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Chlorine in PDB 3vh9: Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol

Enzymatic activity of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol

All present enzymatic activity of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol:
3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol, PDB code: 3vh9 was solved by S.Saijo, K.Hanaya, M.Suetsugu, K.Kobayashi, I.Yamato, S.Aoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.62 / 1.29
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.463, 108.463, 90.737, 90.00, 90.00, 120.00
R / Rfree (%) 13.1 / 15.3

Other elements in 3vh9:

The structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol (pdb code 3vh9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol, PDB code: 3vh9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 3vh9

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Chlorine binding site 1 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl313

b:18.5
occ:1.00
 OG A:SER215 3.0 16.6 1.0
O A:HOH615 3.2 28.2 1.0
N A:SER215 3.3 11.2 1.0
C A:LEU213 3.4 9.3 1.0
O A:HOH649 3.5 27.9 1.0
CA A:LEU213 3.5 9.2 1.0
N A:PRO214 3.6 9.8 1.0
CB A:SER215 3.6 15.3 1.0
CD A:PRO214 3.8 11.2 1.0
O A:LEU213 3.9 9.5 1.0
CA A:SER215 3.9 12.7 1.0
CB A:LEU213 4.2 9.4 1.0
CD2 A:LEU213 4.2 11.7 1.0
N A:LEU216 4.3 9.8 1.0
C A:PRO214 4.3 12.0 1.0
CG A:PRO214 4.4 12.8 1.0
CG A:LEU216 4.5 10.3 1.0
CA A:PRO214 4.5 11.7 1.0
C A:SER215 4.5 12.1 1.0
O A:TYR212 4.6 9.9 1.0
N A:LEU213 4.7 8.5 1.0
CG A:LEU213 4.9 10.0 1.0
CD2 A:LEU216 4.9 11.3 1.0

Chlorine binding site 2 out of 9 in 3vh9

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Chlorine binding site 2 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl314

b:15.2
occ:1.00
 O A:HOH590 3.0 24.8 1.0
NZ A:LYS273 3.1 15.2 1.0
N A:ALA19 3.2 7.7 1.0
O A:HOH531 3.7 24.4 1.0
CB A:ALA19 3.8 9.0 1.0
O A:VAL17 3.9 9.7 1.0
CE A:LYS273 3.9 12.9 1.0
CA A:ASP18 3.9 8.7 1.0
CD A:LYS273 4.0 10.9 1.0
C A:ASP18 4.1 7.7 1.0
CA A:ALA19 4.1 8.4 1.0
OD1 A:ASP18 4.1 13.6 1.0
C A:VAL17 4.8 8.2 1.0
O A:HOH557 4.8 20.2 1.0
CG A:ASP18 4.8 13.3 1.0
N A:ASP18 4.8 8.3 1.0
O A:HOH735 4.8 36.0 1.0
N A:SER20 4.9 7.7 1.0
CB A:ASP18 4.9 11.3 1.0

Chlorine binding site 3 out of 9 in 3vh9

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Chlorine binding site 3 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl315

b:9.8
occ:1.00
 O A:HOH612 3.1 15.7 1.0
O A:HOH511 3.2 20.1 1.0
N A:THR258 3.4 7.4 1.0
CA A:THR257 3.5 7.2 1.0
CB A:THR257 3.6 8.6 1.0
CG2 A:THR258 3.7 9.8 1.0
C A:THR257 3.9 7.3 1.0
O A:HOH542 4.1 13.5 0.5
CB A:ILE102 4.3 10.9 1.0
CG2 A:THR257 4.3 8.9 1.0
OG1 A:THR258 4.3 9.9 1.0
CG2 A:ILE102 4.4 10.1 1.0
CD1 A:ILE102 4.4 13.3 1.0
O A:HIS256 4.4 8.7 1.0
CB A:THR258 4.4 8.6 1.0
CA A:THR258 4.5 7.5 1.0
N A:THR257 4.7 7.1 1.0
OG1 A:THR257 4.8 8.2 1.0
CG1 A:ILE102 4.9 13.0 1.0
NE2 A:HIS105 4.9 18.6 0.5

