Sodium in PDB 7zgm: Plant N-Glycan Specific Alpha-1,3-Mannosidase

The structure of Plant N-Glycan Specific Alpha-1,3-Mannosidase, PDB code: 7zgm was solved by A.Basle, L.Crouch, D.Bolam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.29 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.941, 84.335, 132.581, 90, 90, 90
R / Rfree (%)	13.3 / 17.3

The structure of Plant N-Glycan Specific Alpha-1,3-Mannosidase also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Plant N-Glycan Specific Alpha-1,3-Mannosidase (pdb code 7zgm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Plant N-Glycan Specific Alpha-1,3-Mannosidase, PDB code: 7zgm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:23.0 occ:1.00 OG A:SER406 2.4 21.9 1.0 O A:TYR354 2.6 15.9 1.0 OE1 A:GLU410 2.6 22.8 1.0 HG A:SER406 2.9 20.1 1.0 HB2 A:TYR354 2.9 13.3 1.0 HB2 A:PRO658 3.0 18.0 1.0 HA A:VAL407 3.1 14.0 1.0 HB3 A:PRO658 3.2 17.9 1.0 HA A:TYR354 3.2 13.6 1.0 HG21 A:VAL407 3.3 15.5 1.0 HD2 A:TYR354 3.3 12.8 1.0 HD3 A:PRO359 3.4 13.9 1.0 C A:TYR354 3.5 13.5 1.0 CB A:PRO658 3.5 18.1 1.0 CD A:GLU410 3.6 17.2 1.0 CB A:SER406 3.6 17.1 1.0 HB2 A:GLU410 3.6 14.5 1.0 CA A:TYR354 3.6 13.6 1.0 CB A:TYR354 3.7 13.3 1.0 HB3 A:SER406 3.7 17.2 1.0 C A:SER406 3.7 14.9 1.0 O A:SER406 3.7 16.6 1.0 N A:VAL407 3.8 13.2 1.0 HB2 A:HIS358 3.8 13.8 1.0 HG2 A:PRO658 3.8 20.4 1.0 CA A:VAL407 3.9 13.8 1.0 HB3 A:GLU410 3.9 14.7 1.0 HB3 A:HIS358 3.9 14.0 1.0 HG23 A:VAL407 3.9 15.6 1.0 CG2 A:VAL407 4.0 15.6 1.0 HG3 A:PRO359 4.1 14.8 1.0 CD2 A:TYR354 4.1 12.5 1.0 CB A:GLU410 4.1 14.2 1.0 CG A:PRO658 4.2 21.8 1.0 H A:VAL407 4.2 13.5 1.0 CD A:PRO359 4.3 13.7 1.0 CA A:SER406 4.3 14.8 1.0 CB A:HIS358 4.3 14.2 1.0 HG21 A:VAL659 4.3 17.9 1.0 HB2 A:SER406 4.4 15.9 1.0 CG A:TYR354 4.4 12.6 1.0 CG A:GLU410 4.4 15.0 1.0 OE2 A:GLU410 4.4 19.2 1.0 HB3 A:TYR354 4.4 13.2 1.0 NA A:NA810 4.6 27.4 1.0 CB A:VAL407 4.6 15.5 1.0 CG A:PRO359 4.6 14.9 1.0 HG3 A:PRO658 4.7 20.7 1.0 HG3 A:GLU410 4.8 15.0 1.0 N A:ARG355 4.8 12.8 1.0 HA A:SER406 4.8 14.9 1.0 HD2 A:PRO359 4.8 13.6 1.0 HG22 A:VAL407 4.8 15.7 1.0 CA A:PRO658 4.9 15.5 1.0 HG2 A:PRO359 4.9 14.9 1.0 HE2 A:TYR469 5.0 15.6 1.0 C A:VAL407 5.0 14.8 1.0

Sodium binding site 2 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na805 b:23.2 occ:1.00 HE22 A:GLN549 2.3 22.1 1.0 HE21 A:GLN549 2.4 21.5 1.0 O A:PRO655 2.5 15.7 1.0 HG3 A:PRO658 2.6 20.7 1.0 O A:ARG355 2.6 17.6 1.0 NE2 A:GLN549 2.6 24.1 1.0 HD3 A:PRO658 2.6 16.3 1.0 HA A:ARG355 2.8 13.0 1.0 O A:VAL656 3.2 14.9 1.0 HB3 A:ARG355 3.2 13.2 1.0 CG A:PRO658 3.2 21.8 1.0 NA A:NA807 3.2 23.8 1.0 CD A:PRO658 3.3 16.0 1.0 HG2 A:PRO658 3.4 20.4 1.0 CA A:ARG355 3.4 12.9 1.0 C A:ARG355 3.4 14.6 1.0 HE2 A:TYR654 3.5 14.4 1.0 HA A:VAL656 3.7 13.2 1.0 C A:VAL656 3.7 12.7 1.0 C A:PRO655 3.7 15.1 1.0 CB A:ARG355 3.7 13.0 1.0 HG2 A:ARG355 3.8 12.7 1.0 HD2 A:PRO658 3.9 16.2 1.0 HG2 A:PRO655 4.0 13.5 1.0 CD A:GLN549 4.0 18.5 1.0 CA A:VAL656 4.1 13.1 1.0 CE2 A:TYR654 4.1 14.3 1.0 OH A:TYR654 4.1 15.4 1.0 HB3 A:HIS600 4.2 14.2 1.0 CG A:ARG355 4.3 12.8 1.0 N A:PRO658 4.3 14.6 1.0 HB2 A:PRO655 4.4 13.9 1.0 N A:VAL656 4.4 13.6 1.0 HG2 A:GLN549 4.5 15.6 1.0 CZ A:TYR654 4.5 13.8 1.0 N A:ASP657 4.6 13.5 1.0 HB2 A:ARG355 4.6 13.1 1.0 CB A:PRO658 4.6 18.1 1.0 HA A:ASP657 4.6 14.2 1.0 N A:ALA356 4.7 12.7 1.0 HH A:TYR654 4.7 14.8 1.0 N A:ARG355 4.7 12.8 1.0 CG A:PRO655 4.8 13.4 1.0 CG A:GLN549 4.8 15.7 1.0 HB3 A:PRO658 4.8 17.9 1.0 CA A:PRO655 4.9 14.9 1.0 CB A:PRO655 4.9 13.9 1.0 HE2 A:TYR354 4.9 13.3 1.0 HA A:PRO658 4.9 15.7 1.0 OE1 A:GLN549 4.9 16.7 1.0 O A:HOH1243 4.9 16.1 1.0 HG3 A:ARG355 4.9 12.7 1.0 CA A:PRO658 5.0 15.5 1.0 CA A:ASP657 5.0 14.2 1.0 O A:TYR354 5.0 15.9 1.0

Sodium binding site 3 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na806 b:25.0 occ:1.00 H A:THR259 1.6 17.0 1.0 OG1 A:THR259 2.4 18.4 1.0 N A:THR259 2.5 17.1 1.0 O A:ILE322 2.6 18.8 1.0 OD1 A:ASP324 2.6 22.2 1.0 HG1 A:THR259 2.8 17.1 1.0 HA A:SER258 3.1 15.5 1.0 HG23 A:THR260 3.2 18.3 1.0 CB A:THR259 3.2 14.8 1.0 CA A:THR259 3.3 14.5 1.0 HG23 A:THR259 3.4 14.5 1.0 HG21 A:THR259 3.4 15.0 1.0 HA A:SER323 3.4 14.2 1.0 H A:THR260 3.4 15.4 1.0 H A:ASP324 3.4 14.6 1.0 HA A:TYR329 3.4 13.9 1.0 OG A:SER258 3.5 17.1 1.0 HE3 A:MET58 3.5 19.5 1.0 CG2 A:THR259 3.5 14.6 1.0 CG A:ASP324 3.6 15.9 1.0 C A:SER258 3.6 15.4 1.0 N A:ASP324 3.6 14.5 1.0 CA A:SER258 3.7 15.2 1.0 C A:ILE322 3.7 15.9 1.0 HG21 A:THR260 3.8 18.0 1.0 N A:THR260 3.8 16.3 1.0 O A:LEU328 3.9 15.5 1.0 C A:SER323 3.9 14.3 1.0 CG2 A:THR260 3.9 18.4 1.0 C A:THR259 4.0 14.6 1.0 CA A:SER323 4.0 13.8 1.0 HB A:THR259 4.1 13.9 1.0 OD2 A:ASP324 4.2 17.0 1.0 HA A:THR259 4.2 14.4 1.0 CB A:SER258 4.2 15.3 1.0 HA A:ASP324 4.3 16.2 1.0 CE A:MET58 4.3 19.3 1.0 N A:SER323 4.4 14.7 1.0 CA A:TYR329 4.4 13.9 1.0 H A:ARG330 4.4 14.8 1.0 CA A:ASP324 4.4 16.2 1.0 HD21 A:ASN268 4.4 16.4 1.0 HE2 A:MET58 4.4 19.2 1.0 HB2 A:TYR329 4.5 13.3 1.0 HG22 A:THR259 4.5 14.7 1.0 CB A:ASP324 4.5 16.4 1.0 HB3 A:TYR329 4.6 13.1 1.0 O A:SER323 4.6 16.6 1.0 HG22 A:THR260 4.6 18.3 1.0 HB2 A:SER258 4.6 15.6 1.0 HB A:ILE322 4.7 15.7 1.0 O A:SER258 4.7 15.6 1.0 CB A:THR260 4.7 17.0 1.0 CB A:TYR329 4.8 13.1 1.0 OG1 A:THR260 4.8 17.4 1.0 C A:LEU328 4.8 15.8 1.0 CA A:THR260 4.9 15.8 1.0 HB2 A:ASP324 4.9 15.8 1.0 CA A:ILE322 5.0 15.6 1.0 SD A:MET58 5.0 19.2 1.0 HA A:ILE322 5.0 15.5 1.0 HB3 A:SER258 5.0 15.2 1.0

Sodium binding site 4 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na807 b:23.8 occ:1.00 OH A:TYR654 2.4 15.4 1.0 HE2 A:TYR654 2.6 14.4 1.0 HB3 A:ARG355 2.7 13.2 1.0 HB2 A:HIS599 2.8 13.5 1.0 O A:HOH1243 2.8 16.1 1.0 HB3 A:HIS600 2.9 14.2 1.0 HB3 A:HIS599 3.0 13.2 1.0 HH A:TYR654 3.0 14.8 1.0 CZ A:TYR654 3.2 13.8 1.0 CE2 A:TYR654 3.2 14.3 1.0 NA A:NA805 3.2 23.2 1.0 CB A:HIS599 3.3 13.1 1.0 H A:HIS600 3.3 13.7 1.0 HE22 A:GLN549 3.3 22.1 1.0 N A:HIS600 3.3 13.6 1.0 HD3 A:ARG355 3.5 13.1 1.0 C A:HIS599 3.6 13.0 1.0 CB A:HIS600 3.7 14.0 1.0 CB A:ARG355 3.7 13.0 1.0 HA A:HIS600 3.8 13.4 1.0 CA A:HIS600 3.9 13.5 1.0 HG2 A:ARG355 3.9 12.7 1.0 CA A:HIS599 4.0 13.6 1.0 ND1 A:HIS600 4.1 15.0 1.0 NE2 A:GLN549 4.1 24.1 1.0 CG A:ARG355 4.1 12.8 1.0 HB2 A:ARG355 4.2 13.1 1.0 CD A:ARG355 4.2 12.9 1.0 HE21 A:GLN641 4.2 13.3 1.0 O A:HIS599 4.2 14.9 1.0 O A:ARG355 4.3 17.6 1.0 CG A:HIS600 4.4 14.1 1.0 HB2 A:HIS600 4.4 13.9 1.0 HD2 A:ARG355 4.4 13.0 1.0 HD1 A:TRP645 4.5 14.2 1.0 H A:HIS599 4.5 13.6 1.0 HE21 A:GLN549 4.5 21.5 1.0 HA A:VAL656 4.5 13.2 1.0 CE1 A:TYR654 4.5 13.4 1.0 HA A:ARG355 4.5 13.0 1.0 CG A:HIS599 4.5 13.6 1.0 CD2 A:TYR654 4.6 14.0 1.0 CA A:ARG355 4.6 12.9 1.0 N A:HIS599 4.6 13.9 1.0 O A:GLU596 4.6 15.7 1.0 C A:ARG355 4.6 14.6 1.0 HE22 A:GLN641 4.8 13.3 1.0 NE2 A:GLN641 4.8 13.8 1.0 HB2 A:ALA356 4.8 14.3 1.0 HA A:HIS599 4.8 13.4 1.0 O A:PRO655 4.9 15.7 1.0 HE1 A:TYR654 4.9 13.7 1.0 ND1 A:HIS599 4.9 14.6 1.0 HD2 A:TYR654 4.9 13.8 1.0 HH11 A:ARG355 4.9 14.7 1.0

Sodium binding site 5 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na808 b:26.4 occ:1.00 O A:HOH904 2.2 39.6 1.0 OD1 A:ASN204 2.4 44.5 1.0 O A:VAL208 2.6 29.1 1.0 OE1 A:GLN210 2.6 27.5 1.0 HB3 A:GLN210 2.9 20.1 1.0 O A:HOH1241 3.0 22.4 1.0 HB2 A:GLN210 3.2 20.5 1.0 H A:VAL206 3.2 28.4 1.0 H A:VAL208 3.3 22.9 1.0 HG11 A:VAL208 3.3 27.8 1.0 CB A:GLN210 3.5 20.7 1.0 HG13 A:VAL208 3.5 27.6 1.0 CG A:ASN204 3.6 34.8 1.0 K A:K801 3.6 23.6 1.0 H A:TRP207 3.6 24.6 1.0 CD A:GLN210 3.7 21.6 1.0 C A:VAL208 3.7 25.6 1.0 O A:ASN204 3.8 43.0 1.0 CG1 A:VAL208 3.9 27.9 1.0 C A:ASN204 3.9 31.7 1.0 N A:VAL206 3.9 28.2 1.0 N A:SER205 4.0 31.2 1.0 H A:GLN210 4.0 19.4 1.0 HB2 A:ASN204 4.1 37.5 1.0 HB A:VAL206 4.1 28.5 1.0 H A:SER205 4.1 31.4 1.0 N A:VAL208 4.1 22.2 1.0 O A:HOH1326 4.2 71.1 1.0 CG A:GLN210 4.2 20.9 1.0 CB A:ASN204 4.3 39.7 1.0 N A:GLN210 4.4 19.9 1.0 C A:SER205 4.4 35.6 1.0 N A:TRP207 4.5 22.7 1.0 CA A:VAL208 4.5 22.5 1.0 HB2 A:TRP207 4.5 19.4 1.0 ND2 A:ASN204 4.5 43.7 1.0 HG12 A:VAL208 4.6 26.4 1.0 CA A:SER205 4.6 39.5 1.0 CA A:ASN204 4.6 31.1 1.0 CA A:GLN210 4.6 17.2 1.0 HA A:SER205 4.6 38.7 1.0 O A:HOH1185 4.7 25.9 1.0 HG2 A:GLN210 4.8 21.1 1.0 HD21 A:ASN204 4.8 40.7 1.0 HA A:ASN209 4.8 27.4 1.0 CB A:VAL208 4.8 25.5 1.0 CA A:VAL206 4.8 28.8 1.0 N A:ASN209 4.8 27.6 1.0 HD21 A:LEU97 4.9 20.1 1.0 NE2 A:GLN210 4.9 18.2 1.0 CB A:VAL206 4.9 28.0 1.0 H A:ASN204 4.9 22.8 1.0 HG3 A:GLN210 5.0 20.0 1.0 HD1 A:TRP207 5.0 21.9 1.0

Sodium binding site 6 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na809 b:25.6 occ:1.00 HD1 A:HIS358 1.7 16.1 1.0 ND1 A:HIS358 2.5 15.9 1.0 O A:HIS358 2.6 15.1 1.0 HB2 A:TYR361 2.8 13.0 1.0 HA A:HIS358 2.8 12.9 1.0 HB3 A:HIS358 2.9 14.0 1.0 HD2 A:TYR361 3.0 13.3 1.0 C A:HIS358 3.2 12.6 1.0 CA A:HIS358 3.2 12.8 1.0 CB A:HIS358 3.2 14.2 1.0 CG A:HIS358 3.3 13.4 1.0 HG21 A:THR362 3.3 15.6 1.0 NA A:NA810 3.3 27.4 1.0 HG22 A:VAL369 3.4 16.9 1.0 HG23 A:THR362 3.4 15.7 1.0 HG13 A:VAL407 3.6 15.7 1.0 CE1 A:HIS358 3.7 15.7 1.0 HG21 A:VAL369 3.8 16.9 1.0 CB A:TYR361 3.8 13.0 1.0 CG2 A:THR362 3.8 15.8 1.0 HD2 A:PHE372 3.9 15.1 1.0 CD2 A:TYR361 3.9 12.8 1.0 HG11 A:VAL369 3.9 16.5 1.0 HE1 A:HIS358 3.9 14.9 1.0 H A:THR362 3.9 13.8 1.0 CG2 A:VAL369 4.0 16.9 1.0 HB3 A:TYR361 4.2 13.3 1.0 HB2 A:HIS358 4.2 13.8 1.0 HG13 A:VAL369 4.3 16.3 1.0 CG A:TYR361 4.3 13.6 1.0 N A:THR362 4.3 13.7 1.0 HG22 A:THR362 4.4 15.3 1.0 N A:PRO359 4.5 12.4 1.0 H A:TYR361 4.5 12.4 1.0 CG1 A:VAL407 4.5 15.5 1.0 CG1 A:VAL369 4.5 16.4 1.0 CD2 A:HIS358 4.5 14.0 1.0 HA A:VAL369 4.6 15.7 1.0 HG11 A:VAL407 4.6 15.7 1.0 N A:HIS358 4.7 11.9 1.0 OE1 A:GLU410 4.7 22.8 1.0 CA A:TYR361 4.7 13.2 1.0 NE2 A:HIS358 4.7 14.7 1.0 C A:TYR361 4.8 13.6 1.0 CD2 A:PHE372 4.8 15.4 1.0 CB A:VAL369 4.8 16.1 1.0 HG23 A:VAL369 4.8 16.5 1.0 HG12 A:VAL407 4.8 15.5 1.0 HE2 A:PHE372 4.8 14.3 1.0 N A:TYR361 4.9 12.3 1.0 HA A:THR362 4.9 14.0 1.0 O A:ALA357 5.0 13.4 1.0 CE2 A:TYR361 5.0 13.5 1.0 HA A:PRO359 5.0 13.6 1.0

Sodium binding site 7 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na810 b:27.4 occ:1.00 O A:VAL407 2.5 16.4 1.0 OE1 A:GLU410 2.6 22.8 1.0 HB3 A:GLU410 2.7 14.7 1.0 HA A:VAL407 2.9 14.0 1.0 HG13 A:VAL407 3.1 15.7 1.0 CD A:GLU410 3.1 17.2 1.0 H A:ALA411 3.2 14.3 1.0 HB3 A:HIS358 3.3 14.0 1.0 NA A:NA809 3.3 25.6 1.0 HG11 A:VAL407 3.3 15.7 1.0 HB2 A:ALA411 3.4 15.2 1.0 HG2 A:GLU410 3.4 14.9 1.0 C A:VAL407 3.4 14.8 1.0 CG A:GLU410 3.5 15.0 1.0 CB A:GLU410 3.5 14.2 1.0 CA A:VAL407 3.5 13.8 1.0 HG22 A:THR362 3.6 15.3 1.0 CG1 A:VAL407 3.6 15.5 1.0 HG23 A:THR362 3.6 15.7 1.0 N A:ALA411 3.6 14.1 1.0 HG21 A:THR362 3.8 15.6 1.0 CG2 A:THR362 3.9 15.8 1.0 HD1 A:HIS358 4.0 16.1 1.0 OE2 A:GLU410 4.0 19.2 1.0 CB A:VAL407 4.1 15.5 1.0 CB A:ALA411 4.1 15.2 1.0 HA A:ALA411 4.1 15.3 1.0 HG21 A:VAL407 4.1 15.5 1.0 HB2 A:GLU410 4.1 14.5 1.0 CA A:ALA411 4.2 15.5 1.0 CB A:HIS358 4.2 14.2 1.0 C A:GLU410 4.3 14.0 1.0 HB3 A:ALA411 4.3 15.2 1.0 HG11 A:VAL369 4.4 16.5 1.0 CA A:GLU410 4.4 15.1 1.0 O A:HIS358 4.4 15.1 1.0 HG13 A:VAL369 4.4 16.3 1.0 HG3 A:GLU410 4.5 15.0 1.0 HG12 A:VAL407 4.5 15.5 1.0 ND1 A:HIS358 4.5 15.9 1.0 NA A:NA804 4.6 23.0 1.0 O A:SER406 4.6 16.6 1.0 CG2 A:VAL407 4.7 15.6 1.0 H A:GLU410 4.7 14.2 1.0 CG A:HIS358 4.7 13.4 1.0 C A:HIS358 4.7 12.6 1.0 N A:ILE408 4.7 14.3 1.0 HB2 A:HIS358 4.7 13.8 1.0 N A:VAL407 4.8 13.2 1.0 N A:GLU410 4.9 14.3 1.0 CG1 A:VAL369 4.9 16.4 1.0 HB1 A:ALA411 4.9 15.2 1.0 HB A:VAL407 4.9 15.5 1.0

Sodium binding site 8 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na811 b:31.9 occ:1.00 H A:GLU135 1.7 18.8 1.0 O A:SER121 2.6 28.0 1.0 N A:GLU135 2.6 18.7 1.0 HB2 A:GLU135 2.7 17.9 1.0 HG21 A:VAL134 2.8 15.6 1.0 HB2 A:LEU124 2.8 23.6 1.0 O A:HOH907 2.9 30.3 1.0 HG22 A:VAL134 3.0 15.0 1.0 H A:SER121 3.2 31.5 1.0 HB2 A:PHE120 3.2 20.2 1.0 HA A:VAL134 3.3 15.3 1.0 O A:GLU135 3.3 18.1 1.0 CG2 A:VAL134 3.3 15.2 1.0 CA A:GLU135 3.4 16.9 1.0 HD2 A:PHE120 3.5 19.2 1.0 CB A:GLU135 3.5 17.7 1.0 C A:LEU124 3.5 21.5 1.0 HB2 A:GLU125 3.5 15.6 1.0 OG A:SER121 3.6 32.7 0.5 N A:GLU125 3.6 15.4 1.0 C A:VAL134 3.6 16.0 1.0 CB A:LEU124 3.6 23.3 1.0 C A:SER121 3.7 24.9 1.0 H A:LEU124 3.7 19.8 1.0 O A:LEU124 3.7 25.9 1.0 N A:SER121 3.7 32.5 1.0 H A:GLU125 3.8 16.5 1.0 C A:GLU135 3.8 15.4 1.0 CA A:VAL134 3.8 15.0 1.0 HB3 A:LEU124 3.8 23.4 1.0 HA A:GLU125 3.9 14.8 1.0 HB3 A:SER121 3.9 33.5 0.5 CA A:LEU124 3.9 21.7 1.0 HG23 A:VAL134 4.1 15.2 1.0 CA A:SER121 4.1 30.6 0.5 CA A:GLU125 4.1 15.0 1.0 CA A:SER121 4.1 30.9 0.5 N A:LEU124 4.2 18.9 1.0 CB A:PHE120 4.2 20.2 1.0 HB3 A:GLU135 4.2 17.7 1.0 HG2 A:GLU135 4.2 17.7 1.0 CB A:VAL134 4.2 14.5 1.0 CB A:GLU125 4.3 16.0 1.0 HA A:GLU135 4.3 16.5 1.0 CD2 A:PHE120 4.3 19.0 1.0 CG A:GLU135 4.3 17.6 1.0 CB A:SER121 4.4 32.4 0.5 HG3 A:GLU135 4.4 17.8 1.0 CB A:SER121 4.5 33.4 0.5 HA A:PHE120 4.6 22.2 1.0 HD11 A:LEU124 4.6 29.8 1.0 C A:PHE120 4.6 26.5 1.0 HB3 A:SER121 4.6 32.6 0.5 CA A:PHE120 4.7 22.6 1.0 HB3 A:PHE120 4.7 20.2 1.0 HB A:VAL134 4.8 14.9 1.0 CG A:PHE120 4.8 17.9 1.0 O A:VAL134 4.8 13.5 1.0 HB3 A:GLU125 4.8 15.7 1.0 CG A:LEU124 4.9 25.2 1.0 N A:LYS122 4.9 21.3 1.0 HA A:LEU124 4.9 21.7 1.0 HG A:LEU124 5.0 25.9 1.0 O A:HOH1230 5.0 18.3 1.0

Sodium binding site 9 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na812 b:41.8 occ:1.00 O A:HOH1438 1.8 53.9 1.0 O A:ALA161 2.5 38.3 1.0 O A:MET245 2.5 25.5 1.0 O A:HOH1143 2.8 34.0 1.0 C A:ALA161 3.2 30.6 1.0 NA A:NA814 3.3 43.9 1.0 HB3 A:ALA161 3.4 29.0 1.0 HA A:ASP162 3.5 32.5 1.0 HE22 A:GLN246 3.6 49.2 1.0 H A:MET245 3.7 23.5 1.0 C A:MET245 3.7 