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Sodium in PDB 4xmt: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid

Enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid

All present enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid, PDB code: 4xmt was solved by A.Addlagatta, R.Gumpena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.14 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.473, 120.473, 170.620, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 16.9

Other elements in 4xmt:

The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid (pdb code 4xmt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid, PDB code: 4xmt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4xmt

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Sodium binding site 1 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:25.2
occ:1.00
O A:HOH1877 2.1 34.3 1.0
O A:GLY335 2.3 19.5 1.0
O A:HOH1776 2.4 26.6 1.0
O A:SER332 2.4 17.8 1.0
O A:HOH1588 2.5 19.3 1.0
O A:ASP333 2.7 16.2 1.0
O A:HOH1014 3.1 25.8 0.5
C A:ASP333 3.3 19.4 1.0
C A:GLY335 3.4 18.6 1.0
C A:SER332 3.5 18.8 1.0
CA A:ASP333 3.7 18.7 1.0
N A:GLY335 3.8 17.0 1.0
N A:ARG337 4.0 19.4 1.0
N A:ASP333 4.1 18.8 1.0
C A:LEU334 4.2 19.6 1.0
O A:HOH1529 4.2 27.9 1.0
N A:LEU334 4.2 17.5 1.0
CA A:GLY335 4.2 19.0 1.0
O A:HOH2077 4.3 44.0 1.0
O A:HOH1775 4.3 48.5 1.0
N A:SER336 4.3 19.9 1.0
O A:HOH1943 4.4 37.2 1.0
CA A:SER336 4.5 19.5 1.0
O A:HOH1500 4.5 32.3 1.0
C A:SER336 4.6 18.6 1.0
CB A:ARG337 4.6 20.3 1.0
CA A:LEU334 4.7 19.4 1.0
O A:LEU334 4.8 19.2 1.0
CA A:SER332 4.8 17.2 1.0
CA A:ARG337 4.8 20.8 1.0

Sodium binding site 2 out of 7 in 4xmt

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Sodium binding site 2 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:41.6
occ:1.00
O A:HOH1897 2.2 47.8 1.0
O A:HOH1893 2.4 43.8 1.0
OD1 A:ASP452 2.4 23.9 1.0
O A:ASP452 2.5 23.9 1.0
O A:HOH1885 2.5 44.1 1.0
O A:HOH1639 2.6 31.1 1.0
C A:ASP452 3.3 24.4 1.0
NA A:NA907 3.4 50.9 1.0
CG A:ASP452 3.5 23.4 1.0
O A:HOH1844 3.7 33.8 1.0
N A:ASP452 3.8 22.2 1.0
CA A:ASP452 3.9 21.1 1.0
O A:HOH1880 4.1 48.4 1.0
CB A:ASP452 4.3 22.9 1.0
N A:ASP453 4.3 25.4 1.0
O A:HOH1872 4.4 49.8 1.0
OD2 A:ASP452 4.4 24.9 1.0
O A:HOH1758 4.5 31.1 1.0
CA A:ASP453 4.5 26.4 1.0

Sodium binding site 3 out of 7 in 4xmt

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Sodium binding site 3 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:42.5
occ:1.00
O A:HOH1653 2.5 44.5 1.0
O A:HOH1718 2.7 25.4 1.0
O A:HOH1491 2.8 36.9 1.0
O A:HOH1393 2.8 26.7 1.0
O A:GLY56 2.9 18.3 1.0
N A:GLY79 3.6 21.7 1.0
C A:GLY56 3.7 18.9 1.0
CA A:GLY79 3.7 23.2 1.0
O A:HOH1940 3.8 57.8 1.0
CA A:GLU57 4.0 19.4 1.0
OH A:TYR130 4.1 26.7 1.0
N A:ALA80 4.1 18.9 1.0
C A:GLY79 4.1 22.2 1.0
N A:GLU57 4.2 16.5 1.0
O A:GLU77 4.2 23.2 1.0
N A:ASP58 4.3 19.3 1.0
C A:GLU57 4.6 20.0 1.0
OE1 A:GLU57 4.7 24.6 1.0
C A:GLU78 4.7 24.8 1.0
CA A:GLY56 4.7 17.2 1.0
CE1 A:TYR130 4.8 22.6 1.0
CZ A:TYR130 4.9 23.8 1.0
O A:GLY79 4.9 18.3 1.0
CD A:GLU57 5.0 25.3 1.0

Sodium binding site 4 out of 7 in 4xmt

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Sodium binding site 4 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:33.3
occ:1.00
O A:HOH1728 2.4 30.6 1.0
O A:LEU138 2.5 18.3 1.0
O A:HOH1965 2.5 36.0 1.0
OE1 A:GLN19 2.6 22.2 1.0
O A:ILE20 2.7 23.9 1.0
CD A:GLN19 3.4 21.2 1.0
C A:LEU138 3.5 19.1 1.0
C A:ILE20 3.6 21.7 1.0
N A:LEU138 3.7 16.2 1.0
CB A:GLN19 4.0 18.6 1.0
O A:HOH1972 4.0 19.9 0.5
CA A:THR21 4.1 18.4 1.0
CA A:LEU138 4.1 17.7 1.0
N A:ILE20 4.1 19.6 1.0
CG A:GLN19 4.1 20.1 1.0
N A:THR21 4.2 18.6 1.0
NE2 A:GLN19 4.3 20.3 1.0
O A:HOH1514 4.4 34.1 1.0
CG2 A:THR21 4.4 21.9 1.0
C A:VAL137 4.5 17.3 1.0
O A:HOH1898 4.5 48.0 1.0
N A:ALA139 4.6 17.8 1.0
CB A:LEU138 4.6 19.5 1.0
CA A:ILE20 4.6 18.9 1.0
O A:HOH2022 4.6 19.8 0.5
CA A:GLN19 4.7 18.0 1.0
CA A:VAL137 4.7 16.5 1.0
CG1 A:VAL137 4.7 18.1 1.0
C A:GLN19 4.8 20.6 1.0
CB A:THR21 4.9 20.7 1.0
CA A:ALA139 4.9 16.9 1.0
O A:HOH1614 5.0 29.4 1.0

Sodium binding site 5 out of 7 in 4xmt

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Sodium binding site 5 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:50.9
occ:1.00
O A:HOH1844 2.3 33.8 1.0
O A:HOH1897 2.4 47.8 1.0
O A:HOH1179 2.5 30.5 1.0
OH A:TYR544 2.7 23.0 1.0
O A:HOH1872 2.8 49.8 1.0
OD1 A:ASP452 2.9 23.9 1.0
CZ A:TYR544 3.4 20.4 1.0
NA A:NA904 3.4 41.6 1.0
CG A:ASP452 3.7 23.4 1.0
OD2 A:ASP452 3.7 24.9 1.0
O A:HOH1995 4.0 43.0 1.0
CE1 A:TYR544 4.0 21.3 1.0
O A:HOH1639 4.1 31.1 1.0
CE2 A:TYR544 4.1 22.5 1.0
NE2 A:GLN550 4.2 33.0 1.0
O A:LYS545 4.3 23.7 1.0
OE1 A:GLN550 4.6 23.5 1.0
O A:HOH1669 4.6 39.1 1.0
O A:HOH1885 4.7 44.1 1.0
CD A:GLN550 4.8 24.9 1.0

Sodium binding site 6 out of 7 in 4xmt

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Sodium binding site 6 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:46.4
occ:1.00
O A:HOH1808 2.4 58.9 1.0
O A:HOH1865 2.4 47.5 1.0
O A:HOH1191 2.4 32.9 1.0
O A:HOH1646 2.5 49.2 1.0
O A:HIS771 2.5 21.0 1.0
O A:PHE774 2.5 21.3 1.0
C A:HIS771 3.5 24.8 1.0
C A:PHE774 3.6 22.8 1.0
O A:ARG772 3.9 25.9 1.0
N A:PHE774 4.0 21.7 1.0
CA A:ARG772 4.0 26.6 1.0
C A:ARG772 4.0 26.1 1.0
N A:ARG772 4.1 24.1 1.0
CA A:PHE774 4.3 21.5 1.0
O A:GLN770 4.3 24.1 1.0
C A:GLN770 4.5 26.3 1.0
N A:HIS771 4.6 23.0 1.0
N A:SER773 4.6 23.1 1.0
CB A:PHE774 4.6 20.1 1.0
CA A:HIS771 4.7 23.0 1.0
N A:THR775 4.7 23.1 1.0
C A:SER773 4.8 23.7 1.0
CA A:THR775 4.9 22.3 1.0
O A:LEU769 4.9 23.3 1.0

Sodium binding site 7 out of 7 in 4xmt

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Sodium binding site 7 out of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid


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 MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:48.4
occ:1.00
OD2 A:ASP24 2.2 26.6 0.5
OD1 A:ASP24 2.3 26.5 0.5
CG A:ASP24 2.5 23.0 0.5
O A:HOH2006 2.7 48.0 1.0
O A:HOH1279 2.7 22.2 1.0
O A:HOH1112 2.8 25.0 1.0
O A:HOH1025 3.2 54.0 1.0
O A:HOH1134 3.5 28.1 1.0
CB A:ASP24 3.8 19.4 0.5
CB A:ASP24 3.8 19.3 0.5
CB A:ASP22 3.9 19.5 1.0
N A:ASP24 4.0 17.2 1.0
C A:ILE23 4.0 17.6 1.0
OG1 A:THR142 4.1 22.4 0.4
O A:ILE23 4.2 16.7 1.0
N A:ILE23 4.2 17.9 1.0
O A:HOH1012 4.2 42.3 1.0
CA A:ASP24 4.3 18.0 0.5
CA A:ASP24 4.3 18.1 0.5
OD2 A:ASP24 4.4 29.4 0.5
C A:ASP22 4.4 19.0 1.0
CA A:ILE23 4.5 17.3 1.0
CG A:ASP24 4.6 22.3 0.5
CA A:ASP22 4.7 18.9 1.0
CG A:ASP22 4.8 22.6 1.0
OD2 A:ASP22 4.8 21.7 1.0
CB A:THR142 4.8 21.1 0.4
O A:ARG140 4.9 18.3 1.0
OG1 A:THR142 4.9 19.8 0.6
O A:ASP22 5.0 17.5 1.0
O A:VAL39 5.0 17.3 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid To Be Published.
Page generated: Tue Dec 15 09:47:22 2020

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