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Sodium in PDB 1rtq: The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica

Enzymatic activity of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica

All present enzymatic activity of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica:
3.4.11.10;

Protein crystallography data

The structure of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica, PDB code: 1rtq was solved by W.Desmarais, D.L.Bienvenue, B.P.Krzysztof, R.C.Holz, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 0.95
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.936, 109.936, 91.369, 90.00, 90.00, 120.00
R / Rfree (%) 13.5 / 15.1

Other elements in 1rtq:

The structure of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica (pdb code 1rtq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica, PDB code: 1rtq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1rtq

Go back to Sodium Binding Sites List in 1rtq
Sodium binding site 1 out of 3 in the The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:7.8
occ:1.00
 O A:HOH1024 2.3 8.1 1.0
O A:HOH1026 2.4 9.7 1.0
O A:HOH1096 2.4 10.2 1.0
OH A:TYR218 2.4 8.2 1.0
O A:HOH1025 2.4 8.7 1.0
O A:HOH1028 2.5 8.6 1.0
HH A:TYR218 2.9 12.3 1.0
HE1 A:TYR218 3.2 9.1 1.0
CZ A:TYR218 3.5 7.5 1.0
CE1 A:TYR218 3.7 7.6 1.0
HB A:THR206 3.7 8.6 1.0
HG1 A:THR206 3.8 10.9 1.0
OG1 A:THR206 3.9 7.3 1.0
OD2 A:ASP210 4.0 8.9 1.0
HE21 A:GLN203 4.1 7.8 1.0
CB A:THR206 4.3 7.1 1.0
O A:HOH1198 4.4 24.3 1.0
OD1 A:ASP210 4.4 8.6 1.0
CG A:ASP210 4.6 7.5 1.0
HG21 A:THR206 4.7 11.4 1.0
CE2 A:TYR218 4.7 7.6 1.0
NE2 A:GLN203 4.8 6.5 1.0
O A:HOH1039 5.0 9.4 1.0
HE22 A:GLN203 5.0 7.8 1.0
HE2 A:TYR218 5.0 9.1 1.0

Sodium binding site 2 out of 3 in 1rtq

Go back to Sodium Binding Sites List in 1rtq
Sodium binding site 2 out of 3 in the The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:11.6
occ:1.00
 HG A:SER51 1.8 15.3 1.0
O A:HOH1046 2.4 13.2 1.0
O A:HOH1086 2.4 16.1 1.0
O A:HOH1048 2.4 12.6 1.0
OG A:SER51 2.5 10.2 1.0
O A:HOH1142 2.5 18.5 1.0
HB3 A:SER51 3.3 9.3 1.0
CB A:SER51 3.4 7.7 1.0
HA A:SER51 3.8 9.5 1.0
HB2 A:SER51 4.2 9.3 1.0
CA A:SER51 4.2 7.9 1.0
O A:HOH1122 4.4 17.5 1.0
O A:HOH1057 4.5 7.9 1.0
O A:HOH1258 4.9 28.8 1.0

Sodium binding site 3 out of 3 in 1rtq

Go back to Sodium Binding Sites List in 1rtq
Sodium binding site 3 out of 3 in the The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase From Aeromonas Proteolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:12.7
occ:1.00
 HG A:SER270 1.9 16.1 1.0
OG A:SER270 2.4 10.8 1.0
O A:HOH1133 2.4 19.4 1.0
O A:HOH1087 2.4 11.0 1.0
O A:HOH1090 2.5 15.2 1.0
OG1 A:THR268 2.5 7.9 1.0
O A:HOH1073 2.5 26.5 1.0
HG1 A:THR268 2.7 11.8 1.0
HB2 A:SER270 3.1 10.2 1.0
HG21 A:THR268 3.1 13.6 1.0
HB A:THR268 3.3 8.9 1.0
CB A:SER270 3.3 8.5 1.0
CB A:THR268 3.3 7.4 1.0
O A:HOH1175 3.5 21.7 1.0
CG2 A:THR268 3.7 9.0 1.0
HB3 A:SER270 3.8 10.2 1.0
H A:SER270 4.0 7.9 1.0
HG22 A:THR268 4.1 13.6 1.0
O A:HOH1054 4.2 10.4 1.0
O A:HOH1116 4.3 24.7 1.0
OD2 A:ASP266 4.4 9.3 1.0
O A:HOH1302 4.4 38.0 1.0
HG23 A:THR268 4.5 13.6 1.0
CA A:SER270 4.5 7.0 1.0
OD1 A:ASP266 4.5 7.6 1.0
N A:SER270 4.5 6.6 1.0
CA A:THR268 4.7 7.0 1.0
O A:HOH1260 4.8 27.9 1.0
HA A:SER270 4.9 8.3 1.0
CG A:ASP266 4.9 7.6 1.0
O A:HOH1180 4.9 31.3 1.0
C A:THR268 5.0 6.6 1.0

Reference:

W.Desmarais, D.L.Bienvenue, K.P.Bzymek, G.A.Petsko, D.Ringe, R.C.Holz. The High-Resolution Structures of the Neutral and the Low pH Crystals of Aminopeptidase From Aeromonas Proteolytica. J.Biol.Inorg.Chem. V. 11 398 2006.
ISSN: ISSN 0949-8257
PubMed: 16596389
DOI: 10.1007/S00775-006-0093-X
Page generated: Sun Oct 6 22:01:48 2024

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