21.3 1.0 HB1 A:ALA161 3.7 29.2 1.0 N A:ASP162 3.8 32.4 1.0 CB A:ALA161 3.9 29.1 1.0 H A:SER163 3.9 29.5 1.0 HA A:GLN246 3.9 23.2 1.0 CA A:ASP162 4.1 31.8 1.0 CA A:ALA161 4.1 28.6 1.0 NE2 A:GLN246 4.3 53.7 1.0 N A:MET245 4.4 23.2 1.0 O A:HOH1245 4.4 41.3 1.0 H A:ASP162 4.4 30.0 1.0 H A:ALA164 4.5 24.9 1.0 HD3 A:PRO247 4.5 26.0 1.0 N A:SER163 4.6 30.0 1.0 CA A:MET245 4.6 21.2 1.0 N A:GLN246 4.6 19.5 1.0 OD1 A:ASP162 4.7 41.1 1.0 CA A:GLN246 4.7 22.9 1.0 HE21 A:GLN246 4.7 48.3 1.0 C A:ASP162 4.8 29.7 1.0 HB2 A:ALA161 4.8 29.3 1.0 HB2 A:MET245 4.8 22.8 1.0 HA A:ALA161 4.8 28.8 1.0 H A:ALA161 4.8 26.0 1.0

Sodium binding site 10 out of 13 in the Plant N-Glycan Specific Alpha-1,3-Mannosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Plant N-Glycan Specific Alpha-1,3-Mannosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na813 b:38.0 occ:1.00 HH12 A:ARG117 2.2 24.8 0.7 HH11 A:ARG117 2.3 25.3 0.7 NH1 A:ARG117 2.4 26.6 0.7 O A:HOH1359 2.7 28.0 1.0 HD2 A:ARG117 2.8 22.9 0.3 O A:HOH1515 2.8 32.3 1.0 O A:HOH952 2.9 32.3 1.0 HD3 A:ARG117 3.0 19.7 0.7 HD2 A:ARG117 3.0 20.3 0.7 CD A:ARG117 3.4 20.1 0.7 HG23 A:ILE82 3.4 19.0 1.0 HE A:ARG117 3.5 24.5 0.3 HD13 A:ILE82 3.5 25.3 1.0 CZ A:ARG117 3.5 21.2 0.7 HD11 A:ILE82 3.6 25.0 1.0 CD A:ARG117 3.7 23.0 0.3 NE A:ARG117 3.9 21.3 0.7 NE A:ARG117 3.9 24.8 0.3 HE1 A:TRP84 4.0 17.8 1.0 HD3 A:ARG117 4.0 22.1 0.3 CD1 A:ILE82 4.0 25.9 1.0 HG22 A:ILE82 4.0 19.4 1.0 CG2 A:ILE82 4.2 19.5 1.0 O A:ALA67 4.3 20.3 1.0 NE1 A:TRP84 4.5 17.5 1.0 HB2 A:ARG117 4.6 18.6 0.3 HB2 A:ARG117 4.6 17.6 0.7 O A:HOH1523 4.6 43.6 1.0 HD12 A:ILE82 4.7 25.0 1.0 NH2 A:ARG117 4.7 24.1 0.7 HE A:ARG117 4.7 20.5 0.7 HB A:ILE82 4.7 18.0 1.0 CG A:ARG117 4.8 18.2 0.7 O A:HOH1334 4.8 32.9 1.0 CG A:ARG117 4.8 20.1 0.3 HH22 A:ARG117 4.8 23.3 0.7 HB3 A:ARG117 4.9 17.6 0.7 CB A:ILE82 4.9 17.8 1.0 HB3 A:ARG117 4.9 18.6 0.3 HG21 A:ILE82 4.9 19.3 1.0 HZ2 A:TRP84 5.0 19.2 1.0 CG1 A:ILE82 5.0 22.0 1.0

L.I.Crouch, P.A.Urbanowicz, A.Basle, Z.P.Cai, L.Liu, J.Voglmeir, J.M.Melo Diaz, S.T.Benedict, D.I.R.Spencer, D.N.Bolam. Plant N -Glycan Breakdown By Human Gut Bacteroides. Proc.Natl.Acad.Sci.Usa V. 119 68119 2022.
ISSN: ESSN 1091-6490
PubMed: 36122227
DOI: 10.1073/PNAS.2208168119