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Sodium in PDB 3b3s: Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine

Enzymatic activity of Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine

All present enzymatic activity of Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine:
3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine, PDB code: 3b3s was solved by N.J.Ataie, Q.Q.Hoang, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.21 / 1.18
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.485, 109.485, 91.022, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 19.6

Other elements in 3b3s:

The structure of Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine (pdb code 3b3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine, PDB code: 3b3s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3b3s

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Sodium binding site 1 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na294

b:23.4
occ:1.00
 OG A:SER215 2.8 21.8 1.0
N A:SER215 3.1 15.7 1.0
O A:HOH519 3.3 28.7 1.0
C A:LEU213 3.3 12.2 1.0
CA A:LEU213 3.5 12.0 1.0
O A:HOH507 3.5 29.8 1.0
N A:PRO214 3.5 13.4 1.0
CB A:SER215 3.6 18.1 1.0
CD A:PRO214 3.8 13.9 1.0
O A:LEU213 3.8 12.2 1.0
CA A:SER215 3.8 15.7 1.0
N A:LEU216 4.2 13.2 1.0
C A:PRO214 4.2 15.0 1.0
CB A:LEU213 4.2 12.4 1.0
CD2 A:LEU213 4.3 15.0 1.0
CG A:PRO214 4.4 16.2 1.0
C A:SER215 4.4 14.8 1.0
CG A:LEU216 4.4 14.1 1.0
CA A:PRO214 4.4 14.8 1.0
O A:TYR212 4.7 12.4 1.0
N A:LEU213 4.7 11.8 1.0
CD2 A:LEU216 4.9 15.1 1.0
CG A:LEU213 4.9 13.3 1.0

Sodium binding site 2 out of 8 in 3b3s

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Sodium binding site 2 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na295

b:22.6
occ:1.00
 O A:HOH564 2.8 33.4 1.0
NZ A:LYS273 3.0 18.6 1.0
N A:ALA19 3.0 11.3 1.0
O A:HOH458 3.5 49.2 1.0
CB A:ALA19 3.6 12.2 1.0
CA A:ASP18 3.8 11.6 1.0
CE A:LYS273 3.9 15.8 1.0
CD A:LYS273 3.9 13.5 1.0
CA A:ALA19 3.9 10.7 1.0
C A:ASP18 3.9 10.8 1.0
O A:VAL17 3.9 13.3 1.0
OD1 A:ASP18 4.1 17.3 1.0
N A:ASP18 4.7 11.4 1.0
C A:VAL17 4.7 11.2 1.0
N A:SER20 4.8 11.1 1.0
O A:HOH452 4.9 26.1 1.0
C A:ALA19 4.9 10.6 1.0
CG A:ASP18 4.9 14.8 1.0
CB A:ASP18 4.9 13.2 1.0

Sodium binding site 3 out of 8 in 3b3s

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Sodium binding site 3 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na296

b:30.6
occ:1.00
 O A:HOH365 3.1 26.8 1.0
OG A:SER51 3.2 14.2 0.6
O A:ASP47 3.5 11.8 1.0
CA A:TRP48 3.7 10.3 1.0
C A:ASP47 3.7 10.1 1.0
N A:TRP48 3.8 10.4 1.0
CB A:SER51 4.0 12.5 0.6
CB A:SER51 4.0 12.2 0.4
CB A:ASP47 4.1 11.4 1.0
O A:HOH342 4.2 16.6 1.0
CB A:TRP48 4.4 11.6 1.0
CA A:ASP47 4.6 10.5 1.0
OG A:SER51 4.6 14.5 0.4
CD1 A:TRP48 4.7 16.7 1.0
O A:HOH495 4.7 35.3 1.0
C A:TRP48 4.8 9.8 1.0
O A:HOH576 4.9 22.9 1.0
NE2 A:GLN44 4.9 22.2 0.5
CG A:TRP48 5.0 13.2 1.0
O A:TRP48 5.0 12.3 1.0

