Sodium in PDB 8wt1: Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus

The structure of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus, PDB code: 8wt1 was solved by K.Chandravanshi, A.Kumar, C.Sen, R.Singh, G.B.Bhange, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	194.123, 75.443, 219.74, 90, 93.27, 90
R / Rfree (%)	21.2 / 25.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus (pdb code 8wt1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus, PDB code: 8wt1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


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 S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na709 b:35.8 occ:1.00 CB A:ALA716 2.5 24.4 1.0 O A:HOH923 2.6 25.6 1.0 OG A:SER607 2.9 25.1 1.0 O A:ASN641 2.9 30.0 1.0 OXT A:ALA716 3.1 36.3 1.0 CB A:SER607 3.3 29.1 1.0 C A:ALA716 3.5 29.7 1.0 CA A:ALA716 3.6 30.4 1.0 C A:ASN641 3.8 27.1 1.0 CB A:LEU644 4.0 30.1 1.0 N A:SER607 4.0 30.7 1.0 CA A:HIS642 4.0 26.7 1.0 OD2 A:ASP610 4.0 29.5 1.0 O A:HIS642 4.0 26.4 1.0 CB A:ARG552 4.1 28.1 1.0 C A:HIS642 4.2 28.1 1.0 N A:HIS642 4.2 29.6 1.0 CA A:SER607 4.3 31.9 1.0 O A:HOH828 4.3 28.7 1.0 CD A:ARG552 4.3 27.4 1.0 O A:ALA716 4.4 34.4 1.0 CD2 A:LEU644 4.5 29.9 1.0 CB A:ASP610 4.5 23.7 1.0 N A:ALA716 4.5 27.2 1.0 CG A:ASP610 4.6 29.0 1.0 N A:LEU644 4.6 25.9 1.0 CG A:ARG552 4.7 27.0 1.0 C A:HIS606 4.7 29.2 1.0 CA A:ASN641 4.8 30.1 1.0 CG A:LEU644 4.9 27.4 1.0 CA A:LEU644 5.0 31.7 1.0

Sodium binding site 2 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


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 S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na710 b:42.1 occ:1.00 OE2 A:GLU404 2.7 39.1 1.0 N A:GLY381 2.7 26.4 1.0 ND2 A:ASN400 2.9 29.8 1.0 OD2 A:ASP382 3.0 37.4 1.0 O A:GLY381 3.1 33.2 1.0 CB A:VAL380 3.3 30.5 1.0 C A:GLY381 3.4 33.7 1.0 O A:HOH876 3.5 38.9 1.0 N A:VAL380 3.5 31.8 1.0 CD A:GLU404 3.6 42.2 1.0 O A:HOH817 3.6 41.9 1.0 CA A:GLY381 3.6 26.3 1.0 CA A:VAL380 3.6 31.9 1.0 C A:VAL380 3.6 32.5 1.0 CG A:ASN400 3.7 35.7 1.0 CB A:ASN400 3.7 38.8 1.0 OE1 A:GLU404 3.8 45.5 1.0 CG A:ASP382 3.8 38.5 1.0 OG A:SER379 3.9 39.4 1.0 CG2 A:VAL380 4.2 34.8 1.0 CG1 A:VAL380 4.2 28.4 1.0 N A:ASP382 4.2 30.9 1.0 C A:SER379 4.3 31.5 1.0 N A:ASN400 4.4 35.3 1.0 OD1 A:ASP382 4.5 34.8 1.0 O A:HOH829 4.6 28.0 1.0 CB A:ASP382 4.6 30.1 1.0 CA A:ASN400 4.7 37.5 1.0 O A:VAL380 4.8 31.4 1.0 OD1 A:ASN400 4.8 35.9 1.0 CA A:SER379 4.8 33.7 1.0 CA A:ASP382 4.9 32.7 1.0 CG A:GLU404 4.9 41.0 1.0 CB A:SER379 5.0 33.9 1.0

Sodium binding site 3 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


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 S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na711 b:43.1 occ:1.00 NE2 A:HIS589 2.7 31.2 1.0 NE A:ARG585 2.8 27.4 1.0 O A:GLY494 3.0 28.5 1.0 NH2 A:ARG585 3.2 31.7 1.0 CE1 A:HIS589 3.3 31.9 1.0 CZ A:ARG585 3.4 34.4 1.0 O A:HOH879 3.4 26.0 1.0 CD2 A:HIS589 3.6 29.0 1.0 CD A:ARG585 3.8 30.8 1.0 C A:GLY494 3.9 25.4 1.0 CG A:ARG585 3.9 28.3 1.0 ND1 A:HIS589 4.3 26.6 1.0 CG A:HIS589 4.4 29.3 1.0 O A:VAL575 4.4 27.6 1.0 CA A:GLY494 4.6 24.3 1.0 N A:ASP495 4.6 23.8 1.0 NH1 A:ARG585 4.7 26.4 1.0 O A:HOH868 4.7 36.4 1.0 CA A:ASP495 4.8 26.5 1.0

Sodium binding site 4 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


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 S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na712 b:41.1 occ:1.00 OG A:SER529 2.5 31.9 1.0 O A:HOH1093 2.6 32.9 1.0 O A:HOH1022 2.7 37.7 1.0 CB A:SER529 2.9 29.4 1.0 N A:GLY450 3.0 31.7 1.0 O2 A:SO4702 3.1 43.7 1.0 N A:TYR530 3.2 24.8 1.0 O A:GLY450 3.5 31.0 1.0 CA A:GLY450 3.6 25.5 1.0 C A:GLY450 3.8 28.3 1.0 CB A:TYR530 3.8 25.7 1.0 C A:GLY449 4.0 25.9 1.0 CA A:SER529 4.0 28.1 1.0 C A:SER529 4.0 28.8 1.0 CA A:GLY449 4.0 24.8 1.0 O1 A:SO4702 4.0 37.9 1.0 CA A:TYR530 4.1 26.7 1.0 S A:SO4702 4.2 40.6 1.0 O A:HOH949 4.2 38.9 1.0 NE2 A:HIS642 4.7 28.5 1.0 O A:GLY528 4.7 25.3 1.0 N A:PRO451 4.9 24.7 1.0

Sodium binding site 5 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na713 b:40.5 occ:1.00 O1 B:SO4709 2.6 40.6 1.0 O B:HOH1123 2.7 36.6 1.0 O B:ARG334 2.9 29.8 1.0 NE2 B:GLN426 2.9 32.8 1.0 NH1 B:ARG336 3.0 34.8 1.0 CZ B:ARG336 3.7 37.2 1.0 CB B:ARG334 3.7 31.0 1.0 S B:SO4709 3.8 46.5 1.0 CE2 B:PHE457 3.8 29.1 1.0 CD B:GLN426 3.9 30.8 1.0 C B:ARG334 4.0 28.6 1.0 O2 B:SO4709 4.0 47.3 1.0 OE1 B:GLN426 4.0 28.6 1.0 NH2 B:ARG336 4.1 38.5 1.0 CZ B:PHE457 4.1 26.7 1.0 O B:HOH801 4.2 38.0 1.0 O B:HOH1086 4.3 38.1 1.0 NE B:ARG334 4.4 30.3 1.0 CA B:ARG334 4.4 25.2 1.0 O3 B:SO4709 4.5 48.5 1.0 O B:HOH1051 4.5 46.1 1.0 NE B:ARG336 4.5 37.2 1.0 CG B:ARG336 4.9 29.3 1.0 O4 B:SO4709 4.9 49.6 1.0 OD1 B:ASN355 4.9 37.2 1.0 CG B:ARG334 4.9 28.4 1.0 CD B:ARG336 5.0 30.4 1.0 CD B:ARG334 5.0 31.9 1.0

Sodium binding site 6 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na714 b:35.2 occ:1.00 O B:VAL539 2.6 34.5 1.0 OG1 B:THR600 2.8 36.3 1.0 OD1 B:ASP543 2.8 39.2 1.0 N B:ARG599 2.8 34.8 1.0 N B:THR600 3.1 40.1 1.0 O B:THR542 3.3 38.5 1.0 C B:VAL539 3.5 33.5 1.0 CA B:ARG599 3.6 35.8 1.0 C B:ARG599 3.6 39.1 1.0 CB B:THR600 3.6 32.9 1.0 O B:HOH1008 3.7 34.4 1.0 C B:MET598 3.8 37.4 1.0 CA B:VAL539 3.8 32.1 1.0 CA B:MET598 3.8 36.3 1.0 O B:HIS597 3.8 39.7 1.0 CB B:VAL539 3.9 31.7 1.0 O B:HOH933 3.9 31.7 1.0 CG B:ASP543 3.9 39.7 1.0 CA B:THR600 4.0 35.0 1.0 CB B:ARG599 4.0 38.4 1.0 CA B:ASP543 4.1 35.6 1.0 C B:THR542 4.3 38.6 1.0 CB B:ASP543 4.5 36.4 1.0 O B:ARG599 4.6 44.2 1.0 N B:ASP543 4.7 37.9 1.0 C B:HIS597 4.7 39.3 1.0 CG B:ARG599 4.7 39.3 1.0 N B:MET598 4.7 34.8 1.0 N B:GLY540 4.8 27.8 1.0 CG2 B:VAL539 4.8 27.7 1.0 CG1 B:VAL539 4.8 32.5 1.0 CB B:MET598 4.9 37.4 1.0 O B:MET598 4.9 34.5 1.0 OD2 B:ASP543 5.0 37.5 1.0 CG2 B:THR600 5.0 32.4 1.0

Sodium binding site 7 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na715 b:34.6 occ:1.00 N B:VAL579 2.7 24.2 1.0 OD1 B:ASP578 2.8 32.2 1.0 O C:HOH852 3.0 33.6 1.0 CG1 B:VAL579 3.0 35.3 1.0 OG B:SER561 3.0 30.4 1.0 CB B:SER561 3.0 31.3 1.0 CA B:ASP578 3.1 26.1 1.0 CB B:ASP578 3.3 29.3 1.0 C B:ASP578 3.4 30.9 1.0 CG B:ASP578 3.5 30.9 1.0 CB B:VAL579 3.8 30.2 1.0 CA B:VAL579 3.8 27.9 1.0 CG2 B:VAL579 4.0 34.0 1.0 OE1 C:GLN627 4.3 30.1 1.0 CD1 B:LEU586 4.4 28.5 1.0 N B:ASP578 4.5 27.4 1.0 CA B:SER561 4.5 25.1 1.0 NE2 C:GLN627 4.6 23.0 1.0 O B:ASP578 4.6 25.5 1.0 O B:CYS577 4.6 26.4 1.0 O B:HOH912 4.6 22.9 1.0 OD2 B:ASP578 4.7 34.2 1.0 O C:HOH951 4.9 27.8 1.0 CD C:GLN627 4.9 26.2 1.0 CB B:THR571 4.9 28.0 1.0 C B:VAL579 4.9 27.0 1.0 NE1 B:TRP580 5.0 33.1 1.0 N B:TRP580 5.0 29.3 1.0 C B:CYS577 5.0 27.7 1.0

Sodium binding site 8 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na716 b:40.5 occ:1.00 O B:SER88 2.8 32.1 1.0 NE1 B:TRP97 2.9 33.9 1.0 OG B:SER91 2.9 35.8 1.0 CB B:SER91 2.9 40.2 1.0 O B:ARG93 2.9 33.6 1.0 N B:SER91 3.1 37.2 1.0 CG B:GLN95 3.4 34.0 1.0 CB B:GLN95 3.4 34.3 1.0 CA B:SER91 3.6 36.9 1.0 N B:GLN95 3.6 33.8 1.0 C B:SER88 3.7 29.2 1.0 CE2 B:TRP97 3.7 33.9 1.0 N B:ARG90 3.7 29.7 1.0 CD1 B:TRP97 3.9 32.8 1.0 C B:ASP89 3.9 34.1 1.0 CZ2 B:TRP97 4.0 33.7 1.0 CA B:GLN95 4.0 31.9 1.0 CA B:ASP89 4.1 31.6 1.0 CG B:ARG90 4.1 35.6 1.0 C B:ARG93 4.2 37.1 1.0 C B:ARG90 4.2 35.0 1.0 N B:ASP89 4.3 28.0 1.0 NE2 B:GLN108 4.4 31.9 1.0 C B:THR94 4.4 32.5 1.0 CA B:ARG90 4.4 37.3 1.0 C B:SER91 4.5 42.0 1.0 O B:ASP89 4.6 39.3 1.0 O B:GLN95 4.6 30.6 1.0 CB B:SER88 4.6 30.7 1.0 CD B:GLN108 4.6 37.6 1.0 C B:GLN95 4.7 30.1 1.0 CA B:SER88 4.7 33.7 1.0 CA B:THR94 4.7 30.2 1.0 N B:GLY92 4.7 42.7 1.0 CD B:GLN95 4.9 37.2 1.0 CB B:ARG90 4.9 32.5 1.0 N B:ARG93 4.9 41.1 1.0 N B:THR94 4.9 37.6 1.0 CD2 B:TRP97 5.0 33.0 1.0 CG B:GLN108 5.0 32.6 1.0 OG B:SER88 5.0 33.6 1.0

Sodium binding site 9 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na708 b:39.0 occ:1.00 OE2 C:GLU404 2.7 39.0 1.0 O C:GLY381 2.8 30.9 1.0 N C:GLY381 2.9 27.6 1.0 OD2 C:ASP382 2.9 36.3 1.0 ND2 C:ASN400 3.0 31.5 1.0 O C:HOH929 3.2 35.7 1.0 CB C:VAL380 3.4 29.9 1.0 C C:GLY381 3.4 34.4 1.0 CB C:ASN400 3.5 33.8 1.0 CG C:ASP382 3.6 33.5 1.0 CD C:GLU404 3.7 41.9 1.0 N C:VAL380 3.7 32.2 1.0 CG C:ASN400 3.7 30.7 1.0 CA C:GLY381 3.7 25.2 1.0 C C:VAL380 3.8 29.8 1.0 CA C:VAL380 3.8 26.8 1.0 OE1 C:GLU404 3.8 44.5 1.0 O C:HOH880 3.9 38.0 1.0 N C:ASN400 4.1 36.5 1.0 OD1 C:ASP382 4.1 30.8 1.0 CG2 C:VAL380 4.3 32.0 1.0 CG1 C:VAL380 4.3 26.4 1.0 OG C:SER379 4.4 36.4 1.0 CA C:ASN400 4.4 38.3 1.0 N C:ASP382 4.4 33.2 1.0 O C:HOH888 4.5 29.9 1.0 C C:SER379 4.5 29.0 1.0 CB C:ASP382 4.6 28.9 1.0 N C:ALA399 4.8 38.8 1.0 C C:ALA399 4.9 38.2 1.0 OD1 C:ASN400 4.9 32.4 1.0 CA C:ASP382 4.9 28.4 1.0 O C:VAL380 5.0 29.4 1.0

Sodium binding site 10 out of 14 in the Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of S9 Carboxypeptidase From Geobacillus Sterothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na709 b:48.0 occ:1.00 O D:HOH1008 2.2 44.4 1.0 O D:HOH966 2.7 38.6 1.0 N D:ASP224 2.8 38.5 1.0 CD D:PRO223 3.0 43.3 1.0 CB D:ASP224 3.1 38.7 1.0 CG D:ASP224 3.2 39.7 1.0 N D:PRO223 3.3 38.9 1.0 OD2 D:ASP224 3.4 39.3 1.0 CA D:ASP224 3.5 39.0 1.0 C D:ASP222 3.6 45.1 1.0 CG D:PRO223 3.7 41.7 1.0 OD1 D:ASP224 3.7 39.3 1.0 C D:PRO223 3.9 37.9 1.0 CA D:ASP222 3.9 37.6 1.0 CA D:PRO223 4.1 39.4 1.0 O D:ASP222 4.2 44.4 1.0 N D:THR225 4.3 39.7 1.0 CB D:ASP222 4.4 43.8 1.0 C D:ASP224 4.4 38.7 1.0 CB D:PRO223 4.5 43.5 1.0 NH2 D:ARG163 4.9 43.1 1.0

K.Chandravanshi, R.Singh, G.N.Bhange, A.Kumar, P.Yadav, A.Kumar, R.D.Makde. Crystal Structure and Solution Scattering of Geobacillus Stearothermophilus S9 Peptidase Reveal Structural Adaptations For Carboxypeptidase Activity. Febs Lett. 2024.
ISSN: ISSN 0014-5793
PubMed: 38426217
DOI: 10.1002/1873-3468.14834