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Calcium in PDB 1fbl: Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller

Enzymatic activity of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller

All present enzymatic activity of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller:
3.4.24.7;

Protein crystallography data

The structure of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller, PDB code: 1fbl was solved by J.Li, P.Brick, D.M.Blow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.00 / 2.50
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 161.140, 161.140, 52.220, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / n/a

Other elements in 1fbl:

The structure of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller (pdb code 1fbl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller, PDB code: 1fbl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1fbl

Go back to Calcium Binding Sites List in 1fbl
Calcium binding site 1 out of 4 in the Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca993

b:22.5
occ:1.00
 O A:GLU199 2.2 20.8 1.0
OE2 A:GLU199 2.2 22.1 1.0
OD2 A:ASP124 2.4 24.5 1.0
O A:GLU201 2.6 22.1 1.0
CG A:ASP124 3.1 24.4 1.0
OD1 A:ASP124 3.2 24.3 1.0
CD A:GLU199 3.3 21.6 1.0
C A:GLU199 3.3 20.9 1.0
C A:GLU201 3.7 21.9 1.0
CG A:GLU199 3.8 21.2 1.0
CA A:GLU199 4.1 20.8 1.0
OG1 A:THR122 4.1 24.0 1.0
CD1 A:TRP203 4.3 19.4 1.0
N A:GLU201 4.4 21.8 1.0
N A:ASP200 4.4 21.2 1.0
OE1 A:GLU199 4.4 21.6 1.0
CB A:GLU199 4.5 20.9 1.0
N A:ARG202 4.5 22.0 1.0
CA A:ARG202 4.5 22.1 1.0
C A:ASP200 4.5 21.7 1.0
CB A:ASP124 4.6 24.7 1.0
CA A:GLU201 4.7 21.8 1.0
CA A:ASP200 4.7 21.5 1.0
N A:TRP203 4.7 21.8 1.0
NE1 A:TRP203 4.8 19.2 1.0
O A:HOH516 4.9 18.5 1.0

Calcium binding site 2 out of 4 in 1fbl

Go back to Calcium Binding Sites List in 1fbl
Calcium binding site 2 out of 4 in the Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca994

b:31.9
occ:1.00
 O A:ASP378 2.2 39.7 1.0
O A:GLN329 2.4 29.9 1.0
O A:ASP285 2.5 27.8 1.0
O A:ASP427 2.5 33.0 1.0
C A:ASP378 3.3 39.8 1.0
C A:GLN329 3.6 29.9 1.0
C A:ASP427 3.6 32.9 1.0
C A:ASP285 3.7 27.6 1.0
CA A:ASP378 3.8 40.1 1.0
CA A:GLN329 4.2 30.0 1.0
CA A:ASP427 4.2 33.5 1.0
N A:ALA379 4.4 39.2 1.0
CB A:ASP378 4.4 39.8 1.0
CA A:ASP285 4.5 27.7 1.0
O A:VAL426 4.6 35.5 1.0
N A:ALA330 4.7 30.1 1.0
N A:ALA286 4.7 27.2 1.0
N A:ALA428 4.8 32.1 1.0
CB A:GLN329 4.8 30.3 1.0
O A:ILE377 4.8 42.1 1.0
CA A:ALA379 4.8 38.8 1.0
CA A:ALA286 4.9 26.9 1.0
CA A:ALA330 5.0 30.4 1.0

Calcium binding site 3 out of 4 in 1fbl

Go back to Calcium Binding Sites List in 1fbl
Calcium binding site 3 out of 4 in the Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca995

b:38.8
occ:1.00
 O A:HOH834 1.3 61.4 1.0
O A:GLY190 2.3 27.3 1.0
O A:GLY192 2.4 24.4 1.0
O A:ASP158 2.5 26.5 1.0
O A:HOH837 2.9 58.4 1.0
OD1 A:ASP194 3.1 22.3 1.0
C A:GLY190 3.5 27.4 1.0
C A:ASP158 3.6 26.3 1.0
C A:GLY192 3.6 24.5 1.0
CG A:ASP194 3.8 22.1 1.0
C A:ILE191 4.0 26.5 1.0
OD2 A:ASP194 4.0 22.0 1.0
N A:GLY192 4.0 25.8 1.0
O A:ALA157 4.1 27.7 1.0
O A:ILE191 4.1 26.5 1.0
O A:GLY188 4.2 28.2 1.0
CA A:ASP158 4.2 26.8 1.0
N A:ILE191 4.3 27.1 1.0
CA A:ILE191 4.3 26.7 1.0
N A:GLY190 4.4 28.3 1.0
CA A:GLY192 4.4 25.0 1.0
CA A:GLY190 4.4 27.7 1.0
O A:HOH659 4.5 39.2 1.0
C A:PRO189 4.6 28.6 1.0
N A:ASP194 4.6 22.8 1.0
N A:ILE159 4.7 25.4 1.0
N A:GLY193 4.7 24.0 1.0
CH2 A:TRP109 4.7 39.0 1.0
O A:HOH594 4.8 35.8 1.0
CG A:MET160 4.9 22.0 1.0
CA A:GLY193 4.9 23.3 1.0
O A:PRO189 4.9 28.7 1.0
CB A:ASP194 4.9 22.3 1.0
CA A:ILE159 5.0 24.4 1.0
C A:GLY193 5.0 23.0 1.0
CZ2 A:TRP109 5.0 38.9 1.0

Calcium binding site 4 out of 4 in 1fbl

Go back to Calcium Binding Sites List in 1fbl
Calcium binding site 4 out of 4 in the Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Full-Length Porcine Synovial Collagenase (MMP1) Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta- Propeller within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:14.4
occ:1.00
 O A:ASN180 2.0 21.1 1.0
O A:GLY176 2.2 25.4 1.0
O A:GLY178 2.2 22.1 1.0
OE2 A:GLU201 2.3 22.1 1.0
OD2 A:ASP198 2.3 19.9 1.0
OD1 A:ASP175 2.4 26.4 1.0
C A:ASN180 3.2 21.2 1.0
C A:GLY178 3.4 22.2 1.0
C A:GLY176 3.4 25.1 1.0
CD A:GLU201 3.5 21.9 1.0
CG A:ASP198 3.5 19.9 1.0
CG A:ASP175 3.5 26.7 1.0
N A:GLY178 3.8 23.6 1.0
N A:ASN180 3.9 21.7 1.0
C A:PRO177 4.0 24.0 1.0
CA A:ASN180 4.0 21.3 1.0
OD2 A:ASP175 4.1 26.4 1.0
N A:GLY176 4.1 25.9 1.0
CA A:GLY178 4.1 22.7 1.0
CB A:ASP198 4.1 20.0 1.0
N A:LEU181 4.2 21.1 1.0
C A:GLY179 4.3 21.7 1.0
CG A:GLU201 4.3 21.5 1.0
N A:PRO177 4.3 24.6 1.0
CB A:ASN180 4.3 21.2 1.0
OE1 A:GLU201 4.3 21.8 1.0
CA A:GLY176 4.4 25.4 1.0
CA A:PRO177 4.4 24.2 1.0
C A:ASP175 4.4 26.5 1.0
N A:GLY179 4.5 21.8 1.0
N A:ASP175 4.5 27.6 1.0
O A:PRO177 4.5 24.1 1.0
OD1 A:ASP198 4.5 19.6 1.0
CA A:LEU181 4.5 20.7 1.0
O A:GLY179 4.7 21.8 1.0
CB A:ASP175 4.7 26.9 1.0
CA A:GLY179 4.7 21.6 1.0
CA A:ASP175 4.7 26.9 1.0
O A:ASP175 5.0 26.3 1.0

Reference:

J.Li, P.Brick, M.C.O'hare, T.Skarzynski, L.F.Lloyd, V.A.Curry, I.M.Clark, H.F.Bigg, B.L.Hazleman, T.E.Cawston, D.M.Blow. Structure of Full-Length Porcine Synovial Collagenase Reveals A C-Terminal Domain Containing A Calcium-Linked, Four-Bladed Beta-Propeller. Structure V. 3 541 1995.
ISSN: ISSN 0969-2126
PubMed: 8590015
DOI: 10.1016/S0969-2126(01)00188-5
Page generated: Thu Jul 11 08:06:02 2024

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