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Zinc 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:

Calcium (Ca) 3 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 1ck7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gelatinase A (Full-Length) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn990

b:35.2
occ:1.00
NE2 A:HIS407 2.2 31.3 1.0
NE2 A:HIS403 2.3 19.4 1.0
NE2 A:HIS413 2.5 54.3 1.0
SG A:CYS102 2.5 38.0 1.0
CD2 A:HIS407 2.9 36.2 1.0
CD2 A:HIS413 2.9 60.6 1.0
CB A:CYS102 3.0 32.5 1.0
CD2 A:HIS403 3.2 21.7 1.0
CE1 A:HIS403 3.2 17.4 1.0
CE1 A:HIS407 3.4 32.8 1.0
CE1 A:HIS413 3.6 53.0 1.0
CB A:ASN104 3.9 32.4 1.0
ND2 A:ASN104 4.0 54.0 1.0
CG A:ASN104 4.1 47.2 1.0
CG A:HIS413 4.1 54.2 1.0
CG A:HIS407 4.2 34.8 1.0
ND1 A:HIS403 4.3 21.2 1.0
ND1 A:HIS407 4.3 39.2 1.0
CG A:HIS403 4.3 16.3 1.0
ND1 A:HIS413 4.4 58.4 1.0
CE A:MET421 4.5 36.6 1.0
CA A:CYS102 4.5 35.3 1.0
N A:ASN104 4.8 41.2 1.0
OD1 A:ASN104 4.8 52.5 1.0
CA A:ASN104 4.9 40.2 1.0

Zinc binding site 2 out of 2 in 1ck7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gelatinase A (Full-Length) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn991

b:28.9
occ:1.00
ND1 A:HIS206 2.1 5.0 1.0
NE2 A:HIS193 2.1 15.8 1.0
NE2 A:HIS178 2.2 33.0 1.0
OD2 A:ASP180 2.3 23.0 1.0
CD2 A:HIS178 2.7 24.3 1.0
CD2 A:HIS193 2.7 6.9 1.0
CE1 A:HIS206 2.9 15.0 1.0
CG A:HIS206 3.1 37.9 1.0
CG A:ASP180 3.2 37.2 1.0
CE1 A:HIS193 3.3 25.4 1.0
CE1 A:HIS178 3.3 41.8 1.0
OD1 A:ASP180 3.5 35.1 1.0
CB A:HIS206 3.5 32.5 1.0
CG A:HIS178 3.9 25.2 1.0
CG A:HIS193 3.9 16.1 1.0
NE2 A:HIS206 4.1 32.9 1.0
ND1 A:HIS178 4.2 20.7 1.0
ND1 A:HIS193 4.2 27.2 1.0
CD2 A:HIS206 4.2 31.5 1.0
CE2 A:PHE195 4.2 39.2 1.0
CB A:ASP180 4.6 43.0 1.0
CZ A:PHE184 4.7 16.1 1.0
CZ A:PHE195 4.7 38.6 1.0
CB A:TYR182 4.8 54.0 1.0
O A:TYR182 4.8 42.3 1.0
O A:HIS193 4.9 27.9 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: Mon Jan 25 16:08:00 2021

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