Atomistry » Calcium » PDB 3uix-3v03 » 3uvc
Atomistry »
  Calcium »
    PDB 3uix-3v03 »
      3uvc »

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

Go back to Calcium Binding Sites List in 3uvc
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

Go back to Calcium Binding Sites List in 3uvc
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

Go back to Calcium Binding Sites List in 3uvc
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: Sat Jul 13 20:19:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy