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Zinc in PDB 1ibq: Aspergillopepsin From Aspergillus Phoenicis

Enzymatic activity of Aspergillopepsin From Aspergillus Phoenicis

All present enzymatic activity of Aspergillopepsin From Aspergillus Phoenicis:
3.4.23.18;

Protein crystallography data

The structure of Aspergillopepsin From Aspergillus Phoenicis, PDB code: 1ibq was solved by S.W.Cho, W.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.34 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.190, 36.620, 104.940, 90.00, 113.49, 90.00
R / Rfree (%) 22.1 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Aspergillopepsin From Aspergillus Phoenicis (pdb code 1ibq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Aspergillopepsin From Aspergillus Phoenicis, PDB code: 1ibq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1ibq

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Zinc binding site 1 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1451

b:22.5
occ:1.00
 OD1 A:ASP148 2.2 3.2 1.0
N A:SER1 2.2 50.8 1.0
OD2 A:ASP148 2.6 16.5 1.0
CG A:ASP148 2.7 11.7 1.0
CA A:SER1 2.8 49.9 1.0
C A:SER1 3.2 46.9 1.0
O A:HOH1001 3.7 11.6 1.0
N A:LYS2 3.7 49.8 1.0
O A:SER1 3.8 32.5 1.0
CB A:ASP148 4.2 9.3 1.0
CB A:SER1 4.3 52.3 1.0
CB A:LYS2 4.7 51.4 1.0
N A:ASP148 4.7 12.3 1.0
CA A:LYS2 4.8 49.5 1.0
CA A:ASP148 4.8 9.7 1.0
CG A:LYS2 4.8 54.1 1.0

Zinc binding site 2 out of 8 in 1ibq

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Zinc binding site 2 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1453

b:20.8
occ:1.00
 OD2 A:ASP256 2.2 18.1 1.0
OD1 A:ASP256 2.5 16.9 1.0
CG A:ASP256 2.7 21.6 1.0
O A:HOH1261 3.9 54.4 1.0
CB A:ASP256 4.1 23.6 1.0
O A:HOH1029 4.5 9.2 1.0
CG1 A:VAL267 5.0 8.2 1.0

Zinc binding site 3 out of 8 in 1ibq

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Zinc binding site 3 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1455

b:21.7
occ:1.00
 OD2 A:ASP54 1.9 14.0 1.0
OD1 A:ASP118 2.3 21.2 1.0
ND1 A:HIS28 2.4 9.5 1.0
CG A:ASP54 3.1 25.9 1.0
CG A:HIS28 3.1 17.2 1.0
CE1 A:HIS28 3.3 15.2 1.0
CB A:HIS28 3.3 8.6 1.0
CG A:ASP118 3.4 32.3 1.0
N A:HIS28 3.7 9.7 1.0
CB A:ASP54 3.8 24.2 1.0
O A:ALA116 3.8 51.9 1.0
OD2 A:ASP118 4.0 36.8 1.0
OD1 A:ASP54 4.1 41.1 1.0
CA A:HIS28 4.1 9.2 1.0
CD2 A:HIS28 4.2 16.0 1.0
NE2 A:HIS28 4.3 17.5 1.0
N A:ASP54 4.4 32.0 1.0
C A:LEU27 4.4 13.9 1.0
CB A:ASP118 4.5 29.1 1.0
CA A:LEU27 4.6 14.8 1.0
CA A:ASP54 4.7 24.6 1.0
C A:ALA116 4.8 44.4 1.0
O A:HIS28 4.9 30.5 1.0
O A:THR26 5.0 35.5 1.0

Zinc binding site 4 out of 8 in 1ibq

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Zinc binding site 4 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1457

b:21.3
occ:1.00
 OD1 A:ASP32 2.0 15.8 1.0
OD1 A:ASP214 2.2 6.7 1.0
OD2 A:ASP214 2.4 18.9 1.0
OD2 A:ASP32 2.4 8.6 1.0
CG A:ASP32 2.5 9.0 1.0
CG A:ASP214 2.6 8.4 1.0
O A:HOH1122 2.9 17.1 1.0
O A:HOH1046 3.0 11.6 1.0
CA A:GLY34 3.6 18.1 1.0
CA A:GLY216 3.7 10.4 1.0
N A:GLY34 3.9 21.7 1.0
C A:GLY216 4.0 15.6 1.0
N A:GLY216 4.0 8.8 1.0
CB A:ASP32 4.0 8.8 1.0
CB A:ASP214 4.1 3.3 1.0
C A:GLY34 4.1 20.1 1.0
OG1 A:THR217 4.3 27.6 1.0
O A:GLY216 4.4 33.8 1.0
N A:THR217 4.4 11.0 1.0
N A:SER35 4.5 17.0 1.0
CA A:ASP32 4.7 11.8 1.0
O A:GLY34 4.7 27.5 1.0
CA A:ASP214 4.9 5.8 1.0
C A:ASP32 4.9 11.3 1.0

Zinc binding site 5 out of 8 in 1ibq

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Zinc binding site 5 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1452

b:19.2
occ:1.00
 OD1 B:ASP54 1.9 11.0 1.0
OD2 B:ASP118 2.2 21.3 1.0
ND1 B:HIS28 2.4 16.2 1.0
O B:HOH1120 2.5 18.2 1.0
CG B:ASP54 2.9 18.3 1.0
O B:HOH1167 3.0 34.7 1.0
CG B:HIS28 3.3 23.9 1.0
CE1 B:HIS28 3.3 20.4 1.0
CG B:ASP118 3.4 28.6 1.0
CB B:HIS28 3.5 21.3 1.0
O B:ALA116 3.7 28.5 1.0
OD2 B:ASP54 3.7 25.6 1.0
N B:HIS28 3.7 15.2 1.0
CB B:ASP54 3.8 14.3 1.0
OD1 B:ASP118 3.8 35.7 1.0
N B:ASP54 4.3 19.2 1.0
CA B:HIS28 4.3 17.3 1.0
NE2 B:HIS28 4.4 22.6 1.0
CD2 B:HIS28 4.4 24.1 1.0
C B:LEU27 4.4 12.6 1.0
CA B:LEU27 4.5 17.9 1.0
CB B:ASP118 4.6 24.2 1.0
CA B:ASP54 4.7 17.2 1.0
C B:ALA116 4.7 29.2 1.0
O B:THR26 4.8 21.3 1.0
O B:HOH1170 4.9 44.5 1.0

Zinc binding site 6 out of 8 in 1ibq

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Zinc binding site 6 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1454

b:18.2
occ:1.00
 N B:SER1 1.9 38.4 1.0
OD2 B:ASP148 2.0 7.6 1.0
CA B:SER1 2.4 40.3 1.0
CG B:ASP148 2.7 20.4 1.0
OD1 B:ASP148 2.8 30.9 1.0
O B:HOH1006 3.1 21.9 1.0
C B:SER1 3.2 36.2 1.0
O B:SER1 3.7 27.8 1.0
CB B:SER1 3.8 41.6 1.0
N B:LYS2 4.0 34.7 1.0
CB B:ASP148 4.2 18.7 1.0
N B:ASP148 4.4 7.4 1.0
O B:HOH1130 4.5 24.5 1.0
CA B:ASP148 4.6 12.6 1.0
OG B:SER1 4.6 50.9 1.0
O B:GLN146 4.7 21.4 1.0
O B:HOH1013 4.8 17.9 1.0

Zinc binding site 7 out of 8 in 1ibq

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Zinc binding site 7 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1456

b:24.4
occ:1.00
 OE1 B:GLU232 2.2 31.7 1.0
CD B:GLU232 3.1 34.6 1.0
OE2 B:GLU232 3.9 41.2 1.0
CG B:GLU232 4.0 31.5 1.0
O B:GLU232 4.4 42.0 1.0

Zinc binding site 8 out of 8 in 1ibq

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Zinc binding site 8 out of 8 in the Aspergillopepsin From Aspergillus Phoenicis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Aspergillopepsin From Aspergillus Phoenicis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1458

b:19.1
occ:1.00
 OD1 B:ASP214 2.1 10.0 1.0
OD2 B:ASP214 2.2 4.4 1.0
OD1 B:ASP32 2.2 11.3 1.0
CG B:ASP214 2.4 4.5 1.0
OD2 B:ASP32 2.6 17.1 1.0
CG B:ASP32 2.7 12.5 1.0
O B:HOH1214 3.0 30.8 1.0
O B:HOH1115 3.3 1.4 1.0
O B:HOH1179 3.6 24.8 1.0
CA B:GLY34 3.6 18.0 1.0
N B:GLY34 3.9 18.9 1.0
CB B:ASP214 3.9 2.5 1.0
CA B:GLY216 4.0 12.4 1.0
OG1 B:THR217 4.1 18.5 1.0
C B:GLY34 4.1 18.9 1.0
C B:GLY216 4.2 22.5 1.0
CB B:ASP32 4.2 11.3 1.0
N B:GLY216 4.2 6.4 1.0
N B:THR217 4.5 23.0 1.0
N B:SER35 4.5 16.8 1.0
O B:GLY34 4.6 16.5 1.0
O B:GLY216 4.6 22.4 1.0
CA B:ASP214 4.8 6.9 1.0
CA B:ASP32 4.9 14.9 1.0
C B:ASP214 5.0 11.4 1.0

Reference:

S.W.Cho, N.Kim, M.U.Choi, W.Shin. Structure of Aspergillopepsin I From Aspergillus Phoenicis: Variations of the S1'-S2 Subsite in Aspartic Proteinases. Acta Crystallogr.,Sect.D V. 57 948 2001.
ISSN: ISSN 0907-4449
PubMed: 11418762
DOI: 10.1107/S0907444901005972
Page generated: Sun Oct 13 03:04:54 2024

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