Atomistry » Calcium » PDB 3s7w-3sle » 3shi
Atomistry »
  Calcium »
    PDB 3s7w-3sle »
      3shi »

Calcium in PDB 3shi: Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution

Enzymatic activity of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution

All present enzymatic activity of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution:
3.4.24.7;

Protein crystallography data

The structure of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution, PDB code: 3shi was solved by I.Bertini, V.Calderone, L.Cerofolini, M.Fragai, C.F.G.C.Geraldes, P.Hermann, C.Luchinat, G.Parigi, J.Teixeira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.65 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.694, 54.528, 94.905, 90.00, 120.69, 90.00
R / Rfree (%) 20.9 / 27.8

Other elements in 3shi:

The structure of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution (pdb code 3shi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution, PDB code: 3shi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 1 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:24.3
occ:1.00
 O A:ASN180 2.2 23.7 1.0
OE2 A:GLU201 2.2 22.0 1.0
O A:GLY178 2.3 25.6 1.0
OD2 A:ASP198 2.3 25.7 1.0
O A:GLY176 2.4 22.3 1.0
OD1 A:ASP175 2.4 26.5 1.0
C A:ASN180 3.4 22.7 1.0
CG A:ASP198 3.4 23.1 1.0
CD A:GLU201 3.5 21.2 1.0
C A:GLY178 3.5 23.4 1.0
CG A:ASP175 3.6 27.4 1.0
C A:GLY176 3.6 20.9 1.0
N A:GLY178 3.8 21.6 1.0
N A:GLY176 4.0 23.2 1.0
N A:ASN180 4.0 23.8 1.0
CB A:ASP198 4.0 21.3 1.0
C A:PRO177 4.1 22.7 1.0
N A:ASP175 4.2 27.6 1.0
OD2 A:ASP175 4.2 26.6 1.0
C A:ASP175 4.2 25.2 1.0
OE1 A:GLU201 4.2 21.6 1.0
CA A:ASN180 4.3 22.6 1.0
CA A:GLY178 4.3 23.1 1.0
N A:LEU181 4.3 22.2 1.0
OD1 A:ASP198 4.3 21.5 1.0
C A:GLY179 4.4 23.3 1.0
CG A:GLU201 4.4 20.9 1.0
CA A:PRO177 4.5 21.6 1.0
CA A:GLY176 4.5 21.7 1.0
CA A:LEU181 4.5 20.9 1.0
N A:PRO177 4.5 23.8 1.0
N A:GLY179 4.5 21.1 1.0
CA A:ASP175 4.6 26.1 1.0
O A:PRO177 4.6 26.6 1.0
CB A:ASP175 4.7 30.1 1.0
CA A:GLY179 4.7 22.3 1.0
O A:ASP175 4.7 25.2 1.0
CB A:ASN180 4.8 22.7 1.0
CD2 A:LEU181 4.9 20.0 1.0

Calcium binding site 2 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 2 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:25.6
occ:1.00
 OD2 A:ASP124 2.3 24.0 1.0
O A:GLU201 2.4 20.3 1.0
OE2 A:GLU199 2.4 24.1 1.0
O M:HOH287 2.6 25.3 1.0
O A:GLU199 2.6 25.7 1.0
O A:HOH338 2.7 24.8 1.0
O M:HOH1 2.7 21.1 1.0
OD1 A:ASP124 2.8 24.7 1.0
CG A:ASP124 2.9 26.3 1.0
C A:GLU201 3.5 22.6 1.0
CD A:GLU199 3.5 26.0 1.0
C A:GLU199 3.7 25.2 1.0
CG A:GLU199 4.0 23.5 1.0
N A:ARG202 4.2 24.1 1.0
CA A:ARG202 4.2 24.6 1.0
N A:GLU201 4.3 18.1 1.0
OG1 A:THR122 4.3 22.0 1.0
CB A:ASP124 4.4 24.3 1.0
CA A:GLU199 4.4 23.7 1.0
CD1 A:TRP203 4.4 22.8 1.0
O A:HOH74 4.4 32.5 1.0
C A:ASP200 4.5 20.3 1.0
CA A:GLU201 4.6 20.6 1.0
OE1 A:GLU199 4.6 27.7 1.0
N A:ASP200 4.7 22.9 1.0
O M:ASN143 4.7 27.0 1.0
N A:TRP203 4.7 24.9 1.0
CA A:ASP200 4.8 20.3 1.0
CB A:GLU199 4.8 26.9 1.0
O A:ASP200 4.9 19.7 1.0
NH2 A:ARG165 4.9 28.0 1.0
O A:HOH316 5.0 37.9 1.0
NE1 A:TRP203 5.0 22.4 1.0

