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Zinc 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
Calcium (Ca) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the MMP12 in A Complex with the Dimeric Adduct: 5-(5-Phenylhydantoin)-5- Phenylhydantoin, PDB code: 3uvc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3uvc

Go back to Zinc Binding Sites List in 3uvc
Zinc binding site 1 out of 6 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 Zinc with other atoms in the Zn 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:Zn301

b:12.4
occ:1.00
 N2 A:0D2314 1.9 12.7 1.0
NE2 A:HIS222 2.0 11.1 1.0
NE2 A:HIS228 2.0 12.3 1.0
NE2 A:HIS218 2.0 13.1 1.0
C1 A:0D2314 2.9 15.4 1.0
CE1 A:HIS222 2.9 13.6 1.0
CD2 A:HIS218 3.0 11.5 1.0
CD2 A:HIS228 3.0 13.7 1.0
C3 A:0D2314 3.0 14.2 1.0
CE1 A:HIS228 3.0 13.3 1.0
CD2 A:HIS222 3.0 12.0 1.0
CE1 A:HIS218 3.1 12.4 1.0
O12 A:0D2314 3.1 16.6 1.0
O13 A:0D2314 3.3 14.7 1.0
ND1 A:HIS222 4.1 12.9 1.0
ND1 A:HIS228 4.1 14.7 1.0
CG A:HIS228 4.1 13.4 1.0
CG A:HIS218 4.1 11.5 1.0
CG A:HIS222 4.1 10.9 1.0
N4 A:0D2314 4.1 16.1 1.0
ND1 A:HIS218 4.2 11.5 1.0
C5 A:0D2314 4.2 15.3 1.0
CE A:MET236 4.6 13.7 1.0
O A:HOH413 4.6 14.8 1.0
C22 A:0D2314 4.8 17.6 1.0
CA A:PRO238 4.8 15.2 1.0
C21 A:0D2314 4.9 17.7 1.0
O A:HOH464 4.9 21.8 1.0

Zinc binding site 2 out of 6 in 3uvc

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Zinc binding site 2 out of 6 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 Zinc with other atoms in the Zn 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:Zn302

b:12.1
occ:1.00
 NE2 A:HIS168 2.0 10.9 1.0
OD1 A:ASP170 2.0 12.7 1.0
NE2 A:HIS183 2.0 12.7 1.0
ND1 A:HIS196 2.0 11.0 1.0
CD2 A:HIS168 2.9 11.9 1.0
CG A:ASP170 2.9 13.0 1.0
CE1 A:HIS183 2.9 12.6 1.0
CE1 A:HIS196 3.0 11.9 1.0
CE1 A:HIS168 3.1 12.5 1.0
CD2 A:HIS183 3.1 13.0 1.0
CG A:HIS196 3.1 9.8 1.0
OD2 A:ASP170 3.1 12.4 1.0
CB A:HIS196 3.4 10.4 1.0
ND1 A:HIS183 4.1 13.7 1.0
CG A:HIS168 4.1 14.1 1.0
NE2 A:HIS196 4.1 10.8 1.0
ND1 A:HIS168 4.1 13.4 1.0
CG A:HIS183 4.2 11.2 1.0
CD2 A:HIS196 4.2 11.0 1.0
O A:HIS172 4.3 14.6 1.0
CB A:ASP170 4.3 13.6 1.0
CB A:HIS172 4.3 13.3 1.0
CE1 A:PHE185 4.5 18.2 1.0
O A:HOH543 4.7 41.8 1.0
CZ A:PHE174 4.7 12.6 1.0
CZ A:PHE185 4.8 17.6 1.0
CE2 A:PHE174 4.9 12.9 1.0
C A:HIS172 4.9 13.0 1.0
CA A:HIS196 5.0 9.9 1.0

Zinc binding site 3 out of 6 in 3uvc

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Zinc binding site 3 out of 6 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 Zinc with other atoms in the Zn 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:Zn306

b:13.8
occ:0.90
 ND1 A:HIS172 2.0 14.0 1.0
ND1 B:HIS228 2.1 14.3 1.0
N3 A:IMD307 2.1 14.7 0.9
CL B:CL301 2.2 14.4 1.0
CE1 B:HIS228 2.9 13.9 1.0
CE1 A:HIS172 3.0 14.9 1.0
C4 A:IMD307 3.0 16.9 0.9
C2 A:IMD307 3.1 17.2 0.9
CG A:HIS172 3.1 13.0 1.0
CG B:HIS228 3.2 13.1 1.0
CB A:HIS172 3.5 13.3 1.0
CB B:HIS228 3.8 13.6 1.0
NE2 B:HIS228 4.1 12.7 1.0
NE2 A:HIS172 4.1 16.6 1.0
CA A:HIS172 4.2 12.5 1.0
CD2 A:HIS172 4.2 15.4 1.0
O A:HOH412 4.2 12.8 1.0
N1 A:IMD307 4.2 18.0 0.9
C5 A:IMD307 4.2 18.6 0.9
CD2 B:HIS228 4.3 14.6 1.0
CB B:PRO238 4.4 18.4 1.0
CB A:HIS183 4.5 10.3 1.0
CG A:HIS183 4.6 11.2 1.0
CG B:PRO238 4.6 19.1 1.0
ND1 A:HIS183 4.7 13.7 1.0
C8 A:0D2314 4.9 16.5 1.0
O B:HOH474 4.9 33.0 1.0
O A:HOH439 4.9 17.5 1.0

