Calcium in PDB 6dwo: Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583

The structure of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583, PDB code: 6dwo was solved by A.J.Fisher, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.18 / 2.15
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.350, 168.990, 258.520, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.9

The structure of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 (pdb code 6dwo). 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 Alpha-1-2-Mannosidase From Enterococcus Faecalis V583, PDB code: 6dwo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


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 Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:38.5 occ:1.00 OD2 A:ASP604 2.4 32.1 1.0 OE1 A:GLN563 2.4 27.2 1.0 O3 A:GOL808 2.5 55.0 1.0 O A:HOH952 2.6 20.2 1.0 OD1 A:ASN562 2.6 25.8 1.0 O A:HOH1052 2.7 28.9 1.0 O2 A:GOL808 3.3 81.4 1.0 O1 A:GOL807 3.3 30.5 1.0 CD A:GLN563 3.4 29.0 1.0 C3 A:GOL808 3.5 63.9 1.0 CG A:ASP604 3.5 30.9 1.0 NE2 A:GLN563 3.6 26.7 1.0 CG A:ASN562 3.8 23.7 1.0 C2 A:GOL808 4.0 69.5 1.0 CB A:ASP602 4.1 24.0 1.0 OD1 A:ASP604 4.1 28.4 1.0 OD1 A:ASP313 4.2 40.6 1.0 C1 A:GOL807 4.4 51.7 1.0 OE2 A:GLU494 4.4 40.5 1.0 N A:GLN563 4.5 24.3 1.0 CA A:ASN562 4.5 22.9 1.0 O A:ASP602 4.5 26.2 1.0 CZ3 A:TRP312 4.6 43.7 1.0 O A:HOH942 4.6 22.4 1.0 ND2 A:ASN562 4.6 27.6 1.0 CB A:ASN562 4.7 23.4 1.0 OD2 A:ASP602 4.7 30.6 1.0 CB A:ASP604 4.7 27.8 1.0 CG A:GLN563 4.8 26.1 1.0 O A:SER561 4.8 24.5 1.0 CG A:ASP602 4.9 27.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


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 Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:42.9 occ:1.00 OD1 B:ASN562 2.5 25.5 1.0 OD2 B:ASP604 2.5 28.3 1.0 O B:HOH1166 2.5 21.7 1.0 OE1 B:GLN563 2.5 26.4 1.0 O B:HOH1429 2.5 23.5 1.0 O3 B:GOL1007 2.6 63.5 1.0 O2 B:GOL1007 2.8 61.7 1.0 O1 B:GOL1006 3.2 28.4 1.0 CD B:GLN563 3.4 27.5 1.0 CG B:ASP604 3.6 27.6 1.0 NE2 B:GLN563 3.6 27.1 1.0 CG B:ASN562 3.7 26.8 1.0 C3 B:GOL1007 3.7 66.4 1.0 C2 B:GOL1007 3.8 67.8 1.0 C1 B:GOL1006 3.9 31.9 1.0 OD1 B:ASP604 4.1 29.3 1.0 CB B:ASP602 4.1 21.0 1.0 OD1 B:ASP313 4.3 40.5 1.0 OE2 B:GLU494 4.4 36.2 1.0 N B:GLN563 4.4 24.1 1.0 CA B:ASN562 4.4 22.8 1.0 O B:HOH1142 4.4 22.5 1.0 ND2 B:ASN562 4.5 23.6 1.0 CB B:ASN562 4.6 21.7 1.0 O B:ASP602 4.6 24.6 1.0 CZ3 B:TRP312 4.6 41.8 1.0 C2 B:GOL1006 4.6 43.0 1.0 O B:SER561 4.7 23.9 1.0 OD2 B:ASP602 4.8 27.5 1.0 CB B:ASP604 4.8 24.2 1.0 CG B:GLN563 4.8 26.1 1.0 CG B:ASP602 4.9 27.9 1.0 C B:ASN562 5.0 25.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


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 Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:41.9 occ:1.00 O3 C:GOL1006 2.4 59.0 1.0 OD1 C:ASN562 2.5 24.6 1.0 OD2 C:ASP604 2.5 36.0 1.0 OE1 C:GLN563 2.5 29.1 1.0 O C:HOH1343 2.5 26.9 1.0 O C:HOH1147 2.6 27.6 1.0 O1 C:GOL1005 3.3 31.0 1.0 CD C:GLN563 3.4 30.5 1.0 CG C:ASP604 3.6 34.4 1.0 CG C:ASN562 3.6 28.4 1.0 NE2 C:GLN563 3.6 32.5 1.0 C3 C:GOL1006 3.8 73.2 1.0 O2 C:GOL1006 3.9 88.5 1.0 OD1 C:ASP604 4.1 32.8 1.0 CB C:ASP602 4.1 26.2 1.0 C1 C:GOL1005 4.2 44.0 1.0 C2 C:GOL1006 4.3 76.3 1.0 OD1 C:ASP313 4.3 40.3 1.0 OE1 C:GLU494 4.4 44.0 1.0 N C:GLN563 4.4 26.3 1.0 CA C:ASN562 4.4 24.8 1.0 O C:HOH1137 4.4 23.4 1.0 ND2 C:ASN562 4.4 28.8 1.0 CB C:ASN562 4.5 23.8 1.0 O C:ASP602 4.5 25.7 1.0 O C:SER561 4.6 21.9 1.0 CZ3 C:TRP312 4.6 60.6 1.0 CB C:ASP604 4.8 29.7 1.0 OD2 C:ASP602 4.8 33.3 1.0 CG C:GLN563 4.8 25.9 1.0 C2 C:GOL1005 4.9 51.5 1.0 CG C:ASP602 4.9 29.7 1.0 C C:ASN562 5.0 25.8 1.0 OE2 C:GLU546 5.0 31.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


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 Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:39.5 occ:1.00 O3 D:GOL1007 2.4 42.4 1.0 OD2 D:ASP604 2.5 26.0 1.0 OE1 D:GLN563 2.5 27.9 1.0 OD1 D:ASN562 2.5 27.3 1.0 O D:HOH1149 2.6 22.3 1.0 O D:HOH1370 2.6 24.7 1.0 O1 D:GOL1006 3.1 33.8 1.0 O2 D:GOL1007 3.3 64.7 1.0 CD D:GLN563 3.4 28.5 1.0 CG D:ASP604 3.6 28.3 1.0 C3 D:GOL1007 3.6 57.0 1.0 NE2 D:GLN563 3.7 29.6 1.0 CG D:ASN562 3.7 29.6 1.0 C2 D:GOL1007 4.1 57.6 1.0 CB D:ASP602 4.1 22.9 1.0 OD1 D:ASP604 4.2 25.1 1.0 C1 D:GOL1006 4.2 43.1 1.0 OD1 D:ASP313 4.3 42.0 1.0 OE2 D:GLU494 4.4 35.8 1.0 O D:HOH1183 4.4 22.6 1.0 N D:GLN563 4.4 26.2 1.0 CA D:ASN562 4.4 24.3 1.0 ND2 D:ASN562 4.6 29.1 1.0 O D:ASP602 4.6 23.6 1.0 CB D:ASN562 4.6 26.6 1.0 CZ3 D:TRP312 4.6 45.7 1.0 C2 D:GOL1006 4.7 50.5 1.0 O D:SER561 4.7 28.2 1.0 CB D:ASP604 4.8 24.8 1.0 OD2 D:ASP602 4.8 25.9 1.0 CG D:GLN563 4.9 25.2 1.0 CG D:ASP602 4.9 27.2 1.0

Y.Li, R.Li, H.Yu, X.Sheng, J.Wang, A.J.Fisher, X.Chen. Enterococcus Faecalis Alpha 1-2-Mannosidase (Efman-I): An Efficient Catalyst For Glycoprotein N-Glycan Modification. Febs Lett. 2019.
ISSN: ISSN 0014-5793
PubMed: 31552675
DOI: 10.1002/1873-3468.13618