Chlorine binding site 4 out of 9 in 3vh9

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Chlorine binding site 4 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl316

b:12.7
occ:1.00
 O A:HOH397 2.9 29.1 1.0
O A:HOH549 3.0 31.0 1.0
O A:HOH379 3.2 36.1 1.0
N A:ASN74 3.3 10.1 1.0
CA A:THR38 3.6 9.0 1.0
ND2 A:ASN74 3.6 12.0 1.0
CA A:TYR73 3.6 10.8 1.0
CG A:ASN74 3.7 10.7 1.0
CB A:THR38 3.8 10.3 1.0
CG2 A:THR38 3.8 10.9 1.0
O A:THR38 3.8 12.2 1.0
CB A:ASN74 3.9 10.1 1.0
C A:TYR73 3.9 10.0 1.0
O A:HOH470 3.9 14.7 1.0
CB A:TYR73 4.0 10.7 1.0
C A:THR38 4.1 9.4 1.0
O A:HOH447 4.1 10.5 1.0
CA A:ASN74 4.2 9.6 1.0
O A:TYR37 4.2 8.4 1.0
OD1 A:ASN74 4.3 11.3 1.0
O A:HOH396 4.5 26.4 1.0
O A:GLY72 4.6 19.0 1.0
N A:THR38 4.7 8.0 1.0
N A:TYR73 4.8 12.3 1.0
NA A:NA312 4.8 22.8 1.0
C A:TYR37 4.9 7.9 1.0
O A:HOH565 5.0 32.0 1.0

Chlorine binding site 5 out of 9 in 3vh9

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Chlorine binding site 5 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl317

b:16.8
occ:1.00
 O A:HOH466 3.1 14.6 1.0
N A:GLY72 3.5 14.1 1.0
CA A:SER71 3.8 13.2 1.0
CB A:SER71 4.2 14.6 1.0
C A:SER71 4.2 12.9 1.0
OG A:SER71 4.2 14.3 0.6
O A:HOH565 4.3 32.0 1.0
CA A:GLY72 4.5 16.3 1.0
O A:HIS70 4.6 10.7 1.0
N A:SER71 4.9 11.1 1.0

Chlorine binding site 6 out of 9 in 3vh9

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Chlorine binding site 6 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl318

b:16.5
occ:1.00
 OG1 A:THR9 3.0 10.1 1.0
N A:THR9 3.4 8.3 1.0
O A:HOH494 3.5 24.6 1.0
CA A:GLN6 3.6 9.7 1.0
C A:GLN6 3.6 8.7 1.0
OE1 A:GLN6 3.7 17.1 1.0
CB A:ALA8 3.7 9.8 1.0
O A:GLN6 3.7 8.8 1.0
CB A:THR9 3.8 8.6 1.0
O A:HOH689 3.8 24.0 1.0
N A:ALA8 3.8 7.9 1.0
CB A:GLN6 4.0 10.6 1.0
CA A:ALA8 4.1 8.8 1.0
CA A:THR9 4.2 7.8 1.0
CD A:GLN6 4.2 15.8 1.0
C A:ALA8 4.2 8.2 1.0
N A:GLN7 4.3 9.4 1.0
O A:THR5 4.5 12.5 1.0
C A:GLN7 4.7 8.3 1.0
CG A:GLN6 4.7 13.5 1.0
N A:GLN6 4.8 9.5 1.0
NE2 A:GLN6 4.9 18.1 1.0

