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Calcium in PDB 1ycm: Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh)

Enzymatic activity of Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh)

All present enzymatic activity of Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh):
3.4.24.65;

Other elements in 1ycm:

The structure of Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh) also contains other interesting chemical elements:

Zinc (Zn) 40 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh) (pdb code 1ycm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh), PDB code: 1ycm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1ycm

Go back to Calcium Binding Sites List in 1ycm
Calcium binding site 1 out of 3 in the Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:1.0
occ:1.00
 OD2 A:ASP124 2.2 1.5 1.0
OE1 A:GLU199 2.2 2.1 1.0
O A:GLU199 2.3 0.8 1.0
O A:GLU201 2.5 1.0 1.0
OG1 A:THR122 2.6 2.4 1.0
OD1 A:ASP124 2.8 2.3 1.0
CG A:ASP124 2.9 1.3 1.0
HG1 A:THR122 3.0 2.7 1.0
HD1 A:TRP203 3.4 1.4 1.0
CD A:GLU199 3.5 2.3 1.0
C A:GLU199 3.5 0.7 1.0
HA A:PHE202 3.5 0.9 1.0
C A:GLU201 3.6 0.9 1.0
HA A:GLU199 3.8 0.9 1.0
CB A:THR122 3.8 2.0 1.0
HG3 A:GLU199 3.8 1.9 1.0
HB A:THR122 3.9 2.4 1.0
HD2 A:PRO123 3.9 1.4 1.0
H A:TRP203 4.0 0.8 1.0
HA A:THR122 4.1 1.7 1.0
CE1 A:PHE202 4.1 5.7 1.0
HE1 A:PHE202 4.1 7.4 1.0
CA A:GLU199 4.2 0.8 1.0
CG A:GLU199 4.2 1.5 1.0
CD1 A:PHE202 4.2 4.1 1.0
HD1 A:PHE202 4.3 4.9 1.0
O A:ASP200 4.3 1.0 1.0
CB A:ASP124 4.3 1.4 1.0
CD1 A:TRP203 4.4 1.1 1.0
CA A:PHE202 4.4 0.9 1.0
N A:PHE202 4.4 0.9 1.0
C A:ASP200 4.4 0.8 1.0
OE2 A:GLU199 4.4 3.7 1.0
HB2 A:ASP124 4.4 1.6 1.0
HE1 A:TRP203 4.5 1.2 1.0
H A:ASP124 4.5 1.1 1.0
CA A:THR122 4.5 1.4 1.0
N A:GLU201 4.5 0.8 1.0
N A:ASP200 4.6 0.8 1.0
CZ A:PHE202 4.6 5.2 1.0
CA A:GLU201 4.7 0.9 1.0
HG23 A:THR122 4.7 2.6 1.0
CB A:GLU199 4.8 1.1 1.0
CG A:PHE202 4.8 2.0 1.0
HB3 A:ASP124 4.8 1.8 1.0
CG2 A:THR122 4.8 2.2 1.0
NE1 A:TRP203 4.8 1.0 1.0
HA A:ASP200 4.8 1.0 1.0
CA A:ASP200 4.9 0.9 1.0
H A:GLU201 5.0 0.8 1.0
CD A:PRO123 5.0 1.3 1.0
N A:TRP203 5.0 0.8 1.0

