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Calcium 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:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7fe1

Go back to Calcium Binding Sites List in 7fe1
Calcium 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 Calcium with other atoms in the Ca 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:Ca803

b:21.3
occ:1.00
 O3 A:MAN802 2.4 19.1 1.0
O A:HOH1191 2.4 16.4 1.0
OD1 A:ASN562 2.5 16.6 1.0
OD2 A:ASP604 2.5 16.2 1.0
OE1 A:GLN563 2.5 16.6 1.0
O A:HOH1078 2.5 15.6 1.0
O2 A:MAN802 2.6 31.4 1.0
O A:HOH997 2.7 19.6 1.0
CD A:GLN563 3.5 17.6 1.0
CG A:ASP604 3.5 16.6 1.0
C3 A:MAN802 3.5 27.8 1.0
C2 A:MAN802 3.6 34.1 1.0
CG A:ASN562 3.6 17.3 1.0
NE2 A:GLN563 3.8 17.8 1.0
OD1 A:ASP604 3.9 16.3 1.0
CB A:ASP602 4.1 15.4 1.0
OD1 A:ASP313 4.2 19.9 1.0
C1 A:MAN802 4.3 29.4 1.0
CZ3 A:TRP312 4.5 25.3 1.0
ND2 A:ASN562 4.5 16.6 1.0
CA A:ASN562 4.5 16.4 1.0
O A:HOH910 4.5 35.6 1.0
N A:GLN563 4.5 15.7 1.0
C4 A:MAN802 4.5 26.4 1.0
CB A:ASN562 4.5 16.2 1.0
O A:ASP602 4.6 15.3 1.0
O A:HOH980 4.6 14.1 1.0
OD2 A:ASP602 4.7 17.1 1.0
OE1 A:GLU546 4.7 17.7 1.0
CB A:ASP604 4.8 16.1 1.0
O A:SER561 4.8 16.2 1.0
CG A:ASP602 4.8 17.0 1.0
CG A:GLN563 4.8 17.4 1.0

Calcium binding site 2 out of 4 in 7fe1

Go back to Calcium Binding Sites List in 7fe1
Calcium 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 Calcium with other atoms in the Ca 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:Ca803

b:20.7
occ:1.00
 O3 B:MAN802 2.4 21.9 1.0
OD2 B:ASP604 2.4 15.9 1.0
OE1 B:GLN563 2.4 17.1 1.0
O B:HOH1208 2.5 15.7 1.0
O B:HOH1176 2.5 17.2 1.0
OD1 B:ASN562 2.6 17.9 1.0
O B:HOH1011 2.6 19.2 1.0
O2 B:MAN802 2.6 29.2 1.0
CG B:ASP604 3.4 17.7 1.0
CD B:GLN563 3.4 17.6 1.0
C3 B:MAN802 3.5 27.7 1.0
C2 B:MAN802 3.5 33.6 1.0
CG B:ASN562 3.7 17.9 1.0
NE2 B:GLN563 3.8 18.1 1.0
OD1 B:ASP604 3.9 17.5 1.0
CB B:ASP602 4.1 16.7 1.0
OD1 B:ASP313 4.2 20.2 1.0
C1 B:MAN802 4.4 30.2 1.0
C4 B:MAN802 4.5 26.5 1.0
CZ3 B:TRP312 4.5 27.0 1.0
N B:GLN563 4.5 16.2 1.0
CA B:ASN562 4.6 16.3 1.0
ND2 B:ASN562 4.6 18.4 1.0
O B:HOH931 4.6 31.0 1.0
CB B:ASN562 4.6 17.4 1.0
O B:HOH1045 4.6 16.0 1.0
O B:ASP602 4.6 14.8 1.0
CB B:ASP604 4.7 16.1 1.0
OD2 B:ASP602 4.7 17.8 1.0
OE1 B:GLU546 4.8 16.6 1.0
CG B:GLN563 4.8 19.3 1.0
O B:SER561 4.9 16.8 1.0
CG B:ASP602 4.9 17.6 1.0

