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Sodium in PDB 5urb: Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine

Enzymatic activity of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine

All present enzymatic activity of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine:
6.1.1.10;

Protein crystallography data

The structure of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine, PDB code: 5urb was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.73 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.910, 108.410, 78.570, 90.00, 90.69, 90.00
R / Rfree (%) 15.6 / 19.4

Other elements in 5urb:

The structure of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine (pdb code 5urb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine, PDB code: 5urb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5urb

Go back to Sodium Binding Sites List in 5urb
Sodium binding site 1 out of 2 in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine


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 Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:37.3
occ:1.00
 O A:HOH919 2.3 30.6 1.0
OD1 A:ASN321 2.4 18.9 0.4
O A:LYS364 2.4 34.7 1.0
O A:HOH866 2.5 26.6 1.0
O A:SER362 2.5 32.0 1.0
CG A:ASN321 3.4 27.3 0.4
C A:LYS364 3.5 34.3 1.0
C A:SER362 3.6 36.6 1.0
NE2 A:GLN27 3.9 25.2 1.0
N A:LYS364 4.0 28.0 1.0
N A:SER362 4.1 28.9 1.0
C A:ASP363 4.2 26.1 1.0
CB A:ASN321 4.2 29.1 0.4
ND2 A:ASN321 4.2 22.9 0.4
O A:HOH783 4.2 35.0 1.0
O A:VAL320 4.3 25.1 1.0
CA A:LYS364 4.4 35.6 1.0
N A:VAL365 4.4 31.2 1.0
CA A:ASN321 4.4 27.1 0.4
CD2 A:LEU361 4.5 32.6 1.0
N A:ASP363 4.5 30.9 1.0
CA A:SER362 4.5 30.2 1.0
CA A:ASN321 4.5 26.4 0.6
CA A:ASP363 4.5 28.3 1.0
CB A:ASN321 4.6 29.5 0.6
CA A:VAL365 4.6 30.6 1.0
O A:ASP363 4.6 32.8 1.0
O A:HOH831 4.6 33.9 1.0
N A:GLU366 4.7 34.3 1.0
OG A:SER362 4.7 33.9 1.0
CG A:GLU366 4.7 43.2 1.0
OE2 A:GLU366 4.8 50.2 1.0
CD A:GLN27 4.9 25.4 1.0

Sodium binding site 2 out of 2 in 5urb

Go back to Sodium Binding Sites List in 5urb
Sodium binding site 2 out of 2 in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine


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 Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:35.8
occ:1.00
 O B:HOH903 2.2 29.0 1.0
OD1 B:ASN321 2.4 25.4 0.6
O B:SER362 2.4 26.4 1.0
O B:HOH1012 2.5 28.3 1.0
O B:LYS364 2.5 36.2 1.0
CG B:ASN321 3.4 22.9 0.6
C B:SER362 3.5 25.8 1.0
C B:LYS364 3.6 36.9 1.0
N B:SER362 4.0 26.7 1.0
NE2 B:GLN27 4.0 25.3 1.0
N B:LYS364 4.0 36.4 1.0
C B:ASP363 4.1 35.2 1.0
CB B:ASN321 4.2 27.0 0.6
O B:HOH814 4.2 33.4 1.0
O B:VAL320 4.3 25.4 1.0
N B:ASP363 4.3 25.4 1.0
CA B:SER362 4.3 22.2 1.0
ND2 B:ASN321 4.4 24.2 0.6
CB B:ASN321 4.4 26.9 0.4
CA B:ASP363 4.4 28.7 1.0
OG B:SER362 4.4 31.5 1.0
CA B:LYS364 4.5 38.7 1.0
CA B:ASN321 4.5 25.9 0.6
O B:HOH852 4.5 30.7 1.0
CA B:ASN321 4.5 25.9 0.4
N B:VAL365 4.5 30.4 1.0
CD2 B:LEU361 4.6 23.1 1.0
O B:ASP363 4.6 34.7 1.0
CA B:VAL365 4.6 25.0 1.0
N B:GLU366 4.7 31.5 1.0
CG B:GLU366 4.7 35.9 1.0
O B:HOH992 4.9 41.8 1.0
OE2 B:GLU366 4.9 52.2 1.0
O B:GLU366 5.0 32.6 1.0
CD B:GLN27 5.0 23.7 1.0

Reference:

D.M.Dranow, D.D.Lorimer, T.E.Edwards. Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine To Be Published.
Page generated: Tue Oct 8 00:39:16 2024

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