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Calcium in PDB 1su3: X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action

Enzymatic activity of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action

All present enzymatic activity of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action:
3.4.24.7;

Protein crystallography data

The structure of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3 was solved by D.Jozic, G.Bourenkov, N.H.Lim, H.Nagase, W.Bode, K.Maskos, Structural Proteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.746, 142.746, 295.308, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.2

Other elements in 1su3:

The structure of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action (pdb code 1su3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1su3

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Calcium binding site 1 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:76.0
occ:1.00
 O A:GLY190 2.6 45.0 1.0
OD1 A:ASP194 2.8 36.6 1.0
O A:ASP158 2.8 39.4 1.0
O A:HOH1027 2.9 51.4 1.0
O A:ALA157 3.1 46.4 1.0
O A:HOH1045 3.1 39.8 1.0
O A:GLY192 3.3 38.6 1.0
C A:ASP158 3.6 41.0 1.0
CG A:ASP194 3.7 37.9 1.0
C A:GLY190 3.8 44.7 1.0
OD2 A:ASP194 3.9 40.2 1.0
CG A:MET160 4.0 39.3 1.0
C A:ALA157 4.2 46.2 1.0
CA A:ILE191 4.3 44.3 1.0
CA A:ASP158 4.3 42.9 1.0
C A:ILE191 4.3 43.2 1.0
N A:MET160 4.4 37.4 1.0
N A:ILE159 4.4 39.6 1.0
C A:GLY192 4.4 40.2 1.0
N A:GLY192 4.4 42.0 1.0
N A:ILE191 4.5 44.3 1.0
CA A:ILE159 4.6 38.6 1.0
O A:ILE191 4.7 43.5 1.0
CB A:MET160 4.7 37.6 1.0
N A:ASP158 4.7 44.3 1.0
C A:ILE159 4.9 37.5 1.0
CA A:GLY190 4.9 45.5 1.0

Calcium binding site 2 out of 8 in 1su3

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Calcium binding site 2 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:37.3
occ:1.00
 OD2 A:ASP124 2.2 37.6 1.0
O A:HOH946 2.4 27.9 1.0
OE2 A:GLU199 2.4 35.9 1.0
O A:GLU199 2.4 35.0 1.0
O A:HOH991 2.5 36.0 1.0
O A:GLU201 2.5 34.8 1.0
OD1 A:ASP124 2.6 37.2 1.0
CG A:ASP124 2.8 38.8 1.0
CD A:GLU199 3.5 37.3 1.0
C A:GLU199 3.5 34.7 1.0
C A:GLU201 3.6 34.5 1.0
OG1 A:THR122 3.9 37.0 1.0
CG A:GLU199 4.0 36.1 1.0
CA A:GLU199 4.2 34.6 1.0
CB A:ASP124 4.3 37.2 1.0
CD1 A:TRP203 4.3 31.3 1.0
N A:ARG202 4.4 34.4 1.0
CA A:ARG202 4.4 34.8 1.0
O A:HOH942 4.4 37.3 1.0
C A:ASP200 4.5 34.4 1.0
N A:GLU201 4.5 34.7 1.0
OE1 A:GLU199 4.6 40.0 1.0
N A:ASP200 4.6 34.3 1.0
CA A:GLU201 4.7 34.4 1.0
N A:TRP203 4.7 33.8 1.0
CA A:ASP200 4.7 34.2 1.0
O A:HOH1073 4.7 45.5 1.0
CB A:GLU199 4.7 34.5 1.0
O A:HOH972 4.8 40.4 1.0
O A:ASP200 4.8 33.6 1.0
NE1 A:TRP203 4.9 32.1 1.0

Calcium binding site 3 out of 8 in 1su3

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Calcium binding site 3 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:34.0
occ:1.00
 OE2 A:GLU201 2.1 33.0 1.0
OD2 A:ASP198 2.2 33.4 1.0
O A:ASN180 2.3 33.6 1.0
O A:GLY176 2.3 37.0 1.0
O A:GLY178 2.3 38.0 1.0
OD1 A:ASP175 2.4 39.7 1.0
CG A:ASP198 3.3 34.6 1.0
C A:ASN180 3.4 34.3 1.0
CD A:GLU201 3.4 34.7 1.0
C A:GLY176 3.5 37.1 1.0
C A:GLY178 3.5 37.4 1.0
CG A:ASP175 3.6 41.7 1.0
N A:GLY178 3.9 37.7 1.0
CB A:ASP198 4.0 32.9 1.0
C A:PRO177 4.0 37.5 1.0
N A:ASN180 4.0 35.7 1.0
N A:GLY176 4.1 38.2 1.0
OE1 A:GLU201 4.1 33.3 1.0
OD2 A:ASP175 4.1 42.3 1.0
CA A:ASN180 4.2 35.9 1.0
CA A:GLY178 4.2 37.6 1.0
N A:ASP175 4.3 40.1 1.0
C A:ASP175 4.3 38.7 1.0
OD1 A:ASP198 4.3 34.3 1.0
N A:LEU181 4.3 33.7 1.0
CA A:PRO177 4.3 37.1 1.0
N A:PRO177 4.3 36.6 1.0
C A:GLY179 4.4 36.3 1.0
O A:PRO177 4.4 37.9 1.0
CA A:GLY176 4.4 37.2 1.0
CG A:GLU201 4.4 35.1 1.0
CA A:LEU181 4.5 33.3 1.0
CB A:ASN180 4.5 36.4 1.0
N A:GLY179 4.6 37.2 1.0
CA A:ASP175 4.7 39.8 1.0
O A:ASP175 4.7 39.3 1.0
CB A:ASP175 4.7 40.0 1.0
CA A:GLY179 4.7 37.0 1.0
O A:HOH1025 4.9 51.4 1.0
O A:GLY179 5.0 37.0 1.0

Calcium binding site 4 out of 8 in 1su3

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Calcium binding site 4 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:39.1
occ:1.00
 O A:HOH1052 2.0 40.4 1.0
O A:ASP427 2.3 41.0 1.0
O A:ASP285 2.4 36.9 1.0
O A:HOH916 2.5 33.6 1.0
O A:ASP378 2.5 40.0 1.0
O A:GLU329 2.5 42.8 1.0
O A:HOH961 2.5 41.0 1.0
C A:ASP427 3.3 41.6 1.0
C A:ASP285 3.5 37.1 1.0
C A:GLU329 3.5 42.8 1.0
C A:ASP378 3.6 40.4 1.0
CA A:ASP427 3.8 43.2 1.0
CA A:GLU329 4.1 44.5 1.0
CA A:ASP378 4.1 41.6 1.0
CA A:ASP285 4.2 38.2 1.0
O A:HOH967 4.4 61.0 1.0
N A:ALA428 4.5 40.7 1.0
N A:ALA286 4.5 36.2 1.0
O A:VAL426 4.6 43.9 1.0
N A:ALA330 4.6 41.9 1.0
N A:ALA379 4.7 38.9 1.0
CB A:ASP427 4.7 43.9 1.0
O A:PHE284 4.7 38.3 1.0
CB A:GLU329 4.7 44.5 1.0
CA A:ALA286 4.8 36.5 1.0
CB A:ASP378 4.8 41.7 1.0
O A:HOH1107 4.9 88.3 1.0
CA A:ALA428 5.0 40.3 1.0
CA A:ALA379 5.0 38.8 1.0
CA A:ALA330 5.0 41.1 1.0
N A:ASP427 5.0 43.1 1.0

Calcium binding site 5 out of 8 in 1su3

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Calcium binding site 5 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:70.2
occ:1.00
 OD1 B:ASP194 2.6 36.0 1.0
O B:GLY190 2.7 40.3 1.0
O B:ASP158 2.8 37.3 1.0
O B:GLY192 2.9 36.6 1.0
O B:ALA157 3.4 37.6 1.0
C B:ASP158 3.6 37.4 1.0
CG B:ASP194 3.6 37.8 1.0
C B:GLY190 3.8 40.5 1.0
OD2 B:ASP194 3.9 39.1 1.0
C B:GLY192 4.0 37.1 1.0
CG B:MET160 4.1 37.0 1.0
C B:ILE191 4.1 40.0 1.0
OE1 B:GLN156 4.2 52.2 1.0
CA B:ASP158 4.3 38.0 1.0
CA B:ILE191 4.3 40.7 1.0
N B:GLY192 4.3 38.7 1.0
N B:ILE159 4.4 36.8 1.0
O B:ILE191 4.4 39.8 1.0
N B:MET160 4.4 36.7 1.0
C B:ALA157 4.5 39.1 1.0
N B:ILE191 4.5 40.5 1.0
CA B:ILE159 4.6 36.9 1.0
N B:ASP194 4.7 36.5 1.0
CA B:GLY192 4.7 37.8 1.0
CB B:MET160 4.8 36.8 1.0
CB B:ASP194 4.9 36.4 1.0
N B:ASP158 4.9 38.6 1.0
C B:ILE159 5.0 37.1 1.0
CA B:GLY190 5.0 40.1 1.0

Calcium binding site 6 out of 8 in 1su3

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Calcium binding site 6 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca906

b:45.3
occ:1.00
 OE2 B:GLU201 2.1 42.6 1.0
O B:GLY178 2.3 42.6 1.0
OD2 B:ASP198 2.3 32.2 1.0
OD1 B:ASP175 2.3 39.6 1.0
O B:GLY176 2.3 44.0 1.0
O B:ASN180 2.3 40.9 1.0
C B:ASN180 3.4 40.3 1.0
CD B:GLU201 3.4 41.5 1.0
CG B:ASP198 3.4 34.9 1.0
C B:GLY178 3.5 43.3 1.0
CG B:ASP175 3.5 43.2 1.0
C B:GLY176 3.5 44.1 1.0
N B:ASN180 3.9 41.7 1.0
N B:GLY176 4.0 43.6 1.0
N B:GLY178 4.0 43.8 1.0
OD2 B:ASP175 4.0 45.1 1.0
CB B:ASP198 4.1 35.3 1.0
OE1 B:GLU201 4.1 42.3 1.0
CA B:ASN180 4.1 41.7 1.0
C B:PRO177 4.2 43.9 1.0
N B:ASP175 4.2 43.1 1.0
C B:GLY179 4.3 42.2 1.0
CA B:GLY178 4.3 43.6 1.0
C B:ASP175 4.3 43.1 1.0
N B:LEU181 4.3 39.5 1.0
CG B:GLU201 4.4 38.7 1.0
OD1 B:ASP198 4.4 35.5 1.0
CA B:GLY176 4.4 43.8 1.0
N B:PRO177 4.5 44.3 1.0
N B:GLY179 4.5 43.1 1.0
CA B:LEU181 4.5 38.6 1.0
CB B:ASN180 4.5 42.0 1.0
CA B:PRO177 4.6 44.4 1.0
O B:PRO177 4.6 44.6 1.0
CA B:ASP175 4.6 43.2 1.0
CA B:GLY179 4.7 42.9 1.0
CB B:ASP175 4.7 42.8 1.0
O B:ASP175 4.8 43.3 1.0
O B:GLY179 4.9 42.3 1.0
CB B:PHE174 4.9 42.3 1.0

Calcium binding site 7 out of 8 in 1su3

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Calcium binding site 7 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca907

b:58.2
occ:1.00
 OE2 B:GLU199 2.2 45.0 1.0
O B:GLU199 2.4 36.8 1.0
OD2 B:ASP124 2.4 43.9 1.0
O B:GLU201 2.4 37.0 1.0
O B:HOH1085 2.9 43.8 1.0
OD1 B:ASP124 2.9 43.8 1.0
CG B:ASP124 3.1 43.1 1.0
CD B:GLU199 3.4 44.5 1.0
C B:GLU199 3.5 37.1 1.0
C B:GLU201 3.6 37.0 1.0
OG1 B:THR122 3.8 40.9 1.0
CG B:GLU199 4.0 40.1 1.0
CA B:GLU199 4.1 37.4 1.0
N B:GLU201 4.3 37.4 1.0
CD1 B:TRP203 4.3 37.6 1.0
N B:ARG202 4.4 37.0 1.0
CA B:ARG202 4.4 37.0 1.0
OE1 B:GLU199 4.4 48.0 1.0
N B:ASP200 4.5 37.0 1.0
C B:ASP200 4.5 37.2 1.0
CB B:ASP124 4.5 42.3 1.0
CA B:GLU201 4.6 37.2 1.0
CB B:GLU199 4.7 37.4 1.0
N B:TRP203 4.7 37.8 1.0
CA B:ASP200 4.7 37.4 1.0
O B:HOH1091 4.8 28.9 0.5
NE1 B:TRP203 4.8 37.3 1.0
CB B:THR122 5.0 41.4 1.0

Calcium binding site 8 out of 8 in 1su3

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Calcium binding site 8 out of 8 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca908

b:35.0
occ:1.00
 O B:HOH1052 2.1 35.0 1.0
O B:ASP378 2.2 36.7 1.0
O B:ASP427 2.3 36.6 1.0
O B:ASP285 2.3 36.7 1.0
O B:HOH1053 2.3 35.7 1.0
O B:GLU329 2.4 36.8 1.0
O B:HOH1080 2.6 41.1 1.0
C B:ASP427 3.3 37.6 1.0
C B:ASP378 3.4 36.4 1.0
C B:GLU329 3.4 36.3 1.0
C B:ASP285 3.5 36.1 1.0
CA B:ASP427 3.9 38.7 1.0
CA B:GLU329 4.0 37.6 1.0
CA B:ASP378 4.0 37.2 1.0
CA B:ASP285 4.3 36.1 1.0
N B:ALA379 4.5 36.0 1.0
N B:ALA286 4.5 35.4 1.0
N B:ALA428 4.5 37.4 1.0
N B:ALA330 4.5 35.4 1.0
O B:VAL426 4.6 40.4 1.0
CB B:GLU329 4.6 37.0 1.0
CB B:ASP427 4.7 39.3 1.0
CA B:ALA286 4.7 35.4 1.0
CA B:ALA379 4.8 35.8 1.0
CB B:ASP378 4.8 36.5 1.0
O B:ILE377 4.8 39.5 1.0
O B:PHE284 4.8 36.0 1.0
CA B:ALA330 4.9 35.1 1.0
CA B:ALA428 4.9 37.1 1.0
CB B:ALA379 4.9 35.6 1.0

Reference:

D.Jozic, G.Bourenkov, N.H.Lim, R.Visse, H.Nagase, W.Bode, K.Maskos. X-Ray Structure of Human Prommp-1: New Insights Into Procollagenase Activation and Collagen Binding. J.Biol.Chem. V. 280 9578 2005.
ISSN: ISSN 0021-9258
PubMed: 15611040
DOI: 10.1074/JBC.M411084200
Page generated: Thu Jul 11 22:50:02 2024

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