Sodium in PDB 3ed4: Crystal Structure of Putative Arylsulfatase From Escherichia Coli

The structure of Crystal Structure of Putative Arylsulfatase From Escherichia Coli, PDB code: 3ed4 was solved by Y.Patskovsky, S.Ozyurt, M.Gilmore, S.Chang, K.Bain, S.Wasserman, J.Koss, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.932, 178.858, 76.284, 90.00, 92.17, 90.00
R / Rfree (%)	19.6 / 24.2

The binding sites of Sodium atom in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli (pdb code 3ed4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli, PDB code: 3ed4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli


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 Putative Arylsulfatase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na518 b:19.9 occ:1.00 O B:HOH891 2.0 33.0 1.0 O A:HOH840 2.1 25.6 1.0 O A:HOH839 2.2 24.0 1.0 O B:HOH881 2.2 23.3 1.0 OE2 A:GLU326 2.2 27.1 1.0 OE2 B:GLU326 2.3 22.7 1.0 CD A:GLU326 3.3 29.0 1.0 CD B:GLU326 3.4 32.4 1.0 O A:HOH606 3.6 27.5 1.0 O B:HOH853 3.8 23.5 1.0 OE1 A:GLU326 3.9 27.3 1.0 O B:HOH730 4.0 26.5 1.0 OE1 B:GLU326 4.0 23.6 1.0 O A:HOH680 4.0 33.5 1.0 OD2 B:ASP430 4.0 27.1 1.0 NH2 A:ARG328 4.1 26.1 1.0 OD2 A:ASP430 4.1 31.4 1.0 NH2 B:ARG328 4.2 21.5 1.0 CG A:GLU326 4.4 25.0 1.0 CG B:GLU326 4.5 21.9 1.0 O B:HOH620 4.5 32.9 1.0 O A:HOH669 4.6 28.5 1.0 O A:HOH795 4.9 24.6 1.0 O B:HOH571 5.0 21.5 1.0 CG B:ASP430 5.0 27.6 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli


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 Putative Arylsulfatase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:24.0 occ:1.00 OD1 A:ASP52 2.2 19.4 1.0 OD1 A:ASP51 2.3 26.1 1.0 OG A:SER91 2.4 22.6 1.0 OD2 A:ASP319 2.6 24.6 1.0 OD1 A:ASP319 2.8 22.6 1.0 OD1 A:ASN320 2.8 19.0 1.0 CG A:ASP319 3.0 19.0 1.0 CG A:ASP52 3.3 18.1 1.0 N A:ASP52 3.4 24.1 1.0 CG A:ASN320 3.5 26.7 1.0 ND2 A:ASN320 3.5 20.4 1.0 CB A:SER91 3.5 24.8 1.0 CG A:ASP51 3.6 34.9 1.0 O3 A:SO4520 3.8 26.4 0.5 CA A:SER91 3.9 27.5 1.0 CA A:ASP52 4.0 19.4 1.0 OD2 A:ASP52 4.0 24.4 1.0 NZ A:LYS144 4.2 25.1 1.0 N A:SER91 4.2 24.6 1.0 CB A:ASP52 4.2 16.7 1.0 C A:ASP51 4.2 23.0 1.0 CD2 A:HIS242 4.3 22.5 1.0 CA A:ASP51 4.3 19.8 1.0 OD2 A:ASP51 4.4 27.9 1.0 NH2 A:ARG95 4.4 24.3 1.0 CB A:ASP319 4.5 21.9 1.0 CE A:LYS346 4.5 23.9 1.0 NZ A:LYS346 4.6 20.7 1.0 CB A:ASP51 4.6 23.9 1.0 N A:ASN320 4.9 18.1 1.0 CB A:ASN320 4.9 21.5 1.0 S A:SO4520 4.9 31.8 0.5 NE A:ARG95 4.9 20.0 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli


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 Putative Arylsulfatase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Na518 b:21.3 occ:1.00 OD1 B:ASP52 2.2 18.8 1.0 OD1 B:ASP51 2.3 21.8 1.0 OG B:SER91 2.4 25.0 1.0 OD2 B:ASP319 2.6 19.4 1.0 OD1 B:ASN320 2.7 18.9 1.0 OD1 B:ASP319 2.8 20.6 1.0 CG B:ASP319 3.0 18.2 1.0 CG B:ASP52 3.3 20.3 1.0 CG B:ASN320 3.4 20.0 1.0 ND2 B:ASN320 3.4 21.3 1.0 N B:ASP52 3.4 18.5 1.0 CB B:SER91 3.5 22.6 1.0 O1 B:SO42 3.6 24.7 0.5 CG B:ASP51 3.6 18.6 1.0 CA B:SER91 3.9 26.8 1.0 CA B:ASP52 4.0 20.3 1.0 OD2 B:ASP52 4.1 23.1 1.0 C B:ASP51 4.2 21.0 1.0 N B:SER91 4.2 19.9 1.0 NZ B:LYS144 4.2 17.1 1.0 CB B:ASP52 4.2 14.3 1.0 CD2 B:HIS242 4.2 24.6 1.0 CA B:ASP51 4.3 20.4 1.0 OD2 B:ASP51 4.4 18.5 1.0 CB B:ASP319 4.4 22.8 1.0 CE B:LYS346 4.5 20.1 1.0 NZ B:LYS346 4.5 18.7 1.0 CB B:ASP51 4.5 19.9 1.0 NH2 B:ARG95 4.5 21.9 1.0 CB B:ASN320 4.8 20.7 1.0 N B:ASN320 4.8 16.7 1.0 S B:SO42 4.9 26.1 0.5 NE2 B:HIS242 5.0 19.2 1.0 NE B:ARG95 5.0 25.8 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli


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 Putative Arylsulfatase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1 b:19.8 occ:1.00 O C:HOH793 2.0 27.9 1.0 O D:HOH849 2.0 33.4 1.0 O D:HOH848 2.1 22.7 1.0 OE2 D:GLU326 2.1 28.1 1.0 OE2 C:GLU326 2.3 26.0 1.0 O C:HOH794 2.3 25.2 1.0 CD D:GLU326 3.3 31.7 1.0 CD C:GLU326 3.4 29.4 1.0 O D:HOH824 3.7 29.3 1.0 O C:HOH770 3.7 24.4 1.0 OE1 D:GLU326 3.7 23.5 1.0 O D:HOH852 3.8 52.9 1.0 OD2 C:ASP430 3.9 28.6 1.0 O D:HOH822 3.9 31.2 1.0 OE1 C:GLU326 3.9 29.6 1.0 OD2 D:ASP430 4.1 31.2 1.0 O C:HOH777 4.1 31.1 1.0 NH2 D:ARG328 4.2 21.6 1.0 NH2 C:ARG328 4.3 24.1 1.0 CG C:GLU326 4.4 20.2 1.0 CG D:GLU326 4.4 20.2 1.0 O D:HOH549 4.6 33.1 1.0 O C:HOH816 4.8 36.6 1.0 CG C:ASP430 4.9 30.6 1.0 O C:HOH572 5.0 26.1 1.0 O D:HOH700 5.0 26.6 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli


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 Putative Arylsulfatase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Na518 b:30.9 occ:1.00 OD1 C:ASP52 2.3 25.8 1.0 OD1 C:ASP51 2.4 28.3 1.0 OG C:SER91 2.4 30.8 1.0 OD2 C:ASP319 2.6 25.5 1.0 OD1 C:ASN320 2.8 31.4 1.0 OD1 C:ASP319 2.9 27.0 1.0 CG C:ASP319 3.1 29.3 1.0 CG C:ASP52 3.3 22.8 1.0 CG C:ASN320 3.5 35.2 1.0 N C:ASP52 3.5 23.3 1.0 CB C:SER91 3.5 22.6 1.0 ND2 C:ASN320 3.6 22.6 1.0 CG C:ASP51 3.6 31.4 1.0 O1 C:SO43 3.7 23.2 0.5 CA C:SER91 3.9 25.7 1.0 NZ C:LYS144 4.1 26.8 1.0 OD2 C:ASP52 4.1 26.8 1.0 CD2 C:HIS242 4.1 27.5 1.0 CA C:ASP52 4.1 22.8 1.0 N C:SER91 4.1 24.9 1.0 CB C:ASP52 4.2 23.6 1.0 C C:ASP51 4.2 20.7 1.0 OD2 C:ASP51 4.4 26.4 1.0 CA C:ASP51 4.4 28.0 1.0 NH2 C:ARG95 4.4 28.1 1.0 CE C:LYS346 4.5 22.7 1.0 CB C:ASP319 4.6 34.0 1.0 NZ C:LYS346 4.6 21.7 1.0 CB C:ASP51 4.6 23.9 1.0 NE2 C:HIS242 4.8 22.6 1.0 S C:SO43 4.9 33.9 0.5 CB C:ASN320 4.9 21.1 1.0 NE C:ARG95 4.9 29.4 1.0 O4 C:SO43 5.0 33.2 0.5 N C:ASN320 5.0 26.9 1.0 CE C:LYS144 5.0 31.1 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Putative Arylsulfatase From Escherichia Coli


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 Putative Arylsulfatase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1 b:27.1 occ:1.00 OD1 D:ASP52 2.2 23.3 1.0 OD1 D:ASP51 2.3 28.1 1.0 OG D:SER91 2.5 29.1 1.0 OD2 D:ASP319 2.6 23.3 1.0 OD1 D:ASN320 2.8 21.4 1.0 OD1 D:ASP319 2.8 25.4 1.0 CG D:ASP319 3.1 23.1 1.0 CG D:ASP52 3.4 28.7 1.0 N D:ASP52 3.4 24.8 1.0 CG D:ASN320 3.5 27.9 1.0 CB D:SER91 3.5 29.9 1.0 ND2 D:ASN320 3.6 24.4 1.0 CG D:ASP51 3.6 32.2 1.0 O1 D:SO44 3.8 25.9 0.5 CA D:SER91 3.9 26.8 1.0 CA D:ASP52 4.0 21.7 1.0 OD2 D:ASP52 4.2 23.2 1.0 N D:SER91 4.2 22.4 1.0 NZ D:LYS144 4.2 23.7 1.0 C D:ASP51 4.2 31.0 1.0 CB D:ASP52 4.2 20.8 1.0 CD2 D:HIS242 4.3 24.9 1.0 CA D:ASP51 4.3 22.8 1.0 OD2 D:ASP51 4.4 27.2 1.0 CB D:ASP319 4.5 30.1 1.0 NZ D:LYS346 4.5 22.0 1.0 NH2 D:ARG95 4.5 24.6 1.0 CE D:LYS346 4.5 26.9 1.0 CB D:ASP51 4.6 22.8 1.0 N D:ASN320 4.8 21.2 1.0 CB D:ASN320 4.9 20.9 1.0 NE2 D:HIS242 5.0 27.4 1.0

Y.Patskovsky, S.Ozyurt, M.Gilