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Calcium in PDB 4auo: Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide

Enzymatic activity of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide

All present enzymatic activity of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide:
3.4.24.7;

Protein crystallography data

The structure of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide, PDB code: 4auo was solved by S.W.Manka, F.Carafoli, R.Visse, D.Bihan, N.Raynal, R.W.Farndale, G.Murphy, J.J.Enghild, E.Hohenester, H.Nagase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 3.00
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.671, 102.241, 80.734, 90.00, 103.75, 90.00
R / Rfree (%) 21.11 / 27.27

Other elements in 4auo:

The structure of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide (pdb code 4auo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide, PDB code: 4auo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4auo

Go back to Calcium Binding Sites List in 4auo
Calcium binding site 1 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:68.3
occ:1.00
O A:GLU180 2.8 31.5 1.0
OE2 A:GLU180 2.9 36.1 1.0
NH2 A:ARG146 3.2 35.3 1.0
OD2 A:ASP105 3.5 44.4 1.0
O A:GLU182 3.5 33.7 1.0
CD A:GLU180 3.7 36.2 1.0
C A:GLU180 3.8 31.5 1.0
CG A:GLU180 3.8 33.8 1.0
CZ A:ARG146 4.2 35.1 1.0
OD1 A:ASP105 4.2 43.9 1.0
CG A:ASP105 4.2 43.1 1.0
CA A:ASP181 4.5 34.4 1.0
NH1 A:ARG146 4.5 35.6 1.0
C A:ASP181 4.5 35.4 1.0
C A:GLU182 4.5 35.1 1.0
N A:ASP181 4.6 32.6 1.0
N A:GLU182 4.6 36.1 1.0
CA A:GLU180 4.8 31.3 1.0
CB A:GLU180 4.9 31.2 1.0
OE1 A:GLU180 4.9 36.3 1.0
O A:ASP181 5.0 35.7 1.0

Calcium binding site 2 out of 8 in 4auo

Go back to Calcium Binding Sites List in 4auo
Calcium binding site 2 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:40.0
occ:1.00
O A:ASP408 2.1 35.8 1.0
O A:ASP266 2.3 18.5 1.0
O A:ASP359 2.3 28.4 1.0
O A:GLU310 2.5 28.6 1.0
C A:ASP408 3.2 37.2 1.0
C A:ASP266 3.4 18.0 1.0
C A:ASP359 3.5 29.3 1.0
C A:GLU310 3.7 29.5 1.0
CA A:ASP408 3.8 39.5 1.0
CA A:ASP266 4.0 19.0 1.0
CA A:ASP359 4.2 28.9 1.0
N A:ALA409 4.3 35.5 1.0
CA A:GLU310 4.4 30.4 1.0
N A:ALA267 4.5 16.6 1.0
O A:VAL407 4.5 42.1 1.0
N A:ALA360 4.5 29.7 1.0
CB A:ASP408 4.6 41.3 1.0
O A:PHE265 4.6 17.7 1.0
CA A:ALA409 4.7 34.4 1.0
N A:ALA311 4.7 29.1 1.0
CA A:ALA360 4.7 29.9 1.0
CA A:ALA267 4.8 16.5 1.0
CA A:ALA311 4.9 28.9 1.0
CB A:ASP359 4.9 31.4 1.0
CB A:ALA360 4.9 28.4 1.0
N A:ASP408 4.9 41.1 1.0
CB A:ASP266 5.0 22.2 1.0

Calcium binding site 3 out of 8 in 4auo

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Calcium binding site 3 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:63.5
occ:1.00
OD1 A:ASP175 2.4 36.2 1.0
O A:GLY173 2.7 27.9 1.0
O A:GLY171 2.7 37.2 1.0
O A:ASP139 2.8 28.4 1.0
CG A:ASP175 3.2 35.0 1.0
C A:ASP139 3.5 28.7 1.0
OD2 A:ASP175 3.6 35.7 1.0
C A:GLY173 3.7 27.8 1.0
C A:GLY171 3.9 34.5 1.0
N A:MET141 3.9 26.3 1.0
O A:ALA138 3.9 37.0 1.0
C A:ILE172 4.0 30.4 1.0
CA A:ILE140 4.0 25.1 1.0
N A:ILE140 4.0 26.9 1.0
O A:ILE172 4.0 29.0 1.0
N A:GLY173 4.1 29.4 1.0
CG A:MET141 4.1 31.3 1.0
N A:ASP175 4.3 30.5 1.0
C A:GLY174 4.4 29.8 1.0
CA A:GLY173 4.4 28.3 1.0
CB A:ASP175 4.4 33.5 1.0
C A:ILE140 4.4 25.8 1.0
CA A:ILE172 4.5 30.9 1.0
CA A:ASP139 4.5 30.0 1.0
N A:GLY174 4.6 27.9 1.0
CA A:ASP175 4.6 30.9 1.0
N A:ILE172 4.6 33.4 1.0
CB A:MET141 4.6 28.4 1.0
CA A:GLY174 4.7 28.6 1.0
O A:GLY174 4.7 30.8 1.0
C A:ALA138 4.9 37.0 1.0
CA A:MET141 4.9 26.6 1.0
CA A:GLY171 4.9 33.1 1.0
O A:GLY169 5.0 33.1 1.0

