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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Dec 15 06:28:54 2020

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