Chlorine binding site 7 out of 9 in 3vh9

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Chlorine binding site 7 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl319

b:12.8
occ:1.00
 O A:GLY24 2.7 7.8 1.0
OG A:SER27 2.7 8.1 1.0
OG A:SER28 2.7 9.7 1.0
O A:HOH493 2.7 16.8 1.0
O A:HOH450 3.2 14.7 1.0
N A:SER28 3.4 7.1 1.0
C A:GLY24 3.6 6.9 1.0
CB A:SER28 3.8 8.6 1.0
CB A:SER27 3.8 7.4 1.0
CA A:SER28 3.9 7.4 1.0
CA A:GLY24 3.9 8.2 1.0
O A:HOH415 3.9 33.6 1.0
C A:SER27 4.0 6.7 1.0
O A:HOH439 4.2 12.0 1.0
CA A:SER27 4.4 6.8 1.0
O A:SER27 4.7 7.8 1.0
N A:SER27 4.8 6.2 1.0
O A:THR23 4.8 7.8 1.0
N A:THR25 4.9 6.6 1.0

Chlorine binding site 8 out of 9 in 3vh9

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Chlorine binding site 8 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl320

b:25.4
occ:1.00
 O A:HOH366 2.8 38.0 1.0
O A:HOH387 3.0 40.3 1.0
N A:LYS184 3.4 8.0 1.0
O A:HOH545 3.5 25.3 1.0
O A:HOH547 3.8 24.1 1.0
CB A:ASP266 3.8 8.9 1.0
CA A:TYR183 3.9 7.2 1.0
O A:HOH334 4.0 28.1 1.0
N A:ASP266 4.0 8.8 1.0
CA A:ASP266 4.1 9.3 1.0
C A:SER265 4.1 9.8 1.0
C A:TYR183 4.1 7.3 1.0
O A:SER265 4.1 11.8 1.0
O A:ASN182 4.2 7.1 1.0
CD1 A:TYR183 4.3 10.5 1.0
CB A:LYS184 4.3 11.1 1.0
CA A:LYS184 4.3 9.2 1.0
CG A:TYR183 4.6 8.1 1.0
CG A:ASP266 4.6 8.4 1.0
CB A:TYR183 4.7 8.0 1.0
O A:LYS184 4.8 10.8 1.0
C A:LYS184 4.9 9.2 1.0
N A:TYR183 4.9 6.5 1.0
CE1 A:TYR183 4.9 11.3 1.0
CA A:SER265 4.9 8.4 1.0
O A:HOH559 4.9 23.2 1.0
C A:ASN182 4.9 6.3 1.0

Chlorine binding site 9 out of 9 in 3vh9

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Chlorine binding site 9 out of 9 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl321

b:16.4
occ:1.00
 O A:HOH345 3.0 30.8 1.0
N A:PHE220 3.3 7.0 1.0
O A:HOH570 3.3 27.9 1.0
CA A:GLY219 3.7 8.6 1.0
CD1 A:PHE220 3.9 9.3 1.0
O A:PHE220 3.9 8.5 1.0
C A:GLY219 4.0 7.4 1.0
NZ A:LYS247 4.0 15.5 0.4
CB A:PHE220 4.1 7.7 1.0
CA A:PHE220 4.2 7.0 1.0
O A:HOH524 4.4 18.1 1.0
CG A:PHE220 4.5 7.5 1.0
CE A:LYS247 4.5 15.4 0.6
C A:PHE220 4.5 7.4 1.0
NZ A:LYS247 4.6 18.0 0.6
O A:HOH701 4.8 33.8 1.0
CE1 A:PHE220 4.9 9.8 1.0

Reference:

K.Hanaya, M.Suetsugu, S.Saijo, I.Yamato, S.Aoki. Potent Inhibition of Dinuclear Zinc(II) Peptidase, An Aminopeptidase From Aeromonas Proteolytica, By 8-Quinolinol Derivatives: Inhibitor Design Based on Zn(2+) Fluorophores, Kinetic, and X-Ray Crystallographic Study. J.Biol.Inorg.Chem. V. 17 517 2012.
ISSN: ISSN 0949-8257
PubMed: 22311113
DOI: 10.1007/S00775-012-0873-4
Page generated: Sun Jul 21 06:55:59 2024

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