Calcium binding site 4 out of 8 in 4auo

Go back to Calcium Binding Sites List in 4auo
Calcium binding site 4 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:25.2
occ:1.00
O A:GLY157 2.2 30.1 1.0
OD2 A:ASP179 2.2 31.7 1.0
O A:GLY159 2.2 30.3 1.0
OD1 A:ASP156 2.5 28.6 1.0
OE2 A:GLU182 2.5 35.1 1.0
O A:ASN161 2.6 21.8 1.0
CG A:ASP179 3.4 30.7 1.0
C A:GLY157 3.4 29.2 1.0
C A:GLY159 3.4 28.9 1.0
CG A:ASP156 3.6 29.2 1.0
C A:ASN161 3.6 20.5 1.0
CD A:GLU182 3.6 36.5 1.0
N A:GLY159 3.7 29.5 1.0
C A:PRO158 3.9 29.4 1.0
CB A:ASP179 4.1 28.5 1.0
N A:GLY157 4.1 29.2 1.0
CA A:GLY159 4.1 29.5 1.0
C A:GLY160 4.1 24.5 1.0
N A:ASN161 4.2 22.1 1.0
CG A:GLU182 4.2 34.9 1.0
OD2 A:ASP156 4.2 28.1 1.0
C A:ASP156 4.2 29.6 1.0
N A:PRO158 4.3 29.0 1.0
CA A:PRO158 4.3 29.2 1.0
O A:GLY160 4.3 25.9 1.0
CA A:GLY157 4.4 29.2 1.0
OD1 A:ASP179 4.4 33.2 1.0
CA A:ASN161 4.4 21.1 1.0
N A:ASP156 4.4 28.9 1.0
N A:GLY160 4.5 27.4 1.0
O A:PRO158 4.5 30.8 1.0
N A:LEU162 4.5 18.6 1.0
O A:ASP156 4.6 29.0 1.0
CA A:LEU162 4.6 16.3 1.0
CA A:GLY160 4.7 25.8 1.0
CA A:ASP156 4.7 29.1 1.0
OE1 A:GLU182 4.7 36.1 1.0
CB A:ASP156 4.7 30.2 1.0
CD2 A:LEU162 4.8 17.1 1.0
CB A:ASN161 4.9 21.1 1.0

Calcium binding site 5 out of 8 in 4auo

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Calcium binding site 5 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1101

b:70.2
occ:1.00
O B:GLU180 2.7 26.2 1.0
O B:GLU182 2.9 28.1 1.0
OD2 B:ASP105 3.2 33.7 1.0
OE2 B:GLU180 3.4 36.9 1.0
OD1 B:ASP105 3.4 36.4 1.0
CG B:ASP105 3.7 34.7 1.0
C B:GLU182 3.8 29.0 1.0
C B:GLU180 3.9 24.6 1.0
NH2 B:ARG146 4.0 37.9 1.0
C B:ASP181 4.2 26.1 1.0
N B:GLU182 4.2 27.0 1.0
CD B:GLU180 4.3 35.1 1.0
O B:ASP181 4.4 24.8 1.0
CG B:GLU180 4.4 32.2 1.0
CA B:ASP181 4.5 26.4 1.0
N B:ARG183 4.5 28.9 1.0
CA B:ARG183 4.6 29.4 1.0
CA B:GLU182 4.6 28.5 1.0
N B:ASP181 4.7 25.0 1.0
CZ B:ARG146 5.0 37.1 1.0
CA B:GLU180 5.0 23.9 1.0
OG1 B:THR103 5.0 27.6 1.0

Calcium binding site 6 out of 8 in 4auo

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Calcium binding site 6 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1102

b:31.5
occ:1.00
O B:ASP359 2.3 30.0 1.0
O B:ASP408 2.4 34.2 1.0
O B:ASP266 2.4 17.1 1.0
O B:GLU310 2.4 27.3 1.0
C B:ASP359 3.4 29.6 1.0
C B:ASP408 3.5 34.7 1.0
C B:ASP266 3.5 18.1 1.0
C B:GLU310 3.6 27.7 1.0
CA B:ASP359 4.0 29.1 1.0
CA B:ASP408 4.0 37.6 1.0
CA B:ASP266 4.2 20.2 1.0
CA B:GLU310 4.3 28.4 1.0
N B:ALA360 4.5 30.1 1.0
O B:VAL407 4.6 40.7 1.0
N B:ALA409 4.6 31.3 1.0
CB B:ASP359 4.6 31.8 1.0
N B:ALA311 4.6 25.8 1.0
N B:ALA267 4.6 16.0 1.0
CA B:ALA311 4.8 24.4 1.0
CA B:ALA360 4.9 29.5 1.0
O B:PHE265 4.9 20.9 1.0
CB B:ASP408 4.9 40.9 1.0
O B:ILE358 4.9 25.5 1.0
CB B:GLU310 4.9 28.9 1.0
CA B:ALA267 5.0 14.7 1.0
CA B:ALA409 5.0 28.0 1.0

Calcium binding site 7 out of 8 in 4auo

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Calcium binding site 7 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1103

b:96.0
occ:1.00
O B:ASP139 2.2 24.4 1.0
O B:GLY173 2.4 25.3 1.0
O B:GLY171 2.7 31.8 1.0
C B:ASP139 3.2 24.4 1.0
OD1 B:ASP175 3.2 31.0 1.0
C B:GLY173 3.6 25.2 1.0
O B:ALA138 3.8 32.4 1.0
C B:GLY171 3.9 29.6 1.0
N B:ILE140 4.0 22.3 1.0
CA B:ASP139 4.0 26.5 1.0
CG B:ASP175 4.1 32.8 1.0
CA B:ILE140 4.2 18.2 1.0
N B:GLY173 4.2 26.9 1.0
O B:GLY169 4.3 25.7 1.0
C B:ILE172 4.4 27.1 1.0
CA B:GLY173 4.4 25.6 1.0
N B:MET141 4.5 18.3 1.0
C B:GLY174 4.5 26.4 1.0
CH2 B:TRP90 4.5 27.3 1.0
N B:GLY174 4.5 24.7 1.0
OD2 B:ASP175 4.6 35.0 1.0
CA B:GLY174 4.6 26.0 1.0
O B:ILE172 4.6 27.2 1.0
N B:GLY171 4.7 27.8 1.0
O B:GLY174 4.7 26.1 1.0
C B:ALA138 4.8 32.1 1.0
N B:ASP175 4.8 27.1 1.0
CA B:GLY171 4.8 29.1 1.0
CG B:MET141 4.8 17.9 1.0
C B:ILE140 4.8 18.7 1.0
N B:ILE172 4.9 29.6 1.0
CA B:ILE172 4.9 27.6 1.0
N B:ASP139 4.9 29.0 1.0

Calcium binding site 8 out of 8 in 4auo

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Calcium binding site 8 out of 8 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1104

b:16.9
occ:1.00
O B:GLY157 2.1 23.8 1.0
O B:GLY159 2.3 23.5 1.0
OD2 B:ASP179 2.3 11.5 1.0
OE2 B:GLU182 2.5 35.3 1.0
O B:ASN161 2.7 15.7 1.0
OD1 B:ASP156 2.7 31.1 1.0
C B:GLY157 3.3 24.3 1.0
C B:GLY159 3.4 23.4 1.0
N B:GLY159 3.5 22.9 1.0
CG B:ASP179 3.5 12.8 1.0
CD B:GLU182 3.6 34.3 1.0
CG B:ASP156 3.8 29.7 1.0
C B:ASN161 3.8 15.8 1.0
C B:PRO158 3.9 23.4 1.0
CA B:GLY159 4.0 23.2 1.0
N B:GLY157 4.0 24.7 1.0
C B:ASP156 4.1 26.2 1.0
CG B:GLU182 4.2 32.1 1.0
CA B:PRO158 4.2 24.3 1.0
N B:PRO158 4.2 24.3 1.0
CB B:ASP179 4.2 14.2 1.0
CA B:GLY157 4.3 24.9 1.0
N B:ASN161 4.3 18.4 1.0
N B:ASP156 4.4 26.9 1.0
O B:ASP156 4.4 26.9 1.0
OD2 B:ASP156 4.4 27.5 1.0
OD1 B:ASP179 4.5 12.3 1.0
C B:GLY160 4.5 20.6 1.0
OE1 B:GLU182 4.5 36.4 1.0
N B:GLY160 4.5 22.7 1.0
O B:PRO158 4.6 24.3 1.0
CA B:ASN161 4.6 16.7 1.0
CA B:ASP156 4.6 26.3 1.0
CB B:ASP156 4.8 28.4 1.0
N B:LEU162 4.8 14.9 1.0
CD2 B:LEU162 4.8 12.7 1.0
CA B:GLY160 4.8 22.1 1.0
CA B:LEU162 4.9 13.9 1.0
O B:GLY160 4.9 21.0 1.0

Reference:

S.W.Manka, F.Carafoli, R.Visse, D.Bihan, N.Raynal, R.W.Farndale, G.Murphy, J.J.Enghild, E.Hohenester, H.Nagase. Structural Insights Into Triple-Helical Collagen Cleavage By Matrix Metalloproteinase 1 Proc.Natl.Acad.Sci.Usa V. 109 12461 2012.
ISSN: ISSN 0027-8424
PubMed: 22761315
DOI: 10.1073/PNAS.1204991109
Page generated: Sat Dec 12 04:39:46 2020

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