Atomistry » Sodium » PDB 3v45-3vi2 » 3vh9
Atomistry »
  Sodium »
    PDB 3v45-3vi2 »
      3vh9 »

Sodium 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:

Chlorine (Cl) 9 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol, PDB code: 3vh9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na304

b:16.3
occ:1.00
 O A:HOH625 2.4 21.2 1.0
O A:THR194 2.4 10.6 1.0
O A:HOH468 2.4 16.9 1.0
O A:THR197 2.5 9.8 1.0
O A:HOH600 2.8 38.8 1.0
C A:THR197 3.4 7.9 1.0
OG1 A:THR197 3.5 8.0 1.0
O A:HOH458 3.5 18.2 1.0
C A:THR194 3.5 8.3 1.0
O A:HOH673 3.6 30.2 1.0
N A:THR197 4.1 7.4 1.0
N A:SER199 4.2 6.8 1.0
CA A:THR197 4.2 7.5 1.0
CA A:THR194 4.2 8.6 1.0
N A:ASP198 4.3 7.2 1.0
CB A:THR197 4.4 7.4 1.0
N A:SCN322 4.5 18.7 1.0
C A:ASP198 4.5 7.1 1.0
CA A:ASP198 4.5 6.9 1.0
N A:ASP195 4.5 7.1 1.0
O A:HOH597 4.6 30.3 1.0
CB A:SER199 4.6 9.0 1.0
CB A:THR194 4.6 9.3 1.0
CA A:ASP195 4.7 8.0 1.0
CA A:SER199 4.7 7.5 1.0
O A:HOH705 4.8 37.6 1.0
N A:TYR196 5.0 7.5 1.0
C A:ASP195 5.0 7.5 1.0

Sodium binding site 2 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na305

b:12.5
occ:1.00
 O A:HOH623 2.4 13.7 1.0
O A:HOH496 2.4 12.9 1.0
O A:HOH501 2.4 16.6 1.0
OD1 A:ASN74 2.4 11.3 1.0
O A:HOH498 2.5 17.5 1.0
CG A:ASN74 3.4 10.7 1.0
NA A:NA312 3.6 22.8 1.0
O A:HOH431 4.0 12.3 1.0
O A:HOH469 4.0 12.2 1.0
CB A:ASN74 4.1 10.1 1.0
ND2 A:ASN74 4.2 12.0 1.0
O A:HOH565 4.2 32.0 1.0
CA A:ASN74 4.3 9.6 1.0
O A:HOH624 4.4 15.6 1.0
O A:HOH466 4.5 14.6 1.0
O A:HOH616 4.7 31.6 1.0

Sodium binding site 3 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na306

b:11.8
occ:1.00
 O A:HOH471 2.4 11.8 1.0
OH A:TYR218 2.4 10.6 1.0
O A:HOH441 2.4 13.9 1.0
O A:HOH455 2.5 11.9 1.0
O A:HOH620 2.5 15.7 1.0
O A:HOH510 2.5 12.4 1.0
CZ A:TYR218 3.4 9.4 1.0
CE1 A:TYR218 3.5 9.5 1.0
OG1 A:THR206 3.9 9.2 1.0
OD2 A:ASP210 4.1 11.8 1.0
CB A:THR206 4.2 8.6 1.0
OD1 A:ASP210 4.3 11.4 1.0
O A:HOH621 4.4 30.7 1.0
CE2 A:TYR218 4.6 9.7 1.0
CG A:ASP210 4.6 10.8 1.0
OE1 A:GLN203 4.8 10.8 1.0
O A:HOH462 4.9 12.1 1.0
CD1 A:TYR218 4.9 10.5 1.0
CG2 A:THR206 5.0 8.8 1.0

Sodium binding site 4 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na307

b:24.7
occ:1.00
 OD1 A:ASN249 2.3 12.4 1.0
O A:HOH442 2.4 11.1 1.0
O A:HOH525 2.5 16.2 1.0
O A:HOH357 2.6 30.5 1.0
O A:HOH561 2.7 25.4 1.0
O A:HOH515 2.8 25.4 1.0
CG A:ASN249 3.3 11.9 1.0
O A:HOH611 3.4 16.2 1.0
O A:HOH626 3.7 19.3 1.0
ND2 A:ASN249 3.8 14.0 1.0
O A:ASN249 4.4 10.3 1.0
O A:HOH631 4.4 11.7 1.0
CB A:ASN249 4.6 9.9 1.0
O A:HOH684 4.7 36.4 1.0
CA A:ASN249 4.8 8.4 1.0

