Atomistry » Calcium » PDB 1ck6-1cxi » 1ck7
Atomistry »
  Calcium »
    PDB 1ck6-1cxi »
      1ck7 »

Calcium in PDB 1ck7: Gelatinase A (Full-Length)

Enzymatic activity of Gelatinase A (Full-Length)

All present enzymatic activity of Gelatinase A (Full-Length):
3.4.24.24;

Protein crystallography data

The structure of Gelatinase A (Full-Length), PDB code: 1ck7 was solved by E.Morgunova, A.Tuuttila, U.Bergmann, M.Isupov, Y.Lindqvist, G.Schneider, K.Tryggvason, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.00 / 2.80
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 121.320, 121.320, 345.110, 90.00, 90.00, 90.00
R / Rfree (%) 28.6 / 32.7

Other elements in 1ck7:

The structure of Gelatinase A (Full-Length) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Gelatinase A (Full-Length) (pdb code 1ck7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Gelatinase A (Full-Length), PDB code: 1ck7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1ck7

Go back to Calcium Binding Sites List in 1ck7
Calcium binding site 1 out of 3 in the Gelatinase A (Full-Length)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Gelatinase A (Full-Length) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca992

b:23.9
occ:1.00
O A:GLY186 2.4 22.6 1.0
O A:LEU190 2.5 18.5 1.0
O A:ASP188 2.6 20.7 1.0
OD2 A:ASP208 2.6 26.7 1.0
OE2 A:GLU211 2.7 26.0 1.0
O A:ASP185 2.9 37.8 1.0
CG A:ASP208 3.4 24.1 1.0
C A:LEU190 3.6 17.0 1.0
C A:GLY186 3.6 24.7 1.0
C A:ASP188 3.8 19.8 1.0
N A:LEU190 3.8 16.7 1.0
OD1 A:ASP185 3.8 26.6 1.0
CD A:GLU211 3.9 24.5 1.0
CB A:ASP208 3.9 8.9 1.0
C A:ASP185 3.9 29.0 1.0
N A:ASP188 4.1 22.7 1.0
C A:LYS187 4.1 27.0 1.0
CA A:LEU190 4.1 14.5 1.0
C A:GLY189 4.2 22.4 1.0
OD1 A:ASP208 4.4 27.6 1.0
CG A:GLU211 4.4 2.6 1.0
CA A:GLY186 4.4 26.1 1.0
N A:LYS187 4.5 26.7 1.0
N A:GLY186 4.5 25.8 1.0
CA A:LYS187 4.5 26.5 1.0
CA A:ASP188 4.5 20.9 1.0
O A:LYS187 4.5 26.1 1.0
CB A:LEU190 4.5 12.7 1.0
N A:LEU191 4.6 17.6 1.0
N A:ASP185 4.6 21.6 1.0
CA A:GLY189 4.7 21.1 1.0
N A:GLY189 4.7 19.1 1.0
CA A:LEU191 4.7 14.2 1.0
O A:GLY189 4.9 24.6 1.0
OE1 A:GLU211 4.9 33.0 1.0
CA A:ASP185 5.0 26.8 1.0

Calcium binding site 2 out of 3 in 1ck7

Go back to Calcium Binding Sites List in 1ck7
Calcium binding site 2 out of 3 in the Gelatinase A (Full-Length)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Gelatinase A (Full-Length) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca993

b:0.7
occ:1.00
O A:GLY200 2.7 47.1 1.0
O A:ALA167 2.9 34.1 1.0
O A:ASP168 2.9 33.5 1.0
OE1 A:GLU166 3.2 58.5 1.0
O A:GLY202 3.4 27.5 1.0
OD1 A:ASP204 3.5 36.5 1.0
C A:ASP168 3.6 33.5 1.0
C A:GLY200 3.8 46.5 1.0
CG A:ASP204 4.0 37.9 1.0
OD2 A:ASP204 4.0 37.4 1.0
C A:ALA167 4.0 35.2 1.0
CD A:GLU166 4.1 58.5 1.0
CA A:ASP168 4.2 33.5 1.0
OE2 A:GLU166 4.2 55.2 1.0
CG A:MET170 4.4 9.8 1.0
N A:ILE169 4.5 36.2 1.0
CA A:GLY200 4.5 51.1 1.0
O A:HOH1003 4.5 29.0 1.0
C A:GLY202 4.5 32.5 1.0
N A:ASP168 4.6 34.3 1.0
N A:GLY200 4.7 55.0 1.0
N A:MET170 4.7 34.5 1.0
N A:GLY202 4.7 39.4 1.0
N A:VAL201 4.8 43.3 1.0
C A:VAL201 4.8 43.0 1.0
CA A:ILE169 4.8 35.4 1.0
CA A:VAL201 5.0 40.2 1.0

Calcium binding site 3 out of 3 in 1ck7

Go back to Calcium Binding Sites List in 1ck7
Calcium binding site 3 out of 3 in the Gelatinase A (Full-Length)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Gelatinase A (Full-Length) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca994

b:63.8
occ:1.00
O A:ASP476 2.5 59.2 1.0
O A:ASP569 2.7 68.5 1.0
O A:ASP618 2.7 0.7 1.0
O A:ASP521 2.8 52.3 1.0
C A:ASP618 3.6 0.8 1.0
C A:ASP569 3.7 66.9 1.0
CB A:ASP618 3.7 99.0 1.0
CA A:ASP618 3.7 0.3 1.0
C A:ASP476 3.7 60.5 1.0
C A:ASP521 3.8 49.9 1.0
CA A:ASP569 4.0 68.0 1.0
CB A:ASP569 4.3 74.6 1.0
CA A:ASP476 4.5 65.5 1.0
CA A:GLY477 4.6 58.0 1.0
N A:GLY477 4.6 58.4 1.0
CA A:ASP521 4.6 49.2 1.0
N A:ALA570 4.7 64.6 1.0
CL A:CL995 4.7 58.6 1.0
N A:ALA619 4.7 0.8 1.0
N A:ALA522 4.8 50.1 1.0
CA A:ALA522 4.8 51.9 1.0
CA A:ALA570 4.9 64.3 1.0
O A:PHE475 4.9 75.4 1.0
CB A:ALA522 5.0 53.2 1.0

Reference:

E.Morgunova, A.Tuuttila, U.Bergmann, M.Isupov, Y.Lindqvist, G.Schneider, K.Tryggvason. Structure of Human Pro-Matrix Metalloproteinase-2: Activation Mechanism Revealed. Science V. 284 1667 1999.
ISSN: ISSN 0036-8075
PubMed: 10356396
DOI: 10.1126/SCIENCE.284.5420.1667
Page generated: Sat Dec 12 02:51:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy