Sodium in PDB 3cmb: Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution

The structure of Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution, PDB code: 3cmb was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.39 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.340, 136.710, 168.120, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 25.9

The structure of Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution (pdb code 3cmb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution, PDB code: 3cmb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na265 b:18.1 occ:1.00 O2 A:PEG273 2.7 39.4 1.0 OH A:TYR144 2.9 17.8 1.0 N D:ALA110 3.0 12.2 1.0 C2 A:PEG273 3.1 26.8 1.0 O A:HOH316 3.1 22.2 1.0 O A:HOH276 3.2 13.5 1.0 CE1 A:TYR144 3.5 21.9 1.0 CZ A:TYR144 3.6 19.2 1.0 N D:THR109 3.6 12.8 1.0 C3 A:PEG273 3.7 29.0 1.0 CB D:ALA110 3.7 14.3 1.0 CA D:ALA110 3.8 13.4 1.0 C D:THR109 3.9 11.4 1.0 CG D:LYS108 3.9 20.1 1.0 CB D:THR109 3.9 11.9 1.0 CA D:THR109 4.0 12.7 1.0 CB A:TYR125 4.2 12.3 1.0 C1 A:PEG273 4.3 21.5 1.0 NE2 A:GLN228 4.6 14.3 1.0 C D:LYS108 4.6 12.1 1.0 CD D:LYS108 4.7 24.8 1.0 CD1 A:TYR125 4.8 17.5 1.0 CD1 A:TYR144 4.8 21.8 1.0 O D:HOH321 4.8 24.3 1.0 CG A:TYR125 4.8 14.9 1.0 CG2 D:THR109 4.8 14.4 1.0 OG1 D:THR109 4.8 15.6 1.0 CE2 A:TYR144 4.9 16.8 1.0 O D:THR109 5.0 15.0 1.0

Sodium binding site 2 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na266 b:22.8 occ:1.00 O A:HOH288 2.8 18.4 1.0 OD2 A:ASP127 2.8 17.1 1.0 OG A:SER143 2.8 11.8 1.0 N A:GLY146 2.9 13.4 1.0 CB A:SER143 3.4 13.0 1.0 N A:GLU145 3.5 16.6 1.0 CG A:ASP127 3.5 13.3 1.0 CA A:GLY146 3.6 12.0 1.0 CB A:ASP127 3.7 14.3 1.0 C A:SER143 3.7 8.4 1.0 O A:SER143 3.9 12.7 1.0 C A:TYR144 3.9 13.8 1.0 C A:GLU145 3.9 13.9 1.0 O A:HOH296 3.9 19.5 1.0 N A:TYR144 3.9 11.2 1.0 O A:HOH407 3.9 31.3 1.0 CA A:GLU145 3.9 16.6 1.0 CA A:TYR144 4.1 10.4 1.0 CA A:SER143 4.2 13.8 1.0 C A:GLY146 4.4 14.0 1.0 O A:HOH320 4.4 22.5 1.0 N A:ASN147 4.5 11.8 1.0 O A:TYR144 4.5 11.9 1.0 OD1 A:ASP127 4.6 14.7 1.0 O A:HOH285 4.6 17.9 1.0 O C:HOH271 4.9 13.1 1.0 O A:HOH275 4.9 12.0 1.0 CA C:GLY146 4.9 14.3 1.0 CA A:ASP127 5.0 11.9 1.0

Sodium binding site 3 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na267 b:30.1 occ:1.00 O A:PRO23 2.6 22.7 1.0 O A:THR25 2.8 18.5 1.0 N A:MSE258 3.0 21.9 1.0 N A:ALA257 3.2 21.0 1.0 C A:ARG256 3.3 22.9 1.0 CA A:ARG256 3.4 20.7 1.0 N A:THR25 3.5 20.1 1.0 CB A:ARG256 3.5 22.2 1.0 C A:PRO23 3.5 21.9 1.0 CB A:MSE258 3.7 22.8 1.0 C A:GLU24 3.7 23.6 1.0 CA A:GLU24 3.7 25.9 1.0 CA A:MSE258 3.7 22.1 1.0 C A:THR25 3.7 19.3 1.0 O A:ARG256 4.0 22.6 1.0 N A:GLU24 4.0 22.1 1.0 C A:ALA257 4.0 23.6 1.0 CA A:THR25 4.1 21.8 1.0 CA A:ALA257 4.1 23.7 1.0 N A:GLY259 4.1 23.8 1.0 C A:MSE258 4.2 23.5 1.0 CG A:MSE258 4.2 24.8 1.0 CZ A:ARG256 4.2 38.5 1.0 CG A:ARG256 4.2 24.2 1.0 NH2 A:ARG256 4.3 47.0 1.0 NE A:ARG256 4.3 28.3 1.0 O A:GLU24 4.4 25.4 1.0 O A:HOH553 4.4 44.8 1.0 CB A:THR25 4.5 23.4 1.0 OE1 A:GLU24 4.6 43.9 1.0 O A:ASP22 4.7 23.3 1.0 CA A:PRO23 4.7 25.5 1.0 CB A:ALA257 4.8 27.3 1.0 NH1 A:ARG256 4.8 30.8 1.0 N A:ARG256 4.8 20.6 1.0 N A:LEU26 4.9 20.1 1.0 CD A:ARG256 4.9 30.9 1.0 CD2 A:LEU26 4.9 23.5 1.0 CD A:GLU24 5.0 36.0 1.0

Sodium binding site 4 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na265 b:23.5 occ:1.00 O A:HOH355 2.6 27.4 1.0 N B:GLU69 2.9 14.5 1.0 O B:GLY75 2.9 14.1 1.0 O B:GLY76 3.3 13.2 1.0 CB B:THR68 3.6 17.4 1.0 CA B:THR68 3.7 12.7 1.0 O A:LEU131 3.7 17.0 1.0 CA B:GLU69 3.7 13.8 1.0 C B:GLY76 3.7 17.1 1.0 C B:THR68 3.7 17.3 1.0 CB B:GLN77 3.8 14.4 0.3 C B:GLY75 3.9 13.2 1.0 CB B:GLN77 3.9 14.0 0.7 OE1 B:GLN77 3.9 21.6 0.3 O B:HOH387 4.1 28.5 1.0 NE2 B:GLN77 4.2 17.1 0.7 N B:GLN77 4.2 13.3 0.7 CG B:GLU69 4.3 19.9 1.0 CA B:GLY76 4.3 12.8 1.0 CG2 B:THR68 4.3 14.6 1.0 N B:GLN77 4.3 14.5 0.3 CG B:GLN77 4.4 16.0 0.7 CD B:GLN77 4.5 16.5 0.7 CG B:GLN77 4.5 10.0 0.3 N B:GLY76 4.5 13.9 1.0 CA B:GLN77 4.5 17.8 0.7 CA B:GLN77 4.5 16.0 0.3 CB B:GLU69 4.6 15.4 1.0 N A:ILE133 4.6 16.0 1.0 CD B:GLN77 4.7 6.7 0.3 O A:HOH344 4.8 26.1 1.0 OG1 B:THR68 4.8 17.1 1.0 CA A:HIS132 4.8 12.1 1.0 N B:ILE70 4.8 14.6 1.0 C A:LEU131 4.8 14.4 1.0 CB A:ILE133 4.9 15.6 1.0 CG1 A:ILE133 4.9 17.3 1.0 C B:GLU69 4.9 15.9 1.0 CD1 A:ILE133 4.9 18.0 1.0 O B:THR68 4.9 15.6 1.0 CA B:GLY75 4.9 14.2 1.0 O B:HOH531 5.0 41.7 1.0

Sodium binding site 5 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na266 b:24.9 occ:1.00 O D:HOH300 2.7 20.9 1.0 OE2 B:GLU129 2.7 18.1 1.0 O B:HOH315 2.8 21.6 1.0 NA B:NA267 2.9 20.5 1.0 CD B:GLU129 3.5 15.1 1.0 CG B:GLU129 3.6 19.7 1.0 CB B:ASP127 3.8 12.5 1.0 C D:GLU145 4.0 12.7 1.0 N D:GLY146 4.0 14.0 1.0 O D:GLU145 4.0 12.4 1.0 CA D:GLY146 4.1 11.1 1.0 N B:GLU129 4.2 13.8 1.0 O B:HOH394 4.2 29.0 1.0 O B:HOH484 4.3 36.3 1.0 C B:ASP127 4.4 13.6 1.0 N B:ILE128 4.4 14.2 1.0 C B:ILE128 4.5 8.9 1.0 O D:HOH425 4.5 34.7 1.0 CA B:GLU129 4.5 15.2 1.0 CA D:GLU145 4.6 13.0 1.0 OG B:SER143 4.6 13.9 1.0 O D:HOH277 4.6 16.1 1.0 CA B:ASP127 4.6 9.5 1.0 O B:HOH288 4.6 17.4 1.0 CB B:GLU129 4.7 14.9 1.0 OE1 B:GLU129 4.7 16.8 1.0 O B:ASP127 4.7 12.6 1.0 O B:THR141 4.9 14.1 1.0 CG B:ASP127 4.9 15.2 1.0 O B:ILE128 4.9 14.2 1.0 CA B:ILE128 4.9 11.0 1.0

Sodium binding site 6 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na267 b:20.5 occ:1.00 OG B:SER143 2.8 13.9 1.0 NA B:NA266 2.9 24.9 1.0 O B:THR141 2.9 14.1 1.0 O B:ASP127 3.2 12.6 1.0 CA D:GLY146 3.4 11.1 1.0 N B:SER143 3.4 13.7 1.0 C B:THR141 3.5 11.0 1.0 C B:ASP127 3.6 13.6 1.0 CB B:SER143 3.7 11.6 1.0 CA B:VAL142 3.9 12.8 1.0 C B:VAL142 3.9 16.6 1.0 N B:VAL142 3.9 11.3 1.0 CB B:ASP127 4.0 12.5 1.0 N B:GLU129 4.1 13.8 1.0 CG B:GLU129 4.1 19.7 1.0 CA B:SER143 4.1 11.9 1.0 N B:ILE128 4.2 14.2 1.0 O D:GLU145 4.2 12.4 1.0 N D:GLY146 4.3 14.0 1.0 CA B:ILE128 4.3 11.0 1.0 O D:GLY146 4.3 12.1 1.0 C D:GLY146 4.3 11.3 1.0 CA B:ASP127 4.4 9.5 1.0 CG2 B:THR141 4.5 13.3 1.0 CB B:THR141 4.5 10.7 1.0 C B:ILE128 4.5 8.9 1.0 C D:GLU145 4.6 12.7 1.0 CA B:THR141 4.7 13.0 1.0 O B:VAL142 4.7 13.1 1.0 OE2 B:GLU129 4.7 18.1 1.0 O D:HOH300 4.8 20.9 1.0 NA B:NA268 4.9 21.4 1.0 O B:SER143 4.9 14.8 1.0 CB B:GLU129 4.9 14.9 1.0 CD B:GLU129 5.0 15.1 1.0 C B:SER143 5.0 10.4 1.0

Sodium binding site 7 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na268 b:21.4 occ:1.00 OD2 B:ASP127 2.6 17.7 1.0 OG B:SER143 2.6 13.9 1.0 O D:HOH277 2.7 16.1 1.0 N B:GLY146 3.0 12.4 1.0 CG B:ASP127 3.4 15.2 1.0 CB B:SER143 3.5 11.6 1.0 N B:GLU145 3.5 12.2 1.0 CB B:ASP127 3.7 12.5 1.0 CA B:GLY146 3.7 11.9 1.0 O B:HOH383 3.7 28.3 1.0 C B:SER143 3.8 10.4 1.0 O D:HOH285 3.9 17.6 1.0 O B:SER143 3.9 14.8 1.0 N B:TYR144 4.0 10.5 1.0 C B:TYR144 4.0 13.4 1.0 C B:GLU145 4.0 14.9 1.0 CA B:GLU145 4.0 15.4 1.0 CA B:TYR144 4.2 11.2 1.0 CA B:SER143 4.3 11.9 1.0 O B:HOH323 4.3 22.4 1.0 O D:HOH300 4.4 20.9 1.0 C B:GLY146 4.5 14.9 1.0 OD1 B:ASP127 4.6 19.4 1.0 N B:ASN147 4.6 15.6 1.0 O B:TYR144 4.7 11.1 1.0 O D:HOH272 4.8 13.5 1.0 CA D:GLY146 4.9 11.1 1.0 NA B:NA267 4.9 20.5 1.0 CA B:ASP127 4.9 9.5 1.0 N B:ASP127 5.0 11.7 1.0

Sodium binding site 8 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na269 b:21.4 occ:1.00 O B:HOH285 2.6 17.2 1.0 ND1 B:HIS137 2.7 21.8 1.0 O B:PHE154 3.5 16.8 1.0 C3 B:PEG271 3.5 41.7 1.0 C B:PHE154 3.5 14.6 1.0 CG B:HIS137 3.6 26.1 1.0 CB B:HIS137 3.6 18.5 1.0 N B:GLU155 3.7 16.3 1.0 CE1 B:HIS137 3.7 25.6 1.0 CB B:GLU155 3.8 17.9 1.0 CA B:GLU155 4.0 15.3 1.0 N B:PHE154 4.0 18.2 1.0 CA B:HIS137 4.1 16.5 1.0 O2 B:PEG271 4.2 47.1 1.0 O B:HOH413 4.3 30.5 1.0 CA B:PHE154 4.3 13.5 1.0 CB B:ASP153 4.3 14.1 1.0 C2 B:PEG271 4.4 46.6 1.0 N B:PHE138 4.5 14.7 1.0 OD1 B:ASP153 4.5 19.7 1.0 O B:PHE138 4.6 16.6 1.0 CG B:GLU155 4.6 19.0 1.0 C B:ASP153 4.7 14.4 1.0 CD2 B:HIS137 4.8 25.5 1.0 C4 B:PEG271 4.8 37.4 1.0 NE2 B:HIS137 4.8 22.5 1.0 C B:HIS137 4.8 17.5 1.0 CG B:ASP153 4.9 23.8 1.0 CA B:ASP153 5.0 15.1 1.0 OE1 B:GLU155 5.0 21.5 1.0

Sodium binding site 9 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na265 b:15.9 occ:1.00 O B:HOH483 2.4 36.3 1.0 OH C:TYR144 3.0 22.7 1.0 N B:ALA110 3.1 15.0 1.0 CL C:CL267 3.2 27.7 1.0 CE1 C:TYR144 3.5 19.5 1.0 N B:THR109 3.6 10.8 1.0 CZ C:TYR144 3.7 17.3 1.0 CB B:ALA110 3.7 16.1 1.0 CB B:THR109 3.8 10.4 1.0 O B:HOH360 3.9 26.6 1.0 CA B:ALA110 3.9 14.0 1.0 CA B:THR109 3.9 10.0 1.0 C B:THR109 3.9 7.9 1.0 CG B:LYS108 4.0 16.3 1.0 CB C:TYR125 4.1 9.1 1.0 O B:HOH346 4.5 25.5 1.0 C B:LYS108 4.6 11.8 1.0 OG1 B:THR109 4.7 14.8 1.0 CD2 C:TYR125 4.7 11.6 1.0 CG C:TYR125 4.7 8.6 1.0 CD1 C:TYR144 4.8 20.6 1.0 CD B:LYS108 4.8 24.2 1.0 NE2 C:GLN228 4.8 14.8 1.0 O C:HOH299 4.8 19.9 1.0 CG2 B:THR109 4.9 10.5 1.0

Sodium binding site 10 out of 12 in the Crystal Structure of Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution


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 Acetoacetate Decarboxylase (YP_001047042.1) From Methanoculleus Marisnigri JR1 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na266 b:26.1 occ:1.00 O C:THR25 2.6 21.6 1.0 O C:PRO23 2.8 20.9 1.0 N C:MSE258 3.0 16.8 1.0 N C:ALA257 3.3 17.8 1.0 C C:ARG256 3.3 17.1 1.0 CA C:ARG256 3.4 18.8 1.0 N C:THR25 3.4 22.2 1.0 CB C:ARG256 3.5 21.0 1.0 CB C:MSE258 3.6 22.9 1.0 C C:THR25 3.6 18.1 1.0 C C:PRO23 3.6 21.7 1.0 C C:GLU24 3.7 23.6 1.0 CA C:MSE258 3.7 19.9 1.0 CA C:GLU24 3.7 23.4 1.0 CG C:MSE258 3.9 23.6 1.0 O C:ARG256 3.9 20.6 1.0 CA C:THR25 3.9 20.3 1.0 N C:GLU24 4.0 19.6 1.0 C C:ALA257 4.0 19.8 1.0 CG C:ARG256 4.1 22.3 1.0 CA C:ALA257 4.2 18.5 1.0 N C:GLY259 4.2 20.5 1.0 C C:MSE258 4.2 21.8 1.0 O C:GLU24 4.4 25.3 1.0 CB C:THR25 4.4 21.9 1.0 NE C:ARG256 4.4 23.1 1.0 CZ C:ARG256 4.6 37.1 1.0 O C:HOH484 4.6 35.5 1.0 NH2 C:ARG256 4.6 36.9 1.0 O C:ASP22 4.7 23.1 1.0 OE1 C:GLU24 4.7 35.3 1.0 N C:LEU26 4.8 21.1 1.0 CA C:PRO23 4.8 22.3 1.0 CB C:ALA257 4.8 21.5 1.0 N C:ARG256 4.8 19.0 1.0 CD2 C:LEU26 4.9 16.6 1.0 CD C:ARG256 5.0 23.4 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.