193 4.7 12.5 1.0
O B:HOH424 4.7 22.8 1.0
O B:HOH555 4.8 64.0 1.0
CA B:ASP194 4.8 12.6 1.0
C B:SER189 4.9 21.8 1.0
CH2 B:TRP109 5.0 15.8 1.0

Calcium binding site 7 out of 7 in 3uvc

Go back to Calcium Binding Sites List in 3uvc
Calcium binding site 7 out of 7 in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca307

b:15.5
occ:1.00
 O B:ILE180 2.2 16.9 1.0
OD1 B:ASP198 2.3 15.5 1.0
OE2 B:GLU201 2.3 20.9 1.0
OD2 B:ASP175 2.3 17.2 1.0
O B:GLY176 2.3 16.4 1.0
O B:GLY178 2.4 18.0 1.0
CG B:ASP198 3.4 12.8 1.0
C B:ILE180 3.4 16.0 1.0
CG B:ASP175 3.5 17.9 1.0
CD B:GLU201 3.5 17.9 1.0
C B:GLY176 3.5 17.6 1.0
C B:GLY178 3.6 18.5 1.0
N B:GLY178 3.8 18.3 1.0
N B:ILE180 3.9 16.6 1.0
OD1 B:ASP175 4.0 19.9 1.0
CB B:ASP198 4.0 12.4 1.0
N B:GLY176 4.1 18.5 1.0
CA B:ILE180 4.1 16.6 0.6
C B:LYS177 4.2 19.1 1.0
CA B:ILE180 4.2 16.4 0.4
C B:GLY179 4.3 17.5 1.0
C B:ASP175 4.3 19.2 1.0
CA B:GLY178 4.3 19.3 1.0
N B:ASP175 4.3 18.1 1.0
OD2 B:ASP198 4.4 13.7 1.0
OE1 B:GLU201 4.4 18.5 1.0
CG B:GLU201 4.4 14.6 1.0
CA B:LYS177 4.4 19.1 0.6
CA B:LYS177 4.4 19.1 0.4
N B:LYS177 4.4 18.3 1.0
CA B:GLY176 4.5 17.9 1.0
N B:LEU181 4.5 13.9 1.0
CB B:ILE180 4.6 17.6 0.6
N B:GLY179 4.6 18.4 1.0
CB B:ILE180 4.6 16.9 0.4
CA B:ASP175 4.6 18.9 1.0
CB B:ASP175 4.6 18.7 1.0
CA B:LEU181 4.7 13.6 1.0
CA B:GLY179 4.7 18.0 1.0
O B:ASP175 4.7 20.3 1.0
O B:LYS177 4.7 20.7 1.0
O B:GLY179 4.8 19.7 1.0
O B:HOH568 5.0 33.0 0.5

Reference:

H.Nordstrom, T.Gossas, D.J.Derbyshire, H.Danielson. Characterization of Fragments Interacting with Mmp-12 To Be Published.
Page generated: Tue Jul 8 17:22:03 2025

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