Zinc in PDB 2yig: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor
Protein crystallography data
The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig
was solved by
S.Gerhardt,
D.Hargreaves,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
67.12 /
1.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.417,
36.074,
95.206,
90.00,
131.49,
90.00
|
R / Rfree (%)
|
18.4 /
22.1
|
Other elements in 2yig:
The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor
(pdb code 2yig). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2yig
Go back to
Zinc Binding Sites List in 2yig
Zinc binding site 1 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:10.9
occ:1.00
|
NE2
|
A:HIS222
|
2.1
|
8.1
|
1.0
|
NE2
|
A:HIS226
|
2.1
|
7.9
|
1.0
|
NE2
|
A:HIS232
|
2.2
|
11.3
|
1.0
|
O
|
A:HOH480
|
2.3
|
13.8
|
1.0
|
CD2
|
A:HIS222
|
2.9
|
8.5
|
1.0
|
CD2
|
A:HIS232
|
3.0
|
11.3
|
1.0
|
CD2
|
A:HIS226
|
3.0
|
7.8
|
1.0
|
CE1
|
A:HIS226
|
3.1
|
8.6
|
1.0
|
CE1
|
A:HIS222
|
3.2
|
8.5
|
1.0
|
CE1
|
A:HIS232
|
3.2
|
11.6
|
1.0
|
OE2
|
A:GLU223
|
4.0
|
8.7
|
1.0
|
CG
|
A:HIS222
|
4.1
|
8.2
|
1.0
|
CG
|
A:HIS232
|
4.2
|
10.4
|
1.0
|
CG
|
A:HIS226
|
4.2
|
7.9
|
1.0
|
ND1
|
A:HIS226
|
4.2
|
8.4
|
1.0
|
ND1
|
A:HIS222
|
4.2
|
8.4
|
1.0
|
ND1
|
A:HIS232
|
4.3
|
10.8
|
1.0
|
OE1
|
A:GLU223
|
4.5
|
8.3
|
1.0
|
CD
|
A:GLU223
|
4.6
|
7.9
|
1.0
|
C20
|
A:5EL301
|
4.6
|
12.6
|
1.0
|
CE
|
A:MET240
|
4.7
|
8.6
|
1.0
|
O
|
A:HOH504
|
4.7
|
16.8
|
1.0
|
C21
|
A:5EL301
|
4.8
|
11.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2yig
Go back to
Zinc Binding Sites List in 2yig
Zinc binding site 2 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn304
b:11.0
occ:1.00
|
OD2
|
A:ASP174
|
2.0
|
9.0
|
1.0
|
NE2
|
A:HIS172
|
2.0
|
7.8
|
1.0
|
ND1
|
A:HIS200
|
2.0
|
9.6
|
1.0
|
NE2
|
A:HIS187
|
2.1
|
11.1
|
1.0
|
CD2
|
A:HIS172
|
2.9
|
8.9
|
1.0
|
CG
|
A:ASP174
|
2.9
|
10.6
|
1.0
|
CE1
|
A:HIS187
|
3.0
|
10.9
|
1.0
|
CE1
|
A:HIS200
|
3.0
|
10.5
|
1.0
|
CG
|
A:HIS200
|
3.1
|
9.3
|
1.0
|
CE1
|
A:HIS172
|
3.1
|
9.0
|
1.0
|
CD2
|
A:HIS187
|
3.1
|
10.0
|
1.0
|
OD1
|
A:ASP174
|
3.1
|
10.5
|
1.0
|
CB
|
A:HIS200
|
3.4
|
8.4
|
1.0
|
CG
|
A:HIS172
|
4.1
|
8.9
|
1.0
|
O
|
A:TYR176
|
4.1
|
10.6
|
1.0
|
ND1
|
A:HIS187
|
4.1
|
11.3
|
1.0
|
ND1
|
A:HIS172
|
4.1
|
8.8
|
1.0
|
NE2
|
A:HIS200
|
4.2
|
10.1
|
1.0
|
CG
|
A:HIS187
|
4.2
|
9.6
|
1.0
|
CD2
|
A:HIS200
|
4.2
|
9.7
|
1.0
|
CB
|
A:ASP174
|
4.3
|
10.5
|
1.0
|
CB
|
A:TYR176
|
4.4
|
13.0
|
1.0
|
CE1
|
A:PHE189
|
4.5
|
11.7
|
1.0
|
CZ
|
A:PHE178
|
4.7
|
9.2
|
1.0
|
CZ
|
A:PHE189
|
4.8
|
12.3
|
1.0
|
CE2
|
A:PHE178
|
4.8
|
8.5
|
1.0
|
C
|
A:TYR176
|
4.8
|
11.2
|
1.0
|
O
|
A:HOH467
|
4.9
|
12.9
|
1.0
|
CA