Sodium binding site 5 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na308

b:18.9
occ:1.00
 OG A:SER270 2.4 10.9 0.8
O A:HOH609 2.5 14.4 1.0
O A:HOH627 2.6 20.7 1.0
OG1 A:THR268 2.6 9.0 1.0
O A:HOH567 2.8 31.6 1.0
O A:HOH355 2.8 39.2 1.0
OG A:SER270 3.1 10.8 0.2
CB A:SER270 3.3 9.8 0.2
CB A:SER270 3.3 9.7 0.8
CB A:THR268 3.4 8.9 1.0
O A:HOH740 3.6 28.2 1.0
CG2 A:THR268 3.7 9.8 1.0
O A:HOH618 4.2 25.3 1.0
O A:HOH500 4.3 16.2 1.0
OD2 A:ASP266 4.5 9.5 1.0
CA A:SER270 4.5 8.1 1.0
OD1 A:ASP266 4.5 8.8 1.0
N A:SER270 4.6 7.9 1.0
O A:HOH652 4.6 28.2 1.0
CA A:THR268 4.8 8.8 1.0
CG A:ASP266 4.9 8.4 1.0

Sodium binding site 6 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na309

b:25.5
occ:1.00
 O A:HOH352 2.6 36.4 1.0
OG1 A:THR11 2.6 10.4 1.0
O A:HOH473 2.7 11.4 0.5
O A:HOH619 2.9 39.7 1.0
O A:HOH353 3.3 33.5 1.0
CB A:THR11 3.4 9.8 1.0
C A:THR11 4.2 9.7 1.0
O A:THR11 4.4 10.3 1.0
CG2 A:THR11 4.4 11.0 1.0
CA A:THR11 4.4 9.1 1.0
N A:ALA12 4.5 8.9 1.0
O A:HOH604 4.7 33.5 1.0
O A:ALA8 4.7 8.9 1.0
O A:HOH414 4.8 32.0 1.0

Sodium binding site 7 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na310

b:15.9
occ:1.00
 O A:HOH451 2.3 12.0 1.0
OE1 A:GLU152 2.3 8.7 1.0
O A:HOH479 2.3 16.8 1.0
O A:HOH535 2.4 17.7 1.0
O A:HOH534 2.5 17.6 1.0
CD A:GLU152 3.5 8.1 1.0
O A:HOH563 3.8 21.9 1.0
ZN A:ZN301 3.9 7.0 1.0
NAH A:HQY303 3.9 9.6 1.0
CA A:GLU152 3.9 7.5 1.0
O A:HOH572 4.0 32.2 1.0
CE1 A:HIS256 4.0 8.0 1.0
OE1 A:GLU151 4.0 7.7 1.0
O A:GLU152 4.1 11.1 1.0
OE2 A:GLU151 4.1 10.7 1.0
O A:HOH662 4.1 26.1 1.0
OAA A:HQY303 4.3 7.8 1.0
OE2 A:GLU152 4.3 8.5 1.0
CAE A:HQY303 4.4 10.5 1.0
NE2 A:HIS256 4.4 6.9 1.0
C A:GLU152 4.4 8.4 1.0
CB A:GLU152 4.4 7.9 1.0
CD A:GLU151 4.4 8.2 1.0
CG A:GLU152 4.5 8.2 1.0
O A:GLU151 4.6 7.0 1.0
CAM A:HQY303 4.6 9.0 1.0
O A:CYS227 4.7 10.4 1.0
CAJ A:HQY303 4.7 8.0 1.0
OH A:TYR225 4.8 14.7 1.0
N A:GLU152 5.0 6.7 1.0

Sodium binding site 8 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na311

b:41.6
occ:1.00
 O A:HOH579 2.7 25.5 1.0
O A:HOH333 2.7 37.5 1.0
O A:HOH416 2.8 33.3 1.0
O A:HOH329 2.8 26.9 1.0
O A:HOH359 2.9 34.4 1.0
O A:HOH378 2.9 42.1 1.0
O A:HOH453 3.2 14.4 1.0
O A:HOH720 3.6 23.2 1.0
O A:HOH688 4.1 23.7 1.0
OE1 A:GLN138 4.2 28.9 1.0
O A:HOH607 4.5 12.3 1.0
O A:HOH516 4.5 17.3 1.0
O A:HOH327 4.6 38.1 1.0
O A:HOH376 4.7 29.3 1.0
CD A:GLN138 4.9 27.3 1.0

Sodium binding site 9 out of 9 in 3vh9

Go back to Sodium Binding Sites List in 3vh9
Sodium 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 Sodium with other atoms in the Na 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:Na312

b:22.8
occ:1.00
 O A:HOH501 2.4 16.6 1.0
OD1 A:ASN74 2.5 11.3 1.0
O A:HOH565 2.5 32.0 1.0
O A:HOH549 2.6 31.0 1.0
O A:HOH616 2.8 31.6 1.0
O A:HOH691 2.8 36.1 1.0
CG A:ASN74 3.4 10.7 1.0
ND2 A:ASN74 3.6 12.0 1.0
NA A:NA305 3.6 12.5 1.0
O A:HOH498 4.5 17.5 1.0
O A:HOH623 4.6 13.7 1.0
O A:HOH466 4.7 14.6 1.0
CB A:ASN74 4.7 10.1 1.0
CL A:CL316 4.8 12.7 1.0
N A:ASN74 4.9 10.1 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: Mon Oct 7 13:49:49 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy