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Zinc in PDB 1g4k: X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

Enzymatic activity of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

All present enzymatic activity of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin:
3.4.24.17;

Protein crystallography data

The structure of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin, PDB code: 1g4k was solved by P.Dunten, U.Kammlott, R.Crowther, W.Levin, L.H.Foley, P.Wang, R.Palermo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.800, 103.800, 147.490, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 28.4

Other elements in 1g4k:

The structure of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin also contains other interesting chemical elements:

Calcium (Ca) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin (pdb code 1g4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin, PDB code: 1g4k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1g4k

Go back to Zinc Binding Sites List in 1g4k
Zinc binding site 1 out of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.2
occ:1.00
NE2 A:HIS211 1.9 18.4 1.0
NE2 A:HIS201 1.9 14.8 1.0
N3 A:HQQ306 2.0 27.5 1.0
NE2 A:HIS205 2.1 18.6 1.0
C4 A:HQQ306 2.7 28.6 1.0
CE1 A:HIS201 2.8 12.2 1.0
C2 A:HQQ306 2.9 28.9 1.0
CE1 A:HIS211 2.9 23.0 1.0
O4 A:HQQ306 2.9 27.6 1.0
CD2 A:HIS211 2.9 14.9 1.0
CE1 A:HIS205 3.0 15.4 1.0
O2 A:HQQ306 3.0 29.0 1.0
CD2 A:HIS201 3.1 17.4 1.0
CD2 A:HIS205 3.1 11.7 1.0
ND1 A:HIS201 4.0 14.1 1.0
ND1 A:HIS211 4.0 17.8 1.0
CG A:HIS211 4.1 21.7 1.0
N1 A:HQQ306 4.1 27.8 1.0
CG A:HIS201 4.1 18.6 1.0
C5 A:HQQ306 4.2 27.4 1.0
ND1 A:HIS205 4.2 13.7 1.0
CG A:HIS205 4.2 13.4 1.0
C8 A:HQQ306 4.4 28.9 1.0
O A:HOH313 4.6 18.5 1.0
OE2 A:GLU202 4.6 24.5 1.0
C6 A:HQQ306 4.7 27.6 1.0
C9 A:HQQ306 4.7 27.8 1.0
C13 A:HQQ306 4.8 28.9 1.0
CE A:MET219 4.9 15.6 1.0
O A:HOH358 5.0 36.5 1.0

Zinc binding site 2 out of 6 in 1g4k

Go back to Zinc Binding Sites List in 1g4k
Zinc binding site 2 out of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:18.4
occ:1.00
OD2 A:ASP153 1.9 16.6 1.0
NE2 A:HIS166 2.0 25.5 1.0
NE2 A:HIS151 2.0 20.8 1.0
ND1 A:HIS179 2.1 12.4 1.0
CE1 A:HIS179 2.9 14.4 1.0
CG A:ASP153 2.9 25.4 1.0
CE1 A:HIS166 2.9 25.6 1.0
CD2 A:HIS151 2.9 19.9 1.0
CD2 A:HIS166 3.0 16.6 1.0
CE1 A:HIS151 3.1 18.4 1.0
CG A:HIS179 3.2 12.1 1.0
OD1 A:ASP153 3.2 19.1 1.0
CB A:HIS179 3.6 11.4 1.0
NE2 A:HIS179 4.1 20.4 1.0
ND1 A:HIS166 4.1 23.2 1.0
CG A:HIS151 4.1 22.4 1.0
CG A:HIS166 4.2 20.0 1.0
ND1 A:HIS151 4.2 21.1 1.0
OH A:TYR168 4.2 28.3 1.0
O A:TYR155 4.2 21.5 1.0
CB A:ASP153 4.3 21.4 1.0
CD2 A:HIS179 4.3 16.0 1.0
CE1 A:TYR168 4.5 24.3 1.0
CZ A:PHE157 4.5 15.1 1.0
CE2 A:PHE157 4.7 24.3 1.0
CZ A:TYR168 4.9 26.8 1.0

Zinc binding site 3 out of 6 in 1g4k

Go back to Zinc Binding Sites List in 1g4k
Zinc binding site 3 out of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:13.8
occ:1.00
NE2 B:HIS205 2.0 14.1 1.0
NE2 B:HIS211 2.1 17.6 1.0
NE2 B:HIS201 2.1 14.9 1.0
N3 B:HQQ306 2.1 14.2 1.0
CE1 B:HIS205 2.9 9.7 1.0
C2 B:HQQ306 2.9 13.8 1.0
CD2 B:HIS211 3.0 13.9 1.0
C4 B:HQQ306 3.0 14.0 1.0
O2 B:HQQ306 3.0 15.7 1.0
CD2 B:HIS201 3.0 13.2 1.0
CE1 B:HIS211 3.0 11.1 1.0
CD2 B:HIS205 3.1 11.1 1.0
O4 B:HQQ306 3.1 13.8 1.0
CE1 B:HIS201 3.1 13.8 1.0
ND1 B:HIS205 4.1 10.2 1.0
CG B:HIS211 4.2 12.0 1.0
CG B:HIS201 4.2 12.4 1.0
ND1 B:HIS211 4.2 9.4 1.0
CG B:HIS205 4.2 10.7 1.0
N1 B:HQQ306 4.2 13.8 1.0
ND1 B:HIS201 4.2 12.7 1.0
C5 B:HQQ306 4.4 13.4 1.0
O B:HOH311 4.5 13.8 1.0
C8 B:HQQ306 4.6 13.0 1.0
C9 B:HQQ306 4.7 13.3 1.0
CE B:MET219 4.7 14.8 1.0
OE2 B:GLU202 4.7 17.5 1.0
C6 B:HQQ306 4.8 13.5 1.0
O A:HOH370 4.9 33.5 1.0

Zinc binding site 4 out of 6 in 1g4k

Go back to Zinc Binding Sites List in 1g4k
Zinc binding site 4 out of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:16.7
occ:1.00
OD2 B:ASP153 1.9 16.1 1.0
NE2 B:HIS166 2.0 16.2 1.0
ND1 B:HIS179 2.0 12.5 1.0
NE2 B:HIS151 2.1 18.5 1.0
CE1 B:HIS179 2.9 16.9 1.0
CG B:ASP153 2.9 19.2 1.0
CD2 B:HIS166 2.9 19.8 1.0
CD2 B:HIS151 3.0 16.7 1.0
CE1 B:HIS166 3.0 12.4 1.0
CG B:HIS179 3.1 13.5 1.0
CE1 B:HIS151 3.2 17.5 1.0
OD1 B:ASP153 3.2 17.0 1.0
CB B:HIS179 3.5 10.4 1.0
NE2 B:HIS179 4.0 14.9 1.0
ND1 B:HIS166 4.1 17.9 1.0
CG B:HIS166 4.1 15.7 1.0
CG B:HIS151 4.2 18.3 1.0
CD2 B:HIS179 4.2 11.6 1.0
OH B:TYR168 4.2 25.4 1.0
ND1 B:HIS151 4.2 15.8 1.0
CB B:ASP153 4.2 19.6 1.0
O B:TYR155 4.4 16.6 1.0
CE1 B:TYR168 4.5 19.3 1.0
CZ B:PHE157 4.5 9.9 1.0
CE2 B:PHE157 4.7 12.6 1.0
CZ B:TYR168 4.8 26.3 1.0
CA B:HIS179 5.0 12.1 1.0
O B:HOH316 5.0 15.1 1.0

Zinc binding site 5 out of 6 in 1g4k

Go back to Zinc Binding Sites List in 1g4k
Zinc binding site 5 out of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:34.8
occ:1.00
NE2 C:HIS201 2.0 34.6 1.0
NE2 C:HIS211 2.0 40.1 1.0
N3 C:HQQ306 2.1 44.1 1.0
NE2 C:HIS205 2.2 36.4 1.0
CD2 C:HIS201 2.9 25.8 1.0
CD2 C:HIS211 2.9 31.1 1.0
C2 C:HQQ306 3.0 43.2 1.0
C4 C:HQQ306 3.0 43.4 1.0
O4 C:HQQ306 3.0 42.9 1.0
CD2 C:HIS205 3.1 38.8 1.0
CE1 C:HIS211 3.1 48.8 1.0
O2 C:HQQ306 3.1 42.6 1.0
CE1 C:HIS201 3.2 31.2 1.0
CE1 C:HIS205 3.2 39.6 1.0
CG C:HIS211 4.1 36.5 1.0
CG C:HIS201 4.1 32.4 1.0
ND1 C:HIS211 4.2 39.5 1.0
ND1 C:HIS201 4.2 32.8 1.0
N1 C:HQQ306 4.3 43.6 1.0
CG C:HIS205 4.3 37.4 1.0
ND1 C:HIS205 4.3 36.9 1.0
C5 C:HQQ306 4.4 43.8 1.0
C8 C:HQQ306 4.5 45.1 1.0
C9 C:HQQ306 4.7 45.1 1.0
OE2 C:GLU202 4.7 37.3 1.0
CE C:MET219 4.8 20.4 1.0
C6 C:HQQ306 4.8 44.0 1.0

Zinc binding site 6 out of 6 in 1g4k

Go back to Zinc Binding Sites List in 1g4k
Zinc binding site 6 out of 6 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:45.5
occ:1.00
NE2 C:HIS151 1.6 74.8 1.0
OD2 C:ASP153 1.8 39.9 1.0
NE2 C:HIS166 1.9 50.7 1.0
ND1 C:HIS179 2.2 36.8 1.0
CD2 C:HIS151 2.4 75.5 1.0
CE1 C:HIS166 2.5 56.2 1.0
CE1 C:HIS151 2.8 75.3 1.0
CG C:ASP153 2.8 49.5 1.0
CG C:HIS179 3.1 31.7 1.0
CD2 C:HIS166 3.1 57.8 1.0
OD1 C:ASP153 3.2 47.1 1.0
CE1 C:HIS179 3.2 37.5 1.0
CB C:HIS179 3.4 32.1 1.0
CG C:HIS151 3.6 75.7 1.0
ND1 C:HIS151 3.7 75.2 1.0
ND1 C:HIS166 3.7 54.5 1.0
CG C:HIS166 4.0 54.4 1.0
OH C:TYR168 4.1 48.5 1.0
O C:TYR155 4.1 70.5 1.0
CB C:ASP153 4.2 54.6 1.0
CD2 C:HIS179 4.2 37.5 1.0
NE2 C:HIS179 4.3 33.6 1.0
CE1 C:TYR168 4.7 43.4 1.0
CZ C:PHE157 4.8 41.5 1.0
CA C:HIS179 4.9 37.6 1.0
CZ C:TYR168 4.9 45.4 1.0
CB C:HIS151 4.9 75.3 1.0
CE2 C:PHE157 5.0 44.2 1.0

Reference:

P.Dunten, U.Kammlott, R.Crowther, W.Levin, L.H.Foley, P.Wang, R.Palermo. X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin. Protein Sci. V. 10 923 2001.
ISSN: ISSN 0961-8368
PubMed: 11316871
DOI: 10.1110/PS.48401
Page generated: Sun Oct 13 01:19:46 2024

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