Calcium binding site 3 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 3 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:32.7
occ:1.00
 O A:ASP158 2.2 28.0 1.0
O A:GLY190 2.2 25.9 1.0
OD1 A:ASP194 2.4 26.2 1.0
O A:GLY192 2.4 24.1 1.0
O A:HOH309 2.4 33.0 1.0
O A:HOH17 2.5 20.2 1.0
C A:ASP158 3.4 30.6 1.0
CG A:ASP194 3.5 30.3 1.0
C A:GLY190 3.5 26.8 1.0
C A:GLY192 3.6 26.5 1.0
O A:HOH284 4.0 39.5 1.0
C A:ILE191 4.0 28.7 1.0
OD2 A:ASP194 4.1 28.4 1.0
O A:ILE191 4.1 26.1 1.0
O A:ALA157 4.1 33.9 1.0
N A:ASP194 4.1 27.7 1.0
N A:GLY192 4.1 28.3 1.0
O A:GLY188 4.3 37.2 1.0
CA A:ASP158 4.3 28.9 1.0
CA A:ILE191 4.4 30.0 1.0
N A:ILE191 4.4 28.3 1.0
N A:ILE159 4.4 26.6 1.0
C A:GLY193 4.4 27.8 1.0
CA A:GLY190 4.4 28.9 1.0
CA A:GLY193 4.5 25.9 1.0
CA A:GLY192 4.5 26.2 1.0
N A:GLY190 4.5 34.1 1.0
N A:GLY193 4.5 26.3 1.0
CA A:ILE159 4.6 25.1 1.0
N A:MET160 4.6 29.5 1.0
CB A:ASP194 4.7 27.8 1.0
CA A:ASP194 4.7 27.5 1.0
CH2 A:TRP109 4.7 33.7 1.0
CG A:MET160 4.7 29.3 1.0
C A:PRO189 4.9 35.0 1.0

Calcium binding site 4 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 4 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca303

b:32.4
occ:1.00
 OD2 G:ASP198 2.1 25.0 1.0
O G:GLY178 2.3 39.1 1.0
O G:ASN180 2.3 29.9 1.0
O G:GLY176 2.3 32.5 1.0
OE2 G:GLU201 2.4 31.8 1.0
OD1 G:ASP175 2.5 47.7 1.0
CG G:ASP198 3.3 26.4 1.0
C G:ASN180 3.4 33.5 1.0
C G:GLY178 3.5 44.3 1.0
CG G:ASP175 3.5 40.0 1.0
C G:GLY176 3.5 38.7 1.0
CD G:GLU201 3.7 29.3 1.0
N G:GLY178 3.9 38.3 1.0
OD2 G:ASP175 4.0 37.6 1.0
N G:ASN180 4.0 36.1 1.0
CB G:ASP198 4.0 24.8 1.0
N G:GLY176 4.1 40.9 1.0
C G:PRO177 4.1 39.8 1.0
OD1 G:ASP198 4.2 27.0 1.0
N G:ASP175 4.2 36.2 1.0
C G:ASP175 4.2 39.1 1.0
CA G:GLY178 4.2 40.3 1.0
CA G:ASN180 4.2 37.1 1.0
C G:GLY179 4.4 37.7 1.0
N G:LEU181 4.4 29.2 1.0
OE1 G:GLU201 4.4 30.2 1.0
CA G:GLY176 4.4 37.5 1.0
N G:PRO177 4.5 38.2 1.0
N G:GLY179 4.5 44.0 1.0
O G:PRO177 4.5 37.8 1.0
CA G:PRO177 4.5 37.8 1.0
CA G:ASP175 4.6 40.4 1.0
CG G:GLU201 4.6 28.1 1.0
CA G:LEU181 4.6 30.7 1.0
CB G:ASP175 4.6 40.0 1.0
O G:ASP175 4.7 36.8 1.0
CA G:GLY179 4.7 41.0 1.0
CD2 G:LEU181 4.8 24.1 1.0
CB G:ASN180 4.9 38.2 1.0
O G:GLY179 4.9 39.9 1.0