Zinc binding site 4 out of 6 in 3uvc

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Zinc binding site 4 out of 6 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 Zinc with other atoms in the Zn 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
B:Zn303

b:12.2
occ:1.00
 N3 B:IMD311 2.0 14.9 1.0
NE2 B:HIS228 2.0 12.7 1.0
NE2 B:HIS218 2.0 11.2 1.0
NE2 B:HIS222 2.1 11.5 1.0
C4 B:IMD311 2.9 19.3 1.0
CE1 B:HIS228 3.0 13.9 1.0
CD2 B:HIS218 3.0 12.1 1.0
C2 B:IMD311 3.0 17.2 1.0
CE1 B:HIS218 3.0 10.8 1.0
CD2 B:HIS228 3.0 14.6 1.0
CD2 B:HIS222 3.1 10.4 1.0
CE1 B:HIS222 3.1 13.6 1.0
O B:HOH581 3.3 42.3 1.0
ND1 B:HIS228 4.1 14.3 1.0
ND1 B:HIS218 4.1 11.5 1.0
C5 B:IMD311 4.1 20.6 1.0
N1 B:IMD311 4.1 20.6 1.0
CG B:HIS218 4.1 10.9 1.0
CG B:HIS228 4.1 13.1 1.0
ND1 B:HIS222 4.2 13.5 1.0
CG B:HIS222 4.2 11.4 1.0
O B:HOH442 4.3 27.1 1.0
O B:HOH404 4.6 15.1 1.0
CE B:MET236 4.7 12.5 1.0
O1 B:EDO312 4.8 30.0 0.5
O B:HOH474 4.8 33.0 1.0
O2 B:EDO312 5.0 28.9 0.5
O A:HOH422 5.0 15.8 1.0

Zinc binding site 5 out of 6 in 3uvc

Go back to Zinc Binding Sites List in 3uvc
Zinc binding site 5 out of 6 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 Zinc with other atoms in the Zn 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:Zn304

b:13.3
occ:1.00
 OD1 B:ASP170 1.9 15.1 1.0
NE2 B:HIS168 2.0 12.7 1.0
NE2 B:HIS183 2.0 12.2 1.0
ND1 B:HIS196 2.1 10.5 1.0
CG B:ASP170 2.9 16.0 1.0
CD2 B:HIS168 2.9 14.1 1.0
CE1 B:HIS183 2.9 12.8 1.0
CE1 B:HIS196 3.0 14.5 1.0
CE1 B:HIS168 3.0 15.1 1.0
CD2 B:HIS183 3.1 11.1 1.0
CG B:HIS196 3.1 9.9 1.0
OD2 B:ASP170 3.2 15.9 1.0
CB B:HIS196 3.5 10.8 1.0
ND1 B:HIS183 4.1 12.4 1.0
CG B:HIS168 4.1 15.6 1.0
ND1 B:HIS168 4.1 16.1 1.0
NE2 B:HIS196 4.1 14.2 1.0
CG B:HIS183 4.2 11.9 1.0
O B:HIS172 4.2 17.2 1.0
CD2 B:HIS196 4.2 11.6 1.0
CB B:ASP170 4.2 17.5 1.0
CE1 B:PHE185 4.3 16.5 1.0
CZ B:PHE185 4.6 18.3 1.0
CZ B:PHE174 4.6 14.3 1.0
CE2 B:PHE174 4.7 14.7 1.0
O B:HOH510 4.8 35.1 1.0
CB B:HIS172 4.8 15.6 1.0
O B:HOH410 5.0 18.8 1.0

Zinc binding site 6 out of 6 in 3uvc

Go back to Zinc Binding Sites List in 3uvc
Zinc binding site 6 out of 6 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 Zinc with other atoms in the Zn 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:Zn308

b:19.9
occ:0.80
 O B:HOH446 1.8 21.4 0.3
N1 A:IMD313 2.0 32.3 0.5
NE2 B:HIS172 2.0 18.1 1.0
N3 A:IMD312 2.0 21.5 0.5
N1 A:IMD312 2.0 20.7 0.5
N3 B:IMD309 2.1 29.7 0.7
O A:HOH469 2.1 14.9 0.5
C2 B:IMD309 2.8 30.2 0.7
C2 A:IMD313 2.9 32.2 0.5
CE1 B:HIS172 3.0 19.2 1.0
C4 A:IMD312 3.0 21.5 0.5
C2 A:IMD312 3.0 20.7 0.5
C5 A:IMD312 3.0 19.8 0.5
CD2 B:HIS172 3.0 16.0 1.0
C2 A:IMD312 3.0 20.6 0.5
C5 A:IMD313 3.0 32.1 0.5
C4 B:IMD309 3.3 30.3 0.7
N1 B:IMD309 4.1 30.7 0.7
N3 A:IMD313 4.1 32.5 0.5
ND1 B:HIS172 4.1 17.7 1.0
N3 A:IMD312 4.1 20.7 0.5
CG B:HIS172 4.1 16.0 1.0
C5 A:IMD312 4.1 21.6 0.5
N1 A:IMD312 4.2 20.9 0.5
C4 A:IMD313 4.2 32.8 0.5
C4 A:IMD312 4.2 20.2 0.5
O A:HOH667 4.2 25.0 0.5
C5 B:IMD309 4.3 30.8 0.7
CE2 B:PHE185 4.5 17.6 1.0
O B:ASP170 4.7 19.8 1.0
O A:GLY169 4.7 20.3 1.0

Reference:

H.Nordstrom, T.Gossas, D.J.Derbyshire, H.Danielson. Characterization of Fragments Interacting with Mmp-12 To Be Published.
Page generated: Sat Oct 26 17:27:54 2024

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