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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Jul 8 16:38:50 2025

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