Sodium binding site 4 out of 8 in 3b3s

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Sodium binding site 4 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na297

b:14.2
occ:1.00
 OH A:TYR218 2.4 13.0 1.0
O A:HOH373 2.5 15.8 1.0
O A:HOH555 2.5 18.1 1.0
CZ A:TYR218 3.4 12.0 1.0
CE1 A:TYR218 3.6 11.9 1.0
OG1 A:THR206 4.0 12.2 1.0
OD2 A:ASP210 4.0 14.3 1.0
CB A:THR206 4.4 11.4 1.0
OD1 A:ASP210 4.4 12.6 1.0
CG A:ASP210 4.7 12.7 1.0
CE2 A:TYR218 4.7 12.8 1.0
NE2 A:GLN203 4.8 12.7 1.0
O A:HOH388 4.9 16.9 1.0

Sodium binding site 5 out of 8 in 3b3s

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Sodium binding site 5 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na298

b:18.6
occ:1.00
 O A:HOH306 2.4 21.5 1.0
O A:HOH468 2.5 35.3 1.0
O A:THR194 2.5 12.6 1.0
O A:THR197 2.7 12.0 1.0
O A:HOH367 3.1 24.3 1.0
C A:THR197 3.6 10.1 1.0
C A:THR194 3.6 10.2 1.0
OG1 A:THR197 3.7 11.0 1.0
N A:SER199 4.0 10.6 1.0
O A:HOH467 4.1 31.9 1.0
CA A:THR194 4.2 9.7 1.0
N A:ASP198 4.3 10.4 1.0
N A:THR197 4.4 10.0 1.0
N A:SCN302 4.4 16.6 1.0
CB A:SER199 4.4 12.0 1.0
CA A:THR197 4.4 9.9 1.0
C A:ASP198 4.4 10.4 1.0
CB A:THR194 4.5 10.1 1.0
CA A:ASP198 4.5 10.1 1.0
CA A:SER199 4.5 11.0 1.0
CB A:THR197 4.6 10.8 1.0
N A:ASP195 4.7 9.8 1.0
CA A:ASP195 4.9 10.0 1.0
C A:SCN302 4.9 15.1 1.0

Sodium binding site 6 out of 8 in 3b3s

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Sodium binding site 6 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na299

b:20.3
occ:1.00
 NE2 A:HIS234 2.0 16.9 1.0
CE1 A:HIS234 2.9 15.4 1.0
CD2 A:HIS234 3.0 16.4 1.0
O A:HOH338 3.9 23.8 1.0
ND1 A:HIS234 4.1 15.9 1.0
CG A:HIS234 4.2 13.7 1.0

Sodium binding site 7 out of 8 in 3b3s

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Sodium binding site 7 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na300

b:23.2
occ:1.00
 O A:HOH422 3.2 23.8 1.0
CG A:GLN54 3.8 14.9 1.0
CA A:ALA55 3.9 13.1 0.5
CA A:ALA55 4.0 14.6 0.5
N A:ALA55 4.1 12.9 0.5
N A:ALA55 4.1 13.6 0.5
CB A:ALA55 4.2 13.4 0.5
C A:GLN54 4.3 13.1 1.0
O A:GLN54 4.3 14.9 1.0
CB A:ALA55 4.5 15.0 0.5
CB A:GLN54 4.6 13.5 1.0
CB A:ALA58 4.6 20.5 0.5
CB A:ALA58 4.6 23.3 0.5
NE2 A:GLN54 4.8 19.4 1.0
CD A:GLN54 4.9 16.1 1.0

Sodium binding site 8 out of 8 in 3b3s

Go back to Sodium Binding Sites List in 3b3s
Sodium binding site 8 out of 8 in the Crystal Structure of the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine


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 the M180A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:88.0
occ:1.00
 CB A:SER71 4.2 17.4 1.0
OG A:SER71 4.3 21.1 1.0
N A:GLY72 4.3 19.1 1.0
CA A:SER71 4.5 17.0 1.0
C A:SER71 4.9 17.5 1.0

Reference:

N.J.Ataie, Q.Q.Hoang, M.P.Zahniser, Y.Tu, A.Milne, G.A.Petsko, D.Ringe. Zinc Coordination Geometry and Ligand Binding Affinity: the Structural and Kinetic Analysis of the Second-Shell Serine 228 Residue and the Methionine 180 Residue of the Aminopeptidase From Vibrio Proteolyticus. Biochemistry V. 47 7673 2008.
ISSN: ISSN 0006-2960
PubMed: 18576673
DOI: 10.1021/BI702188E
Page generated: Mon Oct 7 05:58:39 2024

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