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Sodium in PDB 7fe2: Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose

Protein crystallography data

The structure of Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose, PDB code: 7fe2 was solved by T.Miyazaki, S.Alonso-Gil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 162.626, 168.61, 260.282, 90, 90, 90
R / Rfree (%) 16.9 / 19.8

Other elements in 7fe2:

The structure of Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose (pdb code 7fe2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose, PDB code: 7fe2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7fe2

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Sodium binding site 1 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:27.6
occ:1.00
 O A:HOH1327 2.4 34.8 1.0
O A:THR597 2.5 20.9 1.0
OD1 A:ASN20 2.6 19.7 1.0
O A:TYR599 2.6 16.4 1.0
O A:HOH911 2.6 31.2 1.0
O A:HOH1346 3.1 38.6 1.0
O A:HOH1159 3.4 29.3 1.0
C A:TYR599 3.4 17.6 1.0
CG A:ASN20 3.5 19.8 1.0
C A:THR597 3.7 18.9 1.0
CB A:ASN20 3.8 20.3 1.0
N A:TYR599 4.1 18.0 1.0
N A:PRO600 4.1 17.4 1.0
CA A:ASN20 4.1 18.1 1.0
CA A:PRO600 4.1 17.9 1.0
O A:HOH1366 4.2 33.2 1.0
CB A:THR597 4.4 20.5 1.0
CA A:THR597 4.4 17.9 1.0
CA A:TYR599 4.4 16.7 1.0
N A:GLY598 4.6 17.3 1.0
C A:GLY598 4.6 16.6 1.0
ND2 A:ASN20 4.7 21.4 1.0
O A:HOH1037 4.7 37.8 1.0
O A:THR591 4.7 22.6 1.0
C A:PRO600 4.8 19.1 1.0
O A:ASN20 4.9 15.9 1.0
C A:ASN20 5.0 16.9 1.0
CA A:GLY598 5.0 17.8 1.0
O A:SER19 5.0 17.5 1.0

Sodium binding site 2 out of 4 in 7fe2

Go back to Sodium Binding Sites List in 7fe2
Sodium binding site 2 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:29.6
occ:1.00
 O B:HOH963 2.4 32.6 1.0
OD1 B:ASN20 2.4 22.6 1.0
O B:HOH1266 2.4 39.3 1.0
O B:TYR599 2.5 17.4 1.0
O B:THR597 2.5 20.6 1.0
O B:HOH1300 3.1 38.7 1.0
CG B:ASN20 3.4 22.9 1.0
C B:TYR599 3.4 17.6 1.0
O B:HOH1077 3.4 30.0 1.0
C B:THR597 3.5 20.6 1.0
CB B:ASN20 3.7 22.6 1.0
N B:TYR599 4.0 17.5 1.0
CA B:ASN20 4.0 21.4 1.0
N B:PRO600 4.1 17.6 1.0
CA B:PRO600 4.1 18.5 1.0
O B:HOH1313 4.2 26.7 1.0
CB B:THR597 4.2 21.8 1.0
O B:HOH1279 4.3 37.9 1.0
CA B:THR597 4.3 20.0 1.0
CA B:TYR599 4.3 17.6 1.0
N B:GLY598 4.5 19.9 1.0
O B:HOH994 4.5 42.2 1.0
C B:GLY598 4.5 19.1 1.0
ND2 B:ASN20 4.6 22.7 1.0
O B:ASN20 4.8 19.8 1.0
C B:PRO600 4.8 18.8 1.0
O B:THR591 4.8 26.6 1.0
CA B:GLY598 4.8 19.1 1.0
C B:ASN20 4.8 20.1 1.0
O B:SER19 4.9 19.8 1.0
OG1 B:THR597 5.0 22.8 1.0

Sodium binding site 3 out of 4 in 7fe2

Go back to Sodium Binding Sites List in 7fe2
Sodium binding site 3 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:27.4
occ:1.00
 O C:HOH1034 2.3 31.7 1.0
O C:HOH1297 2.4 31.6 1.0
O C:THR597 2.4 20.3 1.0
OD1 C:ASN20 2.6 20.3 1.0
O C:TYR599 2.6 19.2 1.0
O C:HOH1301 2.7 36.8 1.0
C C:TYR599 3.4 19.9 1.0
CG C:ASN20 3.5 21.3 1.0
O C:HOH1086 3.5 27.3 1.0
C C:THR597 3.5 19.8 1.0
CB C:ASN20 3.8 18.1 1.0
N C:TYR599 3.9 20.1 1.0
CA C:ASN20 4.1 18.8 1.0
N C:PRO600 4.1 17.7 1.0
CA C:PRO600 4.2 18.9 1.0
CA C:THR597 4.3 20.4 1.0
O C:HOH1329 4.3 31.6 1.0
CB C:THR597 4.3 21.1 1.0
CA C:TYR599 4.4 18.3 1.0
O C:HOH1307 4.4 36.2 1.0
N C:GLY598 4.5 19.6 1.0
C C:GLY598 4.5 19.1 1.0
ND2 C:ASN20 4.7 21.1 1.0
O C:THR591 4.8 27.4 1.0
CA C:GLY598 4.8 19.4 1.0
O C:ASN20 4.8 17.7 1.0
C C:PRO600 4.8 20.8 1.0
C C:ASN20 4.9 18.6 1.0
O C:SER19 5.0 19.0 1.0
O C:HOH1314 5.0 44.8 1.0
OG1 C:THR597 5.0 20.5 1.0

Sodium binding site 4 out of 4 in 7fe2

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Sodium binding site 4 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na802

b:32.4
occ:1.00
 O D:HOH1279 2.2 41.6 1.0
O D:HOH924 2.4 36.1 1.0
O D:THR597 2.5 21.0 1.0
OD1 D:ASN20 2.5 22.1 1.0
O D:TYR599 2.5 15.3 1.0
O D:HOH1297 2.7 33.4 1.0
C D:TYR599 3.4 16.7 1.0
O D:HOH1111 3.4 24.3 1.0
CG D:ASN20 3.5 22.0 1.0
C D:THR597 3.6 18.2 1.0
CB D:ASN20 3.8 21.5 1.0
N D:TYR599 4.0 17.8 1.0
N D:PRO600 4.1 17.7 1.0
CA D:PRO600 4.1 18.5 1.0
CA D:ASN20 4.1 20.1 1.0
O D:HOH1325 4.2 30.4 1.0
CA D:TYR599 4.4 16.8 1.0
CA D:THR597 4.4 18.5 1.0
CB D:THR597 4.4 22.0 1.0
N D:GLY598 4.5 16.2 1.0
O D:HOH1301 4.5 35.7 1.0
C D:GLY598 4.6 18.1 1.0
ND2 D:ASN20 4.7 23.3 1.0
C D:PRO600 4.8 19.7 1.0
O D:THR591 4.8 24.7 1.0
O D:HOH1043 4.8 32.1 1.0
CA D:GLY598 4.9 17.6 1.0
O D:ASN20 4.9 17.6 1.0
C D:ASN20 5.0 19.9 1.0
O D:HOH1303 5.0 41.2 1.0
O D:SER19 5.0 19.3 1.0

Reference:

S.Alonso-Gil, K.Parkan, J.Kaminsky, R.Pohl, T.Miyazaki. Unlocking the Hydrolytic Mechanism of GH92 Alpha-1,2-Mannosidases: Computation Inspires the Use of C-Glycosides As Michaelis Complex Mimics. Chemistry V. 28 00148 2022.
ISSN: ISSN 0947-6539
PubMed: 35049087
DOI: 10.1002/CHEM.202200148
Page generated: Fri Apr 7 14:46:15 2023

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