Calcium binding site 5 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 5 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca304

b:31.8
occ:1.00
 OE2 G:GLU199 2.3 22.9 1.0
OD2 G:ASP124 2.4 42.1 1.0
O G:GLU201 2.5 25.1 1.0
O G:GLU199 2.5 32.4 1.0
O A:HOH94 2.6 34.4 1.0
O A:HOH16 2.7 27.7 1.0
OD1 G:ASP124 2.7 40.0 1.0
CG G:ASP124 2.9 43.3 1.0
CD G:GLU199 3.4 29.6 1.0
C G:GLU199 3.6 29.6 1.0
C G:GLU201 3.6 27.4 1.0
CG G:GLU199 3.9 25.8 1.0
OG1 G:THR122 4.3 29.6 1.0
CA G:GLU199 4.3 26.1 1.0
CA G:ARG202 4.3 28.4 1.0
CD1 G:TRP203 4.4 28.7 1.0
N G:ARG202 4.4 28.9 1.0
CB G:ASP124 4.4 41.5 1.0
N G:GLU201 4.4 25.4 1.0
O A:ASN143 4.5 32.8 1.0
C G:ASP200 4.5 28.5 1.0
OE1 G:GLU199 4.5 30.3 1.0
N G:ASP200 4.6 29.6 1.0
CA G:ASP200 4.7 29.2 1.0
CA G:GLU201 4.7 25.5 1.0
CB G:GLU199 4.7 26.1 1.0
N G:TRP203 4.7 26.4 1.0
OD1 A:ASN143 4.8 28.4 1.0
NE1 G:TRP203 4.9 28.1 1.0
O G:HOH326 5.0 40.9 1.0

Calcium binding site 6 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 6 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca305

b:32.8
occ:1.00
 O G:HOH285 2.3 28.5 1.0
O G:GLY192 2.3 34.1 1.0
O G:ASP158 2.4 32.4 1.0
OD1 G:ASP194 2.4 36.7 1.0
O G:GLY190 2.4 36.8 1.0
CG G:ASP194 3.3 34.4 1.0
C G:ASP158 3.5 32.6 1.0
C G:GLY192 3.6 28.7 1.0
C G:GLY190 3.7 37.2 1.0
OD2 G:ASP194 3.7 36.2 1.0
C G:ILE191 4.0 35.4 1.0
O G:ALA157 4.0 41.6 1.0
O G:ILE191 4.2 37.7 1.0
O G:GLY188 4.2 36.6 1.0
N G:GLY192 4.2 29.9 1.0
CA G:ASP158 4.2 36.9 1.0
N G:ASP194 4.3 26.5 1.0
N G:GLY190 4.4 37.1 1.0
CA G:ILE191 4.4 38.4 1.0
N G:ILE159 4.4 30.2 1.0
N G:GLY193 4.5 29.8 1.0
CA G:GLY192 4.5 27.9 1.0
N G:ILE191 4.5 38.0 1.0
CA G:GLY193 4.5 26.8 1.0
CA G:GLY190 4.6 35.3 1.0
N G:MET160 4.6 31.9 1.0
O G:HOH332 4.6 57.0 1.0
CB G:ASP194 4.6 30.2 1.0
CG G:MET160 4.7 34.2 1.0
CA G:ILE159 4.7 26.2 1.0
CH2 G:TRP109 4.7 37.3 1.0
C G:PRO189 4.7 39.5 1.0
C G:GLY193 4.8 28.1 1.0
CA G:ASP194 4.9 27.5 1.0
C G:ALA157 4.9 42.2 1.0

Calcium binding site 7 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 7 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca303

b:49.0
occ:1.00
 O M:GLY178 2.1 46.2 1.0
OE2 M:GLU201 2.1 39.5 1.0
OD1 M:ASP175 2.3 50.2 1.0
OD2 M:ASP198 2.3 43.5 1.0
O M:GLY176 2.6 65.9 1.0
O M:ASN180 2.7 55.0 1.0
CG M:ASP175 3.2 57.8 1.0
C M:GLY178 3.3 50.1 1.0
CD M:GLU201 3.4 40.6 1.0
CG M:ASP198 3.5 49.8 1.0
C M:ASN180 3.5 50.2 1.0
OD2 M:ASP175 3.6 52.5 1.0
N M:ASN180 3.7 45.3 1.0
C M:GLY176 3.8 64.1 1.0
N M:GLY178 3.9 61.9 1.0
O M:ASP175 4.0 62.0 1.0
C M:PRO177 4.1 60.1 1.0
OE1 M:GLU201 4.1 41.5 1.0
CA M:ASN180 4.1 49.2 1.0
CB M:ASP198 4.1 46.4 1.0
C M:ASP175 4.2 55.5 1.0
CA M:GLY178 4.2 55.4 1.0
C M:GLY179 4.2 50.9 1.0
N M:GLY179 4.3 45.0 1.0
CG M:GLU201 4.4 39.3 1.0
CA M:GLY179 4.4 46.8 1.0
CA M:PRO177 4.4 61.3 1.0
N M:LEU181 4.4 44.5 1.0
O M:PRO177 4.5 58.6 1.0
OD1 M:ASP198 4.5 47.9 1.0
N M:GLY176 4.5 57.8 1.0
CB M:ASP175 4.5 53.5 1.0
N M:ASP175 4.5 55.9 1.0
N M:PRO177 4.6 63.0 1.0
CA M:ASP175 4.7 57.8 1.0
CA M:LEU181 4.7 39.1 1.0
CD2 M:LEU181 4.8 39.0 1.0
CA M:GLY176 4.8 61.4 1.0
CB M:ASN180 4.8 45.7 1.0
CD1 M:PHE174 4.9 70.8 1.0
O M:GLY179 5.0 41.4 1.0

