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Zinc in PDB 1qia: Crystal Structure of Stromelysin Catalytic Domain

Enzymatic activity of Crystal Structure of Stromelysin Catalytic Domain

All present enzymatic activity of Crystal Structure of Stromelysin Catalytic Domain:
3.4.24.17;

Protein crystallography data

The structure of Crystal Structure of Stromelysin Catalytic Domain, PDB code: 1qia was solved by M.G.Williams, Q.-Z.Ye, F.Molina, L.L.Johnson, D.F.Ortwine, A.G.Pavlovsky, J.R.Rubin, R.W.Skeean, A.D.White, T.L.Blundell, C.Humblet, D.J.Hupe, V.Dhanaraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.200, 57.630, 73.190, 99.25, 109.82, 89.93
R / Rfree (%) 19 / 24

Other elements in 1qia:

The structure of Crystal Structure of Stromelysin Catalytic Domain also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Stromelysin Catalytic Domain (pdb code 1qia). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Stromelysin Catalytic Domain, PDB code: 1qia:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1qia

Go back to Zinc Binding Sites List in 1qia
Zinc binding site 1 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


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 Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.5
occ:1.00
 NE2 A:HIS201 2.3 11.0 1.0
NE2 A:HIS211 2.3 5.7 1.0
NE2 A:HIS205 2.3 13.5 1.0
CD2 A:HIS201 3.2 10.4 1.0
CD2 A:HIS205 3.2 11.3 1.0
CE1 A:HIS211 3.2 8.5 1.0
CD2 A:HIS211 3.3 8.7 1.0
CE1 A:HIS201 3.3 10.8 1.0
CE1 A:HIS205 3.3 11.7 1.0
O C:PHE154 4.0 12.6 1.0
O A:HOH414 4.2 33.5 1.0
CG A:HIS201 4.4 11.8 1.0
CG A:HIS205 4.4 11.7 1.0
ND1 A:HIS211 4.4 9.1 1.0
ND1 A:HIS201 4.4 12.1 1.0
ND1 A:HIS205 4.4 11.3 1.0
CG A:HIS211 4.4 9.4 1.0
O A:HOH306 4.6 16.0 1.0
CE A:MET219 4.8 9.0 1.0
C C:PHE154 5.0 12.6 1.0

Zinc binding site 2 out of 8 in 1qia

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Zinc binding site 2 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


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 Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.8
occ:1.00
 NE2 A:HIS151 2.3 8.9 1.0
NE2 A:HIS166 2.3 7.0 1.0
ND1 A:HIS179 2.3 11.7 1.0
OD2 A:ASP153 2.4 10.6 1.0
CE1 A:HIS166 3.2 5.6 1.0
CG A:ASP153 3.2 11.3 1.0
CD2 A:HIS151 3.2 10.3 1.0
CE1 A:HIS151 3.3 10.1 1.0
CE1 A:HIS179 3.3 10.6 1.0
CG A:HIS179 3.3 11.0 1.0
CD2 A:HIS166 3.4 6.5 1.0
OD1 A:ASP153 3.4 9.4 1.0
CB A:HIS179 3.6 9.7 1.0
OH A:TYR168 4.2 11.5 1.0
ND1 A:HIS166 4.4 6.8 1.0
O A:TYR155 4.4 9.3 1.0
CG A:HIS151 4.4 11.2 1.0
ND1 A:HIS151 4.4 10.1 1.0
NE2 A:HIS179 4.5 9.7 1.0
CG A:HIS166 4.5 7.1 1.0
CD2 A:HIS179 4.5 11.4 1.0
CB A:ASP153 4.5 9.8 1.0
O A:HOH351 4.5 50.4 1.0
CZ A:PHE157 4.6 7.0 1.0
CE2 A:PHE157 4.6 7.5 1.0
CE1 A:TYR168 4.6 13.2 1.0
O A:HOH462 4.9 47.5 1.0
CZ A:TYR168 4.9 12.2 1.0

Zinc binding site 3 out of 8 in 1qia

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Zinc binding site 3 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