|
A:HIS200
|
4.9
|
8.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2yig
Go back to
Zinc Binding Sites List in 2yig
Zinc binding site 3 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:14.8
occ:1.00
|
NE2
|
B:HIS232
|
2.1
|
15.4
|
1.0
|
NE2
|
B:HIS222
|
2.1
|
11.2
|
1.0
|
NE2
|
B:HIS226
|
2.1
|
11.9
|
1.0
|
O
|
B:HOH500
|
2.2
|
24.1
|
1.0
|
CD2
|
B:HIS232
|
2.9
|
14.9
|
1.0
|
CD2
|
B:HIS222
|
3.0
|
10.5
|
1.0
|
CD2
|
B:HIS226
|
3.0
|
11.3
|
1.0
|
CE1
|
B:HIS226
|
3.2
|
13.4
|
1.0
|
CE1
|
B:HIS232
|
3.2
|
15.8
|
1.0
|
CE1
|
B:HIS222
|
3.2
|
10.9
|
1.0
|
OE2
|
B:GLU223
|
4.1
|
10.1
|
1.0
|
CG
|
B:HIS232
|
4.1
|
16.1
|
1.0
|
CG
|
B:HIS222
|
4.2
|
10.5
|
1.0
|
ND1
|
B:HIS232
|
4.2
|
15.6
|
1.0
|
CG
|
B:HIS226
|
4.2
|
11.2
|
1.0
|
ND1
|
B:HIS226
|
4.2
|
11.1
|
1.0
|
ND1
|
B:HIS222
|
4.3
|
11.2
|
1.0
|
O
|
B:HOH493
|
4.5
|
17.3
|
1.0
|
C20
|
B:5EL301
|
4.6
|
15.6
|
1.0
|
OE1
|
B:GLU223
|
4.7
|
11.5
|
1.0
|
CD
|
B:GLU223
|
4.7
|
9.8
|
1.0
|
C21
|
B:5EL301
|
4.8
|
14.9
|
1.0
|
CE
|
B:MET240
|
4.8
|
11.7
|
1.0
|
O
|
B:HOH513
|
4.9
|
36.5
|
1.0
|
O
|
B:HOH483
|
4.9
|
33.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2yig
Go back to
Zinc Binding Sites List in 2yig
Zinc binding site 4 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn303
b:11.0
occ:1.00
|
OD2
|
B:ASP174
|
2.0
|
11.6
|
1.0
|
NE2
|
B:HIS187
|
2.0
|
11.0
|
1.0
|
NE2
|
B:HIS172
|
2.1
|
9.4
|
1.0
|
ND1
|
B:HIS200
|
2.1
|
11.2
|
1.0
|
CG
|
B:ASP174
|
2.9
|
11.4
|
1.0
|
CE1
|
B:HIS187
|
2.9
|
10.2
|
1.0
|
CD2
|
B:HIS172
|
3.0
|
9.7
|
1.0
|
CE1
|
B:HIS200
|
3.0
|
10.3
|
1.0
|
CG
|
B:HIS200
|
3.1
|
10.3
|
1.0
|
CD2
|
B:HIS187
|
3.1
|
11.0
|
1.0
|
OD1
|
B:ASP174
|
3.1
|
10.8
|
1.0
|
CE1
|
B:HIS172
|
3.2
|
10.7
|
1.0
|
CB
|
B:HIS200
|
3.5
|
9.2
|
1.0
|
ND1
|
B:HIS187
|
4.1
|
10.9
|
1.0
|
NE2
|
B:HIS200
|
4.2
|
10.2
|
1.0
|
CG
|
B:HIS172
|
4.2
|
9.6
|
1.0
|
CD2
|
B:HIS200
|
4.2
|
9.7
|
1.0
|
O
|
B:TYR176
|
4.2
|
12.0
|
1.0
|
CG
|
B:HIS187
|
4.3
|
10.1
|
1.0
|
ND1
|
B:HIS172
|
4.3
|
9.8
|
1.0
|
CB
|
B:ASP174
|
4.3
|
11.2
|
1.0
|
CE1
|
B:PHE189
|
4.6
|
16.2
|
1.0
|
CZ
|
B:PHE178
|
4.6
|
9.4
|
1.0
|
CE2
|
B:PHE178
|
4.7
|
9.3
|
1.0
|
O
|
B:HOH436
|
4.8
|
10.1
|
1.0
|
CZ
|
B:PHE189
|
4.8
|
18.2
|
1.0
|
CB
|
B:TYR176
|
4.8
|
12.6
|
1.0
|
CA
|
B:HIS200
|
5.0
|
9.2
|
1.0
|
|
Reference:
C.D.Savi,
A.D.Morley,
A.Ting,
I.Nash,
K.Karabelas,
C.M.Wood,
M.James,
S.J.Norris,
G.Karoutchi,
N.Rankine,
G.Hamlin,
P.A.Macfaul,
D.Ryan,
S.V.Baker,
D.Hargreaves,
S.Gerhardt.
Selective Non Zinc Binding Inhibitors of MMP13. Bioorg.Med.Chem.Lett. V. 21 4215 2011.
ISSN: ISSN 0960-894X
PubMed: 21669521
DOI: 10.1016/J.BMCL.2011.05.075
Page generated: Thu Oct 17 05:51:34 2024
|