Sodium in PDB 5cvy: The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose

The structure of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose, PDB code: 5cvy was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.041, 98.041, 218.956, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 18.9

The structure of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose (pdb code 5cvy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose, PDB code: 5cvy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na825 b:31.3 occ:1.00 OD1 A:ASN165 2.1 28.6 1.0 OG A:SER167 2.6 22.2 1.0 N A:SER167 3.1 16.1 1.0 CG A:ASN165 3.3 27.4 1.0 C A:ASN165 3.3 16.1 1.0 N A:PRO166 3.4 15.5 1.0 CB A:SER167 3.5 19.8 1.0 CA A:ASN165 3.6 18.0 1.0 O A:ASN165 3.7 13.0 1.0 CA A:SER167 3.8 18.7 1.0 CD A:PRO166 3.8 15.2 1.0 CB A:ASN165 3.9 21.6 1.0 C A:PRO166 4.1 16.2 1.0 N A:HIS168 4.2 17.4 1.0 CA A:PRO166 4.3 15.6 1.0 C A:SER167 4.3 19.3 1.0 ND2 A:ASN165 4.5 31.1 1.0 CD2 A:HIS168 4.5 20.5 1.0 NE2 A:HIS168 4.7 20.7 1.0 O A:HOH964 4.9 21.8 0.5 N A:ASN165 4.9 16.6 1.0 CG A:HIS168 5.0 18.6 1.0 CG A:PRO166 5.0 15.8 1.0

Sodium binding site 2 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na826 b:32.8 occ:1.00 O A:HOH1624 2.1 40.7 1.0 OG A:SER466 2.6 22.2 1.0 O A:PRO464 2.7 19.2 1.0 CG A:PRO531 3.5 18.0 1.0 O A:HOH1379 3.7 32.1 1.0 N A:SER466 3.7 21.1 1.0 CB A:SER466 3.7 23.1 1.0 C A:PRO464 3.7 21.9 1.0 CG A:PRO464 4.0 24.8 1.0 CB A:PRO531 4.2 17.9 1.0 C A:VAL465 4.3 20.9 1.0 CA A:SER466 4.3 22.4 1.0 CA A:VAL465 4.5 20.8 1.0 CD A:PRO464 4.5 22.9 1.0 N A:VAL465 4.5 19.9 1.0 CG A:ARG463 4.5 33.0 1.0 O A:HOH1008 4.6 41.6 1.0 CB A:PRO464 4.6 24.1 1.0 CA A:PRO464 4.6 23.6 1.0 N A:PRO464 4.7 25.1 1.0 CD A:PRO531 4.8 17.9 1.0 CD A:ARG463 4.9 42.2 1.0

Sodium binding site 3 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na827 b:36.1 occ:1.00 O A:HOH1260 2.1 35.1 1.0 OG1 A:THR248 2.4 19.2 1.0 O A:HOH1603 2.5 39.4 1.0 O A:HOH1615 2.6 45.6 1.0 O A:HOH1432 2.6 23.8 1.0 OD1 A:ASN246 2.7 14.1 1.0 CB A:THR248 3.4 20.4 1.0 CG A:ASN246 3.5 13.5 1.0 ND2 A:ASN246 3.7 13.1 1.0 N A:THR248 4.1 15.2 1.0 CA A:THR248 4.3 17.5 1.0 O A:HOH1089 4.4 13.4 0.5 OG A:SER247 4.4 17.1 0.5 CG2 A:THR248 4.4 21.5 1.0 O A:HOH1337 4.5 31.1 1.0 CB A:ASN246 4.9 14.8 1.0

Sodium binding site 4 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na828 b:41.4 occ:1.00 O A:HOH946 2.3 13.6 0.5 O1 A:GOL823 2.4 22.9 0.5 OE1 A:GLN364 2.5 10.7 1.0 O1 A:EDO818 2.8 14.7 0.5 CE A:LYS449 3.2 21.2 0.7 NZ A:LYS449 3.3 22.7 0.7 C1 A:GOL823 3.4 23.9 0.5 CG1 A:VAL361 3.6 10.2 1.0 CD A:GLN364 3.6 10.3 1.0 CB A:GLN364 3.7 9.2 1.0 O A:VAL361 3.8 11.3 1.0 C1 A:EDO818 3.9 15.3 0.5 CA A:VAL361 3.9 9.3 1.0 CG A:GLN364 4.0 9.8 1.0 O A:HOH1021 4.1 17.1 1.0 O2 A:GOL823 4.2 27.1 0.5 CB A:VAL361 4.2 10.2 1.0 O A:HOH1310 4.2 34.4 0.5 CD A:LYS449 4.2 9.1 0.1 CG2 A:VAL361 4.3 9.9 1.0 C A:VAL361 4.3 9.5 1.0 C2 A:GOL823 4.4 25.8 0.5 OG A:SER445 4.4 18.6 1.0 CD A:LYS449 4.5 9.3 0.1 CD A:LYS449 4.6 20.2 0.7 CA A:CYS446 4.7 11.6 1.0 NE2 A:GLN364 4.7 10.0 1.0 C3 A:GOL823 4.8 26.5 0.5 O A:HOH934 4.8 4.2 0.3 C2 A:EDO818 4.8 14.8 0.5 N A:CYS446 4.9 11.2 1.0 CB A:CYS446 5.0 12.1 1.0

Sodium binding site 5 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na829 b:27.6 occ:0.70 O A:HOH1069 2.2 22.6 0.7 OE2 A:GLU49 2.2 10.1 0.4 OH A:TYR322 2.4 20.0 1.0 O1 A:EDO811 2.7 24.6 1.0 O1A A:CE6803 3.0 27.7 1.0 O A:HOH1069 3.0 19.8 0.3 CZ A:TYR322 3.0 17.6 1.0 OD1 A:ASP227 3.0 14.5 1.0 CD A:GLU49 3.3 10.2 0.4 CE1 A:TYR322 3.4 17.9 1.0 OD2 A:ASP227 3.5 16.5 1.0 C1 A:EDO811 3.5 29.7 1.0 O A:HOH932 3.6 14.6 0.6 O2 A:EDO811 3.6 32.5 1.0 CG A:ASP227 3.6 13.6 1.0 CE2 A:TYR322 4.0 16.8 1.0 OE1 A:GLU49 4.0 9.2 0.4 CG A:GLU49 4.1 10.3 0.4 O A:HOH947 4.1 37.1 1.0 C2 A:EDO811 4.2 27.5 1.0 CB A:ALA225 4.2 8.2 1.0 O4 A:CBI802 4.3 24.4 1.0 C1A A:CE6803 4.4 27.2 1.0 CD1 A:TYR322 4.6 17.4 1.0 OE2 A:GLU49 4.7 12.5 0.6 O A:HOH953 4.7 28.8 1.0 O5A A:CE6803 4.8 27.3 1.0 O A:HOH1050 4.9 6.5 1.0

Sodium binding site 6 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na830 b:39.1 occ:0.70 O A:HOH1566 2.1 31.6 0.7 O A:HOH1505 2.4 41.5 1.0 O A:HOH1382 2.5 15.2 1.0 O A:HOH1404 2.9 36.4 1.0 O A:HOH1246 3.2 14.8 0.5 O A:HOH1155 3.7 48.2 1.0 O A:GLU38 3.8 14.6 1.0 CZ A:PHE176 3.9 10.6 1.0 O A:HOH1243 4.1 21.9 1.0 N A:VAL184 4.2 9.0 1.0 CE1 A:PHE176 4.2 11.3 1.0 CB A:VAL184 4.3 9.6 1.0 O A:HOH1687 4.4 28.3 1.0 O A:ASP405 4.6 15.2 1.0 CA A:VAL184 4.7 9.6 1.0 CG1 A:VAL184 4.7 9.8 1.0 CA A:ALA39 4.8 10.7 1.0 CD A:PRO406 4.8 11.4 1.0 C A:GLU38 4.8 12.0 1.0 CE2 A:PHE176 4.9 10.1 1.0 C A:SER183 5.0 8.6 1.0 O2A A:CE6803 5.0 22.8 1.0 CA A:SER183 5.0 8.4 1.0 CB A:ALA39 5.0 11.0 1.0

Sodium binding site 7 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na831 b:28.1 occ:1.00 O A:HOH1677 2.4 34.7 1.0 OG A:SER332 2.8 9.4 1.0 O A:HOH1192 2.9 30.5 1.0 O A:HOH1584 3.0 39.0 1.0 CB A:SER332 3.6 10.2 1.0 O A:SER332 3.6 15.3 1.0 C A:SER332 3.7 13.8 1.0 CB A:SER333 3.8 23.0 1.0 CG A:GLU350 3.8 19.1 1.0 N A:SER333 3.9 16.4 1.0 CD2 A:LEU353 3.9 8.6 1.0 CA A:SER333 4.2 19.4 1.0 CA A:SER332 4.3 11.2 1.0 CB A:GLU350 4.3 14.9 1.0 OG A:SER333 4.3 23.0 1.0 CA A:GLU350 4.4 12.2 1.0 CD A:GLU350 4.5 23.3 1.0 CD1 A:TYR329 4.6 14.3 1.0 O A:HOH1237 4.6 9.7 1.0 O A:HOH1271 4.7 15.7 1.0 O A:TYR329 4.8 10.1 1.0 O A:HOH1592 4.9 27.0 0.7 OE2 A:GLU350 4.9 31.0 1.0 CA A:TYR329 5.0 10.8 1.0

Sodium binding site 8 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na832 b:34.5 occ:1.00 O A:GLU79 2.4 12.1 1.0 O A:ILE83 2.5 11.4 1.0 O A:VAL85 2.7 27.7 1.0 O A:HOH1483 2.7 35.4 1.0 O A:HOH1097 2.8 12.4 1.0 OE1 A:GLU92 3.1 22.4 1.0 O A:LYS80 3.2 15.6 1.0 C A:VAL85 3.6 24.1 1.0 C A:GLU79 3.6 12.9 1.0 N A:VAL85 3.6 17.2 1.0 C A:ILE83 3.7 10.2 1.0 C A:LYS80 3.7 13.9 1.0 CA A:LYS80 4.0 14.1 1.0 CD A:GLU92 4.2 21.0 1.0 N A:LYS80 4.3 14.1 1.0 OH A:TYR172 4.3 8.7 1.0 CA A:VAL85 4.3 20.9 1.0 CB A:ASN86 4.3 47.9 1.0 CA A:PRO84 4.4 13.5 1.0 CA A:ASN86 4.4 42.7 1.0 N A:ASN86 4.4 31.9 1.0 C A:PRO84 4.4 15.8 1.0 N A:PRO84 4.5 11.4 1.0 OE2 A:GLU92 4.5 21.4 1.0 N A:TYR81 4.6 12.4 1.0 N A:ILE83 4.6 9.2 1.0 CA A:ILE83 4.7 9.8 1.0 O A:HOH1637 4.7 34.6 1.0 CA A:GLU79 4.8 14.1 1.0 CB A:ILE83 4.9 9.6 1.0

Sodium binding site 9 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na833 b:42.8 occ:1.00 O A:HOH1452 2.5 37.6 1.0 O1' A:CBI802 2.6 45.2 1.0 O A:HOH1479 2.8 32.0 1.0 OE2 A:GLU590 2.9 14.8 1.0 C1' A:CBI802 3.1 32.6 1.0 O5' A:CBI802 3.2 27.7 1.0 CD A:GLU590 3.4 16.2 1.0 CD A:ARG592 3.8 16.8 1.0 OE1 A:GLU590 3.9 17.7 1.0 NH1 A:ARG592 4.1 14.9 1.0 C2 A:EDO819 4.1 55.5 0.7 C5' A:CBI802 4.1 25.9 1.0 NE A:ARG592 4.2 16.2 1.0 CG A:GLU590 4.2 15.9 1.0 NH2 A:ARG682 4.3 10.4 1.0 CB A:GLU590 4.3 15.7 1.0 CZ A:ARG592 4.4 15.3 1.0 C1 A:EDO819 4.4 57.6 0.7 C1 A:EDO819 4.4 54.0 0.3 O A:HOH1077 4.5 21.3 1.0 C2' A:CBI802 4.6 31.3 1.0 C6' A:CBI802 4.8 26.7 1.0 C2 A:EDO819 4.8 53.1 0.3 O1 A:EDO819 4.9 58.6 0.7 O2 A:EDO819 4.9 51.7 0.3 O A:GLU591 4.9 18.1 1.0

Sodium binding site 10 out of 15 in the The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Structure of Bacillus Pumilus GH48 in Complex with Cellobiose and Cellohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na834 b:32.4 occ:1.00 O2 A:EDO818 2.4 16.1 0.5 OD1 A:ASN521 2.6 10.3 1.0 O A:HOH1471 2.7 23.1 1.0 O A:ASP510 2.9 10.8 1.0 C2 A:EDO818 3.4 14.8 0.5 CG A:ASN521 3.5 11.3 1.0 CD1 A:TRP362 3.5 8.3 1.0 ND2 A:ASN521 3.6 12.0 1.0 N A:ASP510 3.7 9.5 1.0 C A:ASP510 3.7 10.4 1.0 O A:TRP362 3.8 8.9 1.0 CB A:ASP510 3.9 12.2 1.0 CA A:ASP510 4.0 10.9 1.0 OG1 A:THR519 4.1 13.4 1.0 NE1 A:TRP362 4.1 7.9 1.0 CB A:PRO509 4.3 8.9 1.0 CE3 A:TRP512 4.3 8.7 1.0 CA A:TRP362 4.4 8.5 1.0 O A:THR511 4.4 8.9 1.0 CG A:TRP362 4.5 7.6 1.0 C A:PRO509 4.6 9.1 1.0 C A:TRP362 4.6 8.8 1.0 C1 A:EDO818 4.6 15.3 0.5 C A:THR511 4.7 9.0 1.0 N A:THR519 4.7 13.5 1.0 CZ3 A:TRP512 4.8 9.3 1.0 CA A:PRO509 4.8 9.1 1.0 N A:THR511 4.8 9.6 1.0 O A:HOH1121 4.9 23.3 1.0 CB A:ASN521 4.9 11.7 1.0 O A:HOH1166 4.9 6.3 1.0 CA A:TRP512 4.9 8.8 1.0 N A:TRP512 4.9 8.9 1.0 CG A:ASP510 5.0 14.8 1.0 CB A:TRP362 5.0 7.9 1.0

R.Brunecky, M.Alahuhta, D.W.Sammond, Q.Xu, M.Chen, D.B.Wilson, J.W.Brady, M.E.Himmel, Y.J.Bomble, V.V.Lunin. Natural Diversity of Glycoside Hydrolase Family 48 Exoglucanases: Insights From Structure. Biotechnol Biofuels V. 10 274 2017.
ISSN: ESSN 1754-6834
PubMed: 29213319
DOI: 10.1186/S13068-017-0951-5