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Sodium in PDB 7fe1: Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside

Protein crystallography data

The structure of Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside, PDB code: 7fe1 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) 48.62 / 1.72
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 163.162, 169.601, 258.659, 90, 90, 90
R / Rfree (%) 14.9 / 17.1

Other elements in 7fe1:

The structure of Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside (pdb code 7fe1). 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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside, PDB code: 7fe1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7fe1

Go back to Sodium Binding Sites List in 7fe1
Sodium binding site 1 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:25.8
occ:1.00
 O A:HOH1471 2.4 30.9 1.0
OD1 A:ASN20 2.5 21.5 1.0
O A:THR597 2.5 17.8 1.0
O A:TYR599 2.6 16.0 1.0
O A:HOH950 2.6 30.6 1.0
O A:HOH1514 3.0 40.5 1.0
O A:HOH1171 3.4 24.8 1.0
CG A:ASN20 3.4 18.4 1.0
C A:TYR599 3.5 15.8 1.0
C A:THR597 3.6 16.5 1.0
CB A:ASN20 3.7 17.4 1.0
N A:TYR599 4.1 14.9 1.0
CA A:ASN20 4.1 15.5 1.0
N A:PRO600 4.2 15.1 1.0
CA A:PRO600 4.2 16.2 1.0
CB A:THR597 4.3 17.8 1.0
CA A:THR597 4.3 16.2 1.0
O A:HOH1564 4.3 25.1 1.0
CA A:TYR599 4.4 15.9 1.0
N A:GLY598 4.5 15.8 1.0
C A:GLY598 4.6 15.2 1.0
ND2 A:ASN20 4.6 20.6 1.0
O A:HOH971 4.7 36.2 1.0
O A:ASN20 4.8 15.1 1.0
C A:PRO600 4.8 15.9 1.0
O A:HOH1497 4.8 38.0 1.0
O A:THR591 4.9 22.7 1.0
OG1 A:THR597 4.9 17.4 1.0
CA A:GLY598 4.9 17.0 1.0
C A:ASN20 4.9 15.7 1.0
O A:SER19 5.0 15.5 1.0

Sodium binding site 2 out of 4 in 7fe1

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


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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na804

b:24.8
occ:1.00
 O B:THR597 2.4 17.7 1.0
O B:HOH978 2.4 30.5 1.0
OD1 B:ASN20 2.4 18.5 1.0
O B:TYR599 2.5 14.9 1.0
O B:HOH1450 2.5 30.5 1.0
O B:HOH1486 2.9 37.9 1.0
CG B:ASN20 3.4 18.2 1.0
C B:TYR599 3.4 15.3 1.0
C B:THR597 3.5 17.6 1.0
O B:HOH1094 3.5 22.8 1.0
CB B:ASN20 3.7 17.1 1.0
N B:TYR599 4.0 17.0 1.0
CA B:ASN20 4.0 17.2 1.0
N B:PRO600 4.2 15.1 1.0
CA B:PRO600 4.2 16.3 1.0
CB B:THR597 4.2 17.3 1.0
CA B:THR597 4.2 15.7 1.0
O B:HOH1547 4.3 23.3 1.0
CA B:TYR599 4.3 15.8 1.0
N B:GLY598 4.4 17.0 1.0
C B:GLY598 4.5 17.1 1.0
ND2 B:ASN20 4.6 19.4 1.0
O B:HOH1139 4.6 36.8 1.0
O B:HOH1382 4.6 43.8 1.0
O B:ASN20 4.8 15.2 1.0
C B:ASN20 4.8 15.5 1.0
C B:PRO600 4.8 15.4 1.0
CA B:GLY598 4.8 18.1 1.0
O B:THR591 4.9 21.7 1.0
OG1 B:THR597 4.9 18.2 1.0
O B:SER19 4.9 15.8 1.0

Sodium binding site 3 out of 4 in 7fe1

Go back to Sodium Binding Sites List in 7fe1
Sodium binding site 3 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na804

b:23.8
occ:1.00
 O C:HOH989 2.4 33.0 1.0
OD1 C:ASN20 2.4 18.4 1.0
O C:HOH1491 2.5 31.4 1.0
O C:TYR599 2.5 16.7 1.0
O C:THR597 2.5 17.4 1.0
O C:HOH1492 2.6 32.6 1.0
CG C:ASN20 3.4 19.0 1.0
C C:TYR599 3.4 17.0 1.0
O C:HOH1196 3.4 23.6 1.0
C C:THR597 3.6 16.5 1.0
CB C:ASN20 3.7 16.6 1.0
N C:TYR599 4.0 16.8 1.0
CA C:ASN20 4.0 16.5 1.0
N C:PRO600 4.1 15.6 1.0
CA C:PRO600 4.1 16.1 1.0
CA C:THR597 4.3 17.6 1.0
O C:HOH1553 4.3 24.4 1.0
CB C:THR597 4.3 18.5 1.0
CA C:TYR599 4.4 16.2 1.0
N C:GLY598 4.5 16.2 1.0
C C:GLY598 4.5 15.4 1.0
ND2 C:ASN20 4.6 18.8 1.0
O C:HOH1051 4.7 34.0 1.0
O C:THR591 4.8 24.3 1.0
O C:ASN20 4.8 15.2 1.0
C C:PRO600 4.8 17.2 1.0
CA C:GLY598 4.8 16.4 1.0
C C:ASN20 4.8 15.9 1.0
O C:HOH1516 4.9 40.6 1.0
O C:SER19 4.9 16.5 1.0
OG1 C:THR597 4.9 19.4 1.0

Sodium binding site 4 out of 4 in 7fe1

Go back to Sodium Binding Sites List in 7fe1
Sodium binding site 4 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na804

b:28.9
occ:1.00
 O D:HOH1434 2.4 36.3 1.0
O D:HOH950 2.4 36.3 1.0
OD1 D:ASN20 2.5 19.7 1.0
O D:THR597 2.5 18.2 1.0
O D:TYR599 2.6 15.7 1.0
O D:HOH1450 2.7 33.9 1.0
O D:HOH1209 3.3 23.0 1.0
CG D:ASN20 3.5 21.1 1.0
C D:TYR599 3.5 16.3 1.0
C D:THR597 3.6 17.5 1.0
CB D:ASN20 3.8 19.4 1.0
CA D:ASN20 4.1 17.6 1.0
CA D:PRO600 4.1 17.0 1.0
N D:TYR599 4.1 17.4 1.0
N D:PRO600 4.1 15.4 1.0
O D:HOH1513 4.2 26.0 1.0
CA D:THR597 4.4 16.7 1.0
CB D:THR597 4.4 20.3 1.0
CA D:TYR599 4.5 16.5 1.0
O D:HOH1456 4.5 31.4 1.0
N D:GLY598 4.5 15.7 1.0
O D:HOH1412 4.5 43.6 1.0
O D:HOH1047 4.6 35.9 1.0
C D:GLY598 4.6 18.9 1.0
ND2 D:ASN20 4.7 22.4 1.0
C D:PRO600 4.8 16.1 1.0
O D:THR591 4.8 23.9 1.0
CA D:GLY598 4.9 17.0 1.0
O D:ASN20 4.9 18.6 1.0
C D:ASN20 4.9 18.0 1.0
O D:SER19 4.9 17.4 1.0
O D:HOH1460 5.0 32.9 1.0
OG1 D:THR597 5.0 21.0 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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