Calcium binding site 8 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 8 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca304

b:41.1
occ:1.00
 O M:GLU199 2.2 31.9 1.0
OD1 M:ASP124 2.4 42.5 1.0
OE2 M:GLU199 2.4 34.7 1.0
O M:GLU201 2.5 34.9 1.0
OD2 M:ASP124 2.5 36.3 1.0
CG M:ASP124 2.8 40.7 1.0
O M:HOH31 2.8 26.2 1.0
C M:GLU199 3.4 41.0 1.0
CD M:GLU199 3.5 43.4 1.0
C M:GLU201 3.7 37.5 1.0
CG M:GLU199 3.8 38.1 1.0
CA M:GLU199 4.2 39.5 1.0
CA M:ARG202 4.2 36.8 1.0
OG1 M:THR122 4.2 40.9 1.0
CB M:ASP124 4.3 37.6 1.0
N M:ARG202 4.3 39.2 1.0
N M:GLU201 4.4 37.2 1.0
CD1 M:TRP203 4.4 40.9 1.0
N M:ASP200 4.5 37.0 1.0
C M:ASP200 4.6 43.9 1.0
OE1 M:GLU199 4.6 44.8 1.0
CB M:GLU199 4.6 35.6 1.0
NH2 M:ARG165 4.6 46.7 1.0
O M:HOH317 4.6 50.8 1.0
CA M:GLU201 4.8 37.8 1.0
N M:TRP203 4.8 44.0 1.0
CA M:ASP200 4.8 42.4 1.0
O M:HOH315 4.9 49.5 1.0
NE1 M:TRP203 4.9 36.7 1.0

Calcium binding site 9 out of 9 in 3shi

Go back to Calcium Binding Sites List in 3shi
Calcium binding site 9 out of 9 in the Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human MMP1 Catalytic Domain at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca305

b:38.5
occ:1.00
 O M:ASP158 2.3 38.5 1.0
OD1 M:ASP194 2.3 42.7 1.0
O M:GLY190 2.3 43.9 1.0
O M:GLY192 2.4 36.2 1.0
CG M:ASP194 3.3 45.9 1.0
C M:ASP158 3.4 38.3 1.0
C M:GLY190 3.5 49.9 1.0
C M:GLY192 3.6 33.5 1.0
OD2 M:ASP194 3.7 51.0 1.0
O M:ALA157 3.8 45.7 1.0
N M:GLY192 3.9 44.5 1.0
C M:ILE191 4.1 43.5 1.0
CA M:ASP158 4.2 39.6 1.0
N M:ASP194 4.2 39.8 1.0
N M:GLY190 4.3 50.7 1.0
CA M:GLY192 4.3 38.4 1.0
CA M:GLY190 4.3 52.1 1.0
O M:GLY188 4.4 49.8 1.0
N M:ILE159 4.4 32.6 1.0
O M:ILE191 4.4 38.9 1.0
N M:ILE191 4.5 47.9 1.0
CA M:ILE191 4.5 48.3 1.0
CB M:ASP194 4.6 39.0 1.0
CA M:ILE159 4.6 30.2 1.0
CH2 M:TRP109 4.6 38.5 1.0
N M:MET160 4.6 32.5 1.0
N M:GLY193 4.7 31.5 1.0
CA M:ASP194 4.7 38.0 1.0
C M:PRO189 4.8 51.0 1.0
C M:ALA157 4.8 40.8 1.0
C M:GLY193 4.8 41.6 1.0
CG M:MET160 4.9 36.1 1.0
CA M:GLY193 4.9 37.4 1.0

Reference:

I.Bertini, V.Calderone, L.Cerofolini, M.Fragai, C.F.Geraldes, P.Hermann, C.Luchinat, G.Parigi, J.M.Teixeira. The Catalytic Domain of Mmp-1 Studied Through Tagged Lanthanides. Febs Lett. V. 586 557 2012.
ISSN: ISSN 0014-5793
PubMed: 21945315
DOI: 10.1016/J.FEBSLET.2011.09.020
Page generated: Sat Dec 12 04:30:01 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy