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Calcium in PDB 1c3i: Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812

Enzymatic activity of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812

All present enzymatic activity of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812:
3.4.24.17;

Protein crystallography data

The structure of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812, PDB code: 1c3i was solved by D.L.Steele, R.U.Kammlott, R.L.Crowther, J.J.Birktoft, P.Dunten, J.E.Engler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.730, 78.060, 105.740, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1c3i:

The structure of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 (pdb code 1c3i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812, PDB code: 1c3i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1c3i

Go back to Calcium Binding Sites List in 1c3i
Calcium binding site 1 out of 6 in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca262

b:8.8
occ:1.00
 O A:HOH276 2.3 9.8 1.0
O A:HOH265 2.4 12.4 1.0
O A:ASP182 2.4 6.8 1.0
OD1 A:ASP107 2.5 14.3 1.0
OD2 A:ASP107 2.5 9.1 1.0
OD1 A:ASP182 2.5 2.0 1.0
O A:GLU184 2.6 5.0 1.0
CG A:ASP107 2.9 7.7 1.0
C A:ASP182 3.3 7.1 1.0
CG A:ASP182 3.5 3.9 1.0
C A:GLU184 3.7 4.0 1.0
CA A:ASP182 3.8 5.2 1.0
CB A:ASP182 3.9 2.0 1.0
OG1 A:THR105 4.1 5.9 1.0
O B:HOH310 4.3 15.8 1.0
CA A:GLN185 4.4 6.8 1.0
CB A:ASP107 4.4 5.8 1.0
N A:GLU184 4.4 4.4 1.0
N A:ASP183 4.4 6.0 1.0
OD2 A:ASP182 4.4 8.6 1.0
N A:GLN185 4.5 5.5 1.0
CD1 A:TRP186 4.6 7.5 1.0
C A:ASP183 4.6 6.2 1.0
OE1 A:GLN185 4.7 12.5 1.0
O B:HOH265 4.7 10.8 1.0
O A:HOH341 4.7 14.9 1.0
CA A:ASP183 4.7 6.4 1.0
CA A:GLU184 4.8 4.5 1.0
N A:TRP186 4.9 8.2 1.0

Calcium binding site 2 out of 6 in 1c3i

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Calcium binding site 2 out of 6 in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca263

b:10.9
occ:1.00
 O A:GLY173 2.1 5.1 1.0
O A:ASN175 2.3 7.7 1.0
O A:HOH266 2.3 6.1 1.0
O A:HOH282 2.3 14.0 1.0
O A:ASP141 2.4 6.1 1.0
OD1 A:ASP177 2.4 7.8 1.0
C A:GLY173 3.3 4.6 1.0
CG A:ASP177 3.4 3.6 1.0
C A:ASN175 3.5 5.7 1.0
C A:ASP141 3.5 5.2 1.0
OD2 A:ASP177 3.8 3.3 1.0
C A:ILE174 3.9 6.3 1.0
N A:ASP177 4.0 2.0 1.0
O A:ILE174 4.0 6.7 1.0
O A:ALA140 4.0 9.9 1.0
N A:ASN175 4.1 6.6 1.0
N A:ILE174 4.2 6.6 1.0
CA A:ASP141 4.2 5.8 1.0
CA A:ILE174 4.3 5.8 1.0
N A:GLY173 4.3 9.2 1.0
C A:GLY176 4.3 2.0 1.0
N A:GLY176 4.3 3.8 1.0
CA A:GLY176 4.3 2.1 1.0
CA A:GLY173 4.3 6.8 1.0
CA A:ASN175 4.4 5.9 1.0
O A:GLY171 4.4 9.4 1.0
O A:HOH285 4.5 17.4 1.0
N A:ILE142 4.6 6.3 1.0
CB A:ASP177 4.6 3.8 1.0
OE2 A:GLU139 4.6 28.2 1.0
C A:PRO172 4.6 9.5 1.0
CA A:ASP177 4.7 2.0 1.0
N A:MET143 4.8 8.2 1.0
CA A:ILE142 4.9 6.5 1.0
O A:HOH307 4.9 4.8 1.0
O A:PRO172 4.9 10.6 1.0
CH2 A:TRP92 4.9 10.5 1.0
C A:ALA140 5.0 8.7 1.0
CG A:MET143 5.0 4.1 1.0

Calcium binding site 3 out of 6 in 1c3i

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Calcium binding site 3 out of 6 in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca264

b:10.5
occ:1.00
 OE2 A:GLU184 2.2 6.7 1.0
OD2 A:ASP181 2.2 6.4 1.0
O A:GLY159 2.3 10.1 1.0
OD2 A:ASP158 2.3 5.8 1.0
O A:VAL163 2.5 3.6 1.0
O A:GLY161 2.5 2.0 1.0
CG A:ASP181 3.3 5.3 1.0
CD A:GLU184 3.4 4.7 1.0
CG A:ASP158 3.5 2.0 1.0
C A:GLY159 3.5 8.0 1.0
C A:GLY161 3.6 3.0 1.0
C A:VAL163 3.6 2.0 1.0
N A:GLY161 3.9 3.4 1.0
C A:PRO160 3.9 2.0 1.0
OD1 A:ASP158 4.0 7.3 1.0
N A:VAL163 4.0 2.0 1.0
CB A:ASP181 4.0 2.0 1.0
OE1 A:GLU184 4.1 9.2 1.0
N A:GLY159 4.1 10.1 1.0
CA A:GLY161 4.2 2.0 1.0
C A:ASP158 4.2 10.8 1.0
O A:PRO160 4.2 2.8 1.0
CA A:VAL163 4.2 4.2 1.0
OD1 A:ASP181 4.3 8.4 1.0
CA A:PRO160 4.3 3.4 1.0
O A:HOH286 4.3 12.0 1.0
N A:ASP158 4.4 9.2 1.0
N A:PRO160 4.4 4.8 1.0
CA A:GLY159 4.5 8.5 1.0
CG A:GLU184 4.5 11.1 1.0
O A:ASP158 4.5 12.5 1.0
C A:ASN162 4.5 2.3 1.0
N A:LEU164 4.6 3.5 1.0
CB A:VAL163 4.6 6.0 1.0
N A:ASN162 4.6 2.0 1.0
CA A:ASP158 4.6 9.5 1.0
CB A:ASP158 4.6 3.0 1.0
CA A:LEU164 4.7 4.3 1.0
CA A:ASN162 5.0 2.9 1.0

Calcium binding site 4 out of 6 in 1c3i

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Calcium binding site 4 out of 6 in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca262

b:8.4
occ:1.00
 O B:HOH280 2.1 11.7 1.0
O B:ASP182 2.2 8.5 1.0
OD1 B:ASP107 2.4 4.2 1.0
O B:GLU184 2.4 8.1 1.0
OD2 B:ASP182 2.5 11.1 1.0
OD2 B:ASP107 2.6 11.8 1.0
O B:HOH298 2.7 9.8 1.0
CG B:ASP107 2.9 7.9 1.0
C B:ASP182 3.2 9.3 1.0
CG B:ASP182 3.5 7.2 1.0
C B:GLU184 3.6 7.5 1.0
CA B:ASP182 3.6 8.1 1.0
CB B:ASP182 3.9 5.6 1.0
OG1 B:THR105 4.0 10.8 1.0
N B:GLU184 4.2 9.6 1.0
CA B:GLN185 4.2 9.1 1.0
CD1 B:TRP186 4.2 7.4 1.0
N B:ASP183 4.3 9.6 1.0
CB B:ASP107 4.4 7.7 1.0
N B:GLN185 4.4 7.9 1.0
O B:HOH299 4.4 15.8 1.0
OD1 B:ASP182 4.5 7.8 1.0
O A:HOH277 4.6 20.2 1.0
C B:ASP183 4.6 12.4 1.0
CA B:GLU184 4.6 9.3 1.0
N B:TRP186 4.6 7.8 1.0
CA B:ASP183 4.7 10.8 1.0
NE1 B:TRP186 4.8 9.3 1.0
CD B:PRO106 4.8 6.8 1.0
OE1 B:GLN185 4.9 28.4 1.0
C B:GLN185 5.0 9.0 1.0

Calcium binding site 5 out of 6 in 1c3i

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Calcium binding site 5 out of 6 in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca263

b:8.8
occ:1.00
 O B:GLY173 2.1 9.3 1.0
OD1 B:ASP177 2.2 10.8 1.0
O B:HOH286 2.2 10.3 1.0
O B:ASP141 2.3 7.1 1.0
O B:ASN175 2.3 7.3 1.0
O B:HOH281 2.4 9.3 1.0
CG B:ASP177 3.2 4.0 1.0
C B:GLY173 3.4 9.1 1.0
C B:ASP141 3.5 6.1 1.0
C B:ASN175 3.5 7.8 1.0
OD2 B:ASP177 3.6 8.4 1.0
O B:ALA140 4.0 8.2 1.0
N B:ASP177 4.1 6.2 1.0
C B:ILE174 4.1 9.6 1.0
N B:ASN175 4.2 8.5 1.0
CA B:ASP141 4.2 7.0 1.0
CA B:GLY173 4.2 8.6 1.0
N B:GLY173 4.3 7.4 1.0
O B:ILE174 4.3 8.6 1.0
N B:ILE174 4.3 9.4 1.0
C B:GLY176 4.4 8.9 1.0
CA B:GLY176 4.4 7.9 1.0
N B:GLY176 4.4 7.9 1.0
CA B:ILE174 4.5 8.9 1.0
N B:ILE142 4.5 6.5 1.0
CA B:ASN175 4.5 9.0 1.0
CB B:ASP177 4.5 7.3 1.0
O B:GLY171 4.5 7.6 1.0
O B:HOH270 4.5 6.4 1.0
C B:PRO172 4.6 6.7 1.0
N B:MET143 4.6 4.4 1.0
CG B:MET143 4.7 2.0 1.0
CA B:ASP177 4.7 5.6 1.0
CA B:ILE142 4.7 5.0 1.0
O B:PRO172 4.9 6.0 1.0
C B:ALA140 4.9 8.3 1.0
CH2 B:TRP92 4.9 11.5 1.0

Calcium binding site 6 out of 6 in 1c3i

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Calcium binding site 6 out of 6 in the Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Stromelysin-1 Catalytic Domain Complexed with Ro-26-2812 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca264

b:10.7
occ:1.00
 OE1 B:GLU184 2.1 10.7 1.0
OD2 B:ASP158 2.2 6.0 1.0
O B:GLY159 2.3 15.5 1.0
O B:VAL163 2.3 11.1 1.0
OD2 B:ASP181 2.4 8.9 1.0
O B:GLY161 2.6 12.4 1.0
CD B:GLU184 3.3 12.1 1.0
CG B:ASP181 3.4 2.0 1.0
CG B:ASP158 3.4 6.5 1.0
C B:VAL163 3.5 8.6 1.0
C B:GLY159 3.5 14.7 1.0
C B:GLY161 3.6 10.8 1.0
N B:GLY161 3.9 11.4 1.0
N B:VAL163 3.9 9.5 1.0
OE2 B:GLU184 4.0 13.5 1.0
C B:PRO160 4.1 12.2 1.0
CB B:ASP181 4.1 11.2 1.0
N B:GLY159 4.1 14.7 1.0
OD1 B:ASP158 4.1 13.8 1.0
C B:ASP158 4.2 13.9 1.0
CA B:VAL163 4.2 10.3 1.0
CA B:GLY161 4.2 10.3 1.0
OD1 B:ASP181 4.2 11.0 1.0
N B:ASP158 4.3 12.6 1.0
CG B:GLU184 4.4 9.0 1.0
CA B:GLY159 4.4 14.5 1.0
C B:ASN162 4.4 10.9 1.0
N B:PRO160 4.4 13.6 1.0
O B:PRO160 4.4 12.5 1.0
N B:LEU164 4.5 8.9 1.0
CA B:PRO160 4.5 13.1 1.0
CA B:ASP158 4.5 12.8 1.0
CB B:ASP158 4.6 2.2 1.0
O B:ASP158 4.6 14.1 1.0
N B:ASN162 4.6 10.5 1.0
O B:HOH283 4.7 18.9 1.0
CA B:LEU164 4.7 7.2 1.0
CB B:VAL163 4.8 5.7 1.0
CA B:ASN162 4.9 10.3 1.0
O B:ASN162 5.0 11.9 1.0
O B:HOH269 5.0 10.6 1.0

Reference:

D.L.Steele, O.El-Kabbani, P.Dunten, L.J.Windsor, R.U.Kammlott, R.L.Crowther, C.Michoud, J.A.Engler, J.J.Birktoft. Expression, Characterization and Structure Determination of An Active Site Mutant (GLU202-Gln) of Mini-Stromelysin-1. Protein Eng. V. 13 397 2000.
ISSN: ISSN 0269-2139
PubMed: 10877850
DOI: 10.1093/PROTEIN/13.6.397
Page generated: Thu Jul 11 06:49:35 2024

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