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 Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:11.0
occ:1.00
 NE2 B:HIS211 2.2 7.8 1.0
NE2 B:HIS201 2.3 7.7 1.0
NE2 B:HIS205 2.3 14.5 1.0
CD2 B:HIS201 3.1 10.0 1.0
CE1 B:HIS211 3.2 9.8 1.0
CD2 B:HIS205 3.2 13.4 1.0
CD2 B:HIS211 3.3 9.3 1.0
CE1 B:HIS201 3.4 9.8 1.0
CE1 B:HIS205 3.4 14.5 1.0
ND1 B:HIS211 4.3 11.7 1.0
CG B:HIS201 4.4 10.6 1.0
CG B:HIS211 4.4 10.1 1.0
CG B:HIS205 4.4 12.9 1.0
ND1 B:HIS201 4.5 13.0 1.0
ND1 B:HIS205 4.5 14.3 1.0
CE B:MET219 4.8 10.8 1.0
OE2 B:GLU202 4.9 10.3 1.0

Zinc binding site 4 out of 8 in 1qia

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Zinc binding site 4 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


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 Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:10.9
occ:1.00
 NE2 B:HIS151 2.2 10.8 1.0
ND1 B:HIS179 2.2 13.3 1.0
NE2 B:HIS166 2.2 4.3 1.0
OD2 B:ASP153 2.4 14.8 1.0
CD2 B:HIS151 3.0 10.4 1.0
CE1 B:HIS166 3.1 5.6 1.0
CG B:ASP153 3.2 12.5 1.0
CG B:HIS179 3.2 12.3 1.0
CE1 B:HIS179 3.3 13.4 1.0
CE1 B:HIS151 3.3 7.1 1.0
CD2 B:HIS166 3.4 6.2 1.0
OD1 B:ASP153 3.4 14.0 1.0
CB B:HIS179 3.4 9.7 1.0
O B:HOH1048 3.5 55.5 1.0
CG B:HIS151 4.3 10.7 1.0
OH B:TYR168 4.3 11.1 1.0
ND1 B:HIS166 4.3 5.1 1.0
O B:TYR155 4.3 11.3 1.0
ND1 B:HIS151 4.4 9.2 1.0
CD2 B:HIS179 4.4 12.3 1.0
NE2 B:HIS179 4.4 13.5 1.0
CZ B:PHE157 4.4 9.1 1.0
CG B:HIS166 4.5 4.9 1.0
CB B:ASP153 4.5 12.0 1.0
CE2 B:PHE157 4.5 10.3 1.0
CE1 B:TYR168 4.8 9.8 1.0
CA B:HIS179 4.9 9.6 1.0

Zinc binding site 5 out of 8 in 1qia

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Zinc binding site 5 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:12.8
occ:1.00
 NE2 C:HIS201 2.3 14.7 1.0
NE2 C:HIS211 2.3 10.8 1.0
NE2 C:HIS205 2.3 15.6 1.0
CD2 C:HIS201 3.1 15.2 1.0
CD2 C:HIS211 3.1 13.7 1.0
CE1 C:HIS205 3.2 15.3 1.0
CE1 C:HIS211 3.3 11.9 1.0
CD2 C:HIS205 3.3 14.1 1.0
CE1 C:HIS201 3.4 16.4 1.0
O A:PHE154 4.2 12.5 1.0
CG C:HIS201 4.3 17.1 1.0
CG C:HIS211 4.3 13.5 1.0
ND1 C:HIS211 4.4 12.9 1.0
ND1 C:HIS205 4.4 12.5 1.0
CG C:HIS205 4.4 13.2 1.0
ND1 C:HIS201 4.4 16.7 1.0
O C:HOH2074 4.6 6.5 1.0
OE2 C:GLU202 4.8 12.2 1.0

Zinc binding site 6 out of 8 in 1qia

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Zinc binding site 6 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:12.5
occ:1.00
 NE2 C:HIS166 2.2 3.2 1.0
NE2 C:HIS151 2.3 13.7 1.0
ND1 C:HIS179 2.3 12.2 1.0
OD2 C:ASP153 2.5 16.0 1.0
CD2 C:HIS151 3.1 14.6 1.0
CE1 C:HIS166 3.1 5.5 1.0
CG C:ASP153 3.3 14.5 1.0
CE1 C:HIS179 3.3 10.5 1.0
CG C:HIS179 3.3 12.7 1.0
CD2 C:HIS166 3.3 6.1 1.0
OD1 C:ASP153 3.4 15.5 1.0
CE1 C:HIS151 3.4 13.0 1.0
CB C:HIS179 3.6 11.9 1.0
OH C:TYR168 4.2 10.3 1.0
O C:TYR155 4.2 12.0 1.0
ND1 C:HIS166 4.3 6.7 1.0
CG C:HIS151 4.3 13.3 1.0
CG C:HIS166 4.4 7.1 1.0
NE2 C:HIS179 4.4 10.4 1.0
ND1 C:HIS151 4.5 13.2 1.0
CD2 C:HIS179 4.5 12.6 1.0
O C:HOH2058 4.5 55.0 1.0
O C:HOH2049 4.6 67.3 1.0
CE2 C:PHE157 4.6 13.9 1.0
CB C:ASP153 4.7 13.6 1.0
CZ C:PHE157 4.7 12.4 1.0
CE1 C:TYR168 4.8 10.1 1.0
CZ C:TYR168 5.0 10.4 1.0

Zinc binding site 7 out of 8 in 1qia

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Zinc binding site 7 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:13.2
occ:1.00
 NE2 D:HIS211 2.2 17.0 1.0
NE2 D:HIS205 2.3 19.3 1.0
NE2 D:HIS201 2.3 14.3 1.0
CD2 D:HIS201 3.2 13.9 1.0
CD2 D:HIS211 3.2 17.2 1.0
CE1 D:HIS211 3.2 16.2 1.0
CE1 D:HIS205 3.2 19.6 1.0
CD2 D:HIS205 3.3 18.8 1.0
CE1 D:HIS201 3.4 14.8 1.0
O D:HOH3077 4.2 31.6 1.0
ND1 D:HIS211 4.3 18.1 1.0
CG D:HIS211 4.3 15.9 1.0
CG D:HIS201 4.4 15.6 1.0
ND1 D:HIS205 4.4 19.3 1.0
CG D:HIS205 4.5 18.5 1.0
ND1 D:HIS201 4.5 14.3 1.0
O D:HOH3053 4.5 13.2 1.0
CE D:MET219 5.0 20.2 1.0
OE1 D:GLU202 5.0 9.7 1.0

Zinc binding site 8 out of 8 in 1qia

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Zinc binding site 8 out of 8 in the Crystal Structure of Stromelysin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Stromelysin Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:12.7
occ:1.00
 NE2 D:HIS166 2.3 13.2 1.0
NE2 D:HIS151 2.3 13.8 1.0
OD2 D:ASP153 2.4 16.5 1.0
ND1 D:HIS179 2.4 10.9 1.0
CE1 D:HIS166 3.2 10.4 1.0
CG D:ASP153 3.2 15.1 1.0
CE1 D:HIS151 3.3 14.1 1.0
CD2 D:HIS151 3.3 13.6 1.0
CD2 D:HIS166 3.3 11.5 1.0
CG D:HIS179 3.4 11.8 1.0
OD1 D:ASP153 3.4 16.1 1.0
CE1 D:HIS179 3.4 10.9 1.0
CB D:HIS179 3.5 11.3 1.0
OH D:TYR168 4.2 14.2 1.0
O D:TYR155 4.3 9.3 1.0
ND1 D:HIS166 4.4 11.7 1.0
ND1 D:HIS151 4.4 13.1 1.0
CG D:HIS166 4.5 10.0 1.0
CG D:HIS151 4.5 14.4 1.0
CZ D:PHE157 4.5 13.0 1.0
CD2 D:HIS179 4.5 9.5 1.0
NE2 D:HIS179 4.6 10.9 1.0
CB D:ASP153 4.6 14.2 1.0
CE2 D:PHE157 4.7 13.9 1.0
CE1 D:TYR168 4.7 13.9 1.0
O D:HOH3040 4.9 51.6 1.0
CZ D:TYR168 5.0 15.5 1.0

Reference:

A.G.Pavlovsky, M.G.Williams, Q.-Z.Ye, D.F.Ortwine, C.F.Purchase Ii, A.D.White, V.Dhanaraj, B.D.Roth, L.L.Johnson, D.J.Hupe, C.Humblet, T.L.Blundell. X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Nonpeptide Inhibitors: Implications For Inhibitor Selectivity Protein Sci. V. 8 1455 1999.
ISSN: ISSN 0961-8368
PubMed: 10422833
Page generated: Mon Jan 25 16:12:14 2021

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