Calcium binding site 2 out of 3 in 1ycm

Go back to Calcium Binding Sites List in 1ycm
Calcium binding site 2 out of 3 in the Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:1.4
occ:1.00
 OD1 A:ASP175 2.2 1.1 1.0
OE2 A:GLU201 2.2 1.0 1.0
OD1 A:ASP198 2.3 2.2 1.0
OD2 A:ASP198 2.4 2.4 1.0
O A:ASP175 2.4 3.7 1.0
O A:GLY178 2.4 1.8 1.0
O A:ILE180 2.4 1.2 1.0
O A:GLY176 2.5 1.6 1.0
CG A:ASP198 2.6 1.3 1.0
H A:GLY178 3.2 2.1 1.0
H A:ASP175 3.2 1.4 1.0
HG3 A:GLU201 3.2 1.9 1.0
C A:ASP175 3.3 2.0 1.0
CD A:GLU201 3.4 1.1 1.0
CG A:ASP175 3.5 1.3 1.0
C A:ILE180 3.6 1.1 1.0
C A:GLY176 3.6 1.5 1.0
C A:GLY178 3.6 1.9 1.0
CB A:ASP198 3.8 0.7 1.0
H A:ILE180 3.8 1.7 1.0
CG A:GLU201 3.8 1.1 1.0
HB3 A:ASP198 3.8 1.6 1.0
HB2 A:ASP198 3.9 1.4 1.0
N A:ASP175 4.0 1.3 1.0
N A:ILE180 4.0 1.6 1.0
N A:GLY178 4.0 2.0 1.0
N A:GLY176 4.0 1.2 1.0
HD12 A:LEU181 4.0 1.4 1.0
CA A:ASP175 4.1 1.6 1.0
HB3 A:ASP200 4.1 1.1 1.0
HA A:LEU181 4.3 0.9 1.0
CB A:ASP175 4.3 1.5 1.0
HB2 A:GLU201 4.3 1.7 1.0
CA A:GLY176 4.3 1.5 1.0
CA A:ILE180 4.4 1.3 1.0
OD2 A:ASP175 4.4 1.6 1.0
HA3 A:GLY179 4.4 2.0 1.0
OE1 A:GLU201 4.4 2.0 1.0
C A:GLY179 4.4 1.7 1.0
CA A:GLY178 4.5 2.1 1.0
H A:GLU201 4.5 0.8 1.0
HA2 A:GLY176 4.6 1.7 1.0
N A:GLY179 4.6 2.0 1.0
N A:LEU181 4.6 0.9 1.0
CB A:GLU201 4.6 1.1 1.0
HB A:ILE180 4.6 1.7 1.0
HA A:LYS177 4.7 2.1 1.0
HG2 A:GLU201 4.7 2.0 1.0
HB2 A:ASP175 4.7 1.9 1.0
N A:LYS177 4.7 1.6 1.0
CA A:GLY179 4.7 1.9 1.0
HD1 A:PHE174 4.7 4.2 1.0
H A:GLY176 4.9 1.9 1.0
HB2 A:ASP200 4.9 1.7 1.0
HA2 A:GLY178 4.9 2.3 1.0
HB3 A:PHE174 4.9 1.4 1.0
N A:GLU201 5.0 0.8 1.0
CB A:ASP200 5.0 1.1 1.0

Calcium binding site 3 out of 3 in 1ycm

Go back to Calcium Binding Sites List in 1ycm
Calcium binding site 3 out of 3 in the Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Solution Structure of Matrix Metalloproteinase 12 (MMP12) in the Presence of N-Isobutyl-N-[4- Methoxyphenylsulfonyl]Glycyl Hydroxamic Acid (Nngh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:1.1
occ:1.00
 OD1 A:ASP194 2.2 1.1 1.0
O A:GLY192 2.4 1.1 1.0
OD2 A:ASP194 2.6 1.5 1.0
O A:GLY190 2.7 1.2 1.0
CG A:ASP194 2.8 0.9 1.0
O A:ILE191 3.0 1.2 1.0
H A:ASP194 3.3 0.8 1.0
HA3 A:GLY193 3.4 0.9 1.0
C A:GLY192 3.5 1.0 1.0
C A:ILE191 3.7 1.1 1.0
HA A:ILE191 3.9 1.2 1.0
C A:GLY190 3.9 1.3 1.0
N A:ASP194 4.0 0.7 1.0
CB A:ASP194 4.1 0.7 1.0
CA A:GLY193 4.1 0.8 1.0
HA A:ILE159 4.2 0.7 1.0
N A:GLY193 4.2 0.9 1.0
N A:GLY192 4.3 1.2 1.0
CA A:ILE191 4.3 1.2 1.0
HB2 A:ASP194 4.4 0.7 1.0
C A:GLY193 4.4 0.8 1.0
CA A:GLY192 4.5 1.1 1.0
O A:ASP158 4.5 0.7 1.0
N A:ILE191 4.6 1.2 1.0
CA A:ASP194 4.6 0.7 1.0
HB3 A:ASP194 4.9 0.8 1.0
HA A:ASP194 4.9 0.6 1.0
HG22 A:ILE159 5.0 0.8 1.0

Reference:

I.Bertini, V.Calderone, M.Cosenza, M.Fragai, Y.M.Lee, C.Luchinat, S.Mangani, B.Terni, P.Turano. Conformational Variability of Matrix Metalloproteinases: Beyond A Single 3D Structure. Proc.Natl.Acad.Sci.Usa V. 102 5334 2005.
ISSN: ISSN 0027-8424
PubMed: 15809432
DOI: 10.1073/PNAS.0407106102
Page generated: Sat Dec 12 03:28:37 2020

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