Calcium binding site 3 out of 4 in 7fe1

Go back to Calcium Binding Sites List in 7fe1
Calcium 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 Calcium with other atoms in the Ca 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:Ca803

b:21.1
occ:1.00
 O C:HOH1216 2.5 15.7 1.0
OE1 C:GLN563 2.5 18.6 1.0
O3 C:MAN802 2.5 21.4 1.0
OD2 C:ASP604 2.5 19.1 1.0
OD1 C:ASN562 2.5 17.9 1.0
O2 C:MAN802 2.5 26.2 1.0
O C:HOH1054 2.5 15.8 1.0
O C:HOH1126 2.5 18.9 1.0
CD C:GLN563 3.5 19.3 1.0
C2 C:MAN802 3.5 27.8 1.0
C3 C:MAN802 3.5 26.8 1.0
CG C:ASP604 3.5 17.0 1.0
CG C:ASN562 3.7 17.5 1.0
NE2 C:GLN563 3.8 20.6 1.0
OD1 C:ASP604 4.0 18.1 1.0
CB C:ASP602 4.1 16.7 1.0
OD1 C:ASP313 4.3 19.5 1.0
C1 C:MAN802 4.4 26.1 1.0
C4 C:MAN802 4.5 25.0 1.0
CZ3 C:TRP312 4.5 24.1 1.0
ND2 C:ASN562 4.5 18.5 1.0
CA C:ASN562 4.5 16.5 1.0
N C:GLN563 4.5 16.6 1.0
CB C:ASN562 4.6 18.8 1.0
O C:ASP602 4.6 17.4 1.0
O C:HOH1029 4.6 16.8 1.0
O C:HOH957 4.6 30.7 1.0
OD2 C:ASP602 4.7 18.9 1.0
OE1 C:GLU546 4.8 20.7 1.0
CB C:ASP604 4.8 17.1 1.0
CG C:GLN563 4.8 19.9 1.0
CG C:ASP602 4.8 19.6 1.0
O C:SER561 4.9 16.5 1.0

Calcium binding site 4 out of 4 in 7fe1

Go back to Calcium Binding Sites List in 7fe1
Calcium 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 Calcium with other atoms in the Ca 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:Ca803

b:21.7
occ:1.00
 OD2 D:ASP604 2.4 20.8 1.0
OD1 D:ASN562 2.4 18.6 1.0
OE1 D:GLN563 2.4 18.0 1.0
O3 D:MAN802 2.5 24.9 1.0
O D:HOH1065 2.5 19.3 1.0
O D:HOH1133 2.5 18.2 1.0
O D:HOH1071 2.6 22.4 1.0
O2 D:MAN802 2.7 31.7 1.0
CD D:GLN563 3.5 20.4 1.0
CG D:ASP604 3.5 18.5 1.0
C3 D:MAN802 3.6 33.8 1.0
CG D:ASN562 3.6 16.9 1.0
C2 D:MAN802 3.6 36.3 1.0
NE2 D:GLN563 3.8 19.8 1.0
OD1 D:ASP604 4.0 20.4 1.0
CB D:ASP602 4.0 16.3 1.0
OD1 D:ASP313 4.3 23.0 1.0
C1 D:MAN802 4.3 34.0 1.0
ND2 D:ASN562 4.4 17.9 1.0
O D:HOH903 4.5 37.1 1.0
CB D:ASN562 4.5 17.4 1.0
CA D:ASN562 4.5 15.8 1.0
N D:GLN563 4.5 18.8 1.0
CZ3 D:TRP312 4.6 28.0 1.0
O D:HOH1023 4.6 18.8 1.0
O D:ASP602 4.6 18.9 1.0
C4 D:MAN802 4.6 34.8 1.0
OD2 D:ASP602 4.7 19.4 1.0
OE1 D:GLU546 4.7 22.0 1.0
CB D:ASP604 4.7 17.4 1.0
CG D:ASP602 4.8 19.8 1.0
O D:SER561 4.8 18.4 1.0
CG D:GLN563 4.8 18.8 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 Jul 19 00:49:20 2024

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