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Zinc in PDB 1cqr: Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution

Enzymatic activity of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution

All present enzymatic activity of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution:
3.4.24.17;

Protein crystallography data

The structure of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution, PDB code: 1cqr was solved by L.Chen, T.J.Rydel, F.Gu, C.M.Dunaway, S.Pikul, K.M.Dunham, B.L.Barnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.200, 79.100, 107.400, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 26.6

Other elements in 1cqr:

The structure of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution (pdb code 1cqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution, PDB code: 1cqr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1cqr

Go back to Zinc Binding Sites List in 1cqr
Zinc binding site 1 out of 4 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:12.6
occ:1.00
 NE2 A:HIS201 2.1 9.6 1.0
NE2 A:HIS211 2.2 16.5 1.0
NE2 A:HIS205 2.2 7.2 1.0
CD2 A:HIS201 3.0 9.8 1.0
CE1 A:HIS211 3.0 18.7 1.0
CD2 A:HIS205 3.1 6.1 1.0
CD2 A:HIS211 3.1 16.8 1.0
CE1 A:HIS205 3.1 4.4 1.0
CE1 A:HIS201 3.2 8.9 1.0
ND1 A:HIS211 4.1 19.1 1.0
CG A:HIS201 4.2 8.9 1.0
O A:HOH14 4.2 24.7 1.0
CG A:HIS211 4.2 15.5 1.0
CG A:HIS205 4.3 5.5 1.0
ND1 A:HIS205 4.3 5.3 1.0
ND1 A:HIS201 4.3 7.3 1.0
O A:HOH15 4.6 23.2 1.0
CE A:MET219 4.8 3.5 1.0
OE2 A:GLU202 4.9 12.6 1.0

Zinc binding site 2 out of 4 in 1cqr

Go back to Zinc Binding Sites List in 1cqr
Zinc binding site 2 out of 4 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:12.4
occ:1.00
 OD2 A:ASP153 2.1 14.5 1.0
NE2 A:HIS151 2.1 6.1 1.0
ND1 A:HIS179 2.1 9.6 1.0
NE2 A:HIS166 2.1 9.8 1.0
CD2 A:HIS151 2.9 6.6 1.0
CE1 A:HIS166 3.0 8.3 1.0
CG A:ASP153 3.0 13.9 1.0
CE1 A:HIS179 3.0 9.1 1.0
CE1 A:HIS151 3.1 5.6 1.0
CG A:HIS179 3.1 8.2 1.0
CD2 A:HIS166 3.1 8.8 1.0
OD1 A:ASP153 3.2 11.3 1.0
CB A:HIS179 3.5 6.5 1.0
CG A:HIS151 4.1 7.1 1.0
ND1 A:HIS166 4.1 8.5 1.0
NE2 A:HIS179 4.1 10.6 1.0
ND1 A:HIS151 4.1 8.0 1.0
CG A:HIS166 4.2 7.6 1.0
CD2 A:HIS179 4.3 8.7 1.0
O A:TYR155 4.3 15.9 1.0
CB A:ASP153 4.4 12.2 1.0
OH A:TYR168 4.4 12.0 1.0
CZ A:PHE157 4.5 7.3 1.0
CE1 A:TYR168 4.6 7.1 1.0
CE1 A:PHE157 4.7 5.1 1.0
CA A:HIS179 4.9 7.4 1.0

Zinc binding site 3 out of 4 in 1cqr

Go back to Zinc Binding Sites List in 1cqr
Zinc binding site 3 out of 4 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2301

b:21.4
occ:1.00
 O B:HOH61 2.0 23.6 1.0
NE2 B:HIS201 2.2 15.0 1.0
NE2 B:HIS205 2.2 15.6 1.0
NE2 B:HIS211 2.2 23.8 1.0
CD2 B:HIS201 2.9 15.3 1.0
CD2 B:HIS205 3.0 14.3 1.0
CE1 B:HIS211 3.1 22.9 1.0
CD2 B:HIS211 3.1 24.8 1.0
CE1 B:HIS201 3.2 13.6 1.0
CE1 B:HIS205 3.2 13.0 1.0
O B:HOH69 3.7 23.9 1.0
OE2 B:GLU202 4.1 14.9 1.0
CG B:HIS201 4.1 14.5 1.0
O B:HOH50 4.1 17.9 1.0
ND1 B:HIS211 4.2 25.6 1.0
CG B:HIS205 4.2 11.0 1.0
CG B:HIS211 4.2 21.6 1.0
ND1 B:HIS201 4.2 15.4 1.0
ND1 B:HIS205 4.3 9.3 1.0
O B:HOH79 4.3 33.4 1.0
OE1 B:GLU202 4.3 12.2 1.0
CD B:GLU202 4.6 11.9 1.0

Zinc binding site 4 out of 4 in 1cqr

Go back to Zinc Binding Sites List in 1cqr
Zinc binding site 4 out of 4 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2302

b:15.9
occ:1.00
 OD2 B:ASP153 2.0 15.7 1.0
NE2 B:HIS166 2.1 8.0 1.0
ND1 B:HIS179 2.1 11.6 1.0
NE2 B:HIS151 2.1 7.7 1.0
CG B:ASP153 2.9 11.6 1.0
CE1 B:HIS166 2.9 8.4 1.0
CE1 B:HIS179 2.9 8.8 1.0
CD2 B:HIS151 3.0 5.2 1.0
OD1 B:ASP153 3.0 13.7 1.0
CE1 B:HIS151 3.1 9.0 1.0
CD2 B:HIS166 3.1 10.3 1.0
CG B:HIS179 3.2 7.7 1.0
CB B:HIS179 3.6 9.5 1.0
OH B:TYR168 3.9 14.1 1.0
ND1 B:HIS166 4.1 10.4 1.0
NE2 B:HIS179 4.1 10.6 1.0
CG B:HIS151 4.2 9.0 1.0
CG B:HIS166 4.2 8.8 1.0
CB B:ASP153 4.2 10.6 1.0
O B:TYR155 4.2 16.3 1.0
ND1 B:HIS151 4.2 8.7 1.0
CD2 B:HIS179 4.3 9.8 1.0
CE1 B:TYR168 4.5 16.1 1.0
CZ B:PHE157 4.6 9.7 1.0
CE1 B:PHE157 4.6 9.1 1.0
CZ B:TYR168 4.7 16.4 1.0
O B:HOH22 5.0 10.8 1.0

Reference:

L.Chen, T.J.Rydel, F.Gu, C.M.Dunaway, S.Pikul, K.M.Dunham, B.L.Barnett. Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution: Inhibitor-Induced Conformational Changes. J.Mol.Biol. V. 293 545 1999.
ISSN: ISSN 0022-2836
PubMed: 10543949
DOI: 10.1006/JMBI.1999.3147
Page generated: Mon Jan 25 16:08:07 2021

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