Atomistry » Calcium » PDB 4aqi-4ayp » 4auo
Atomistry »
  Calcium »
    PDB 4aqi-4ayp »
      4auo »

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

Go back to Calcium Binding Sites List in 4auo
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

Go back to Calcium Binding Sites List in 4auo
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

Go back to Calcium Binding Sites List in 4auo
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

Go back to Calcium Binding Sites List in 4auo
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

Go back to Calcium Binding Sites List in 4auo
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 Jul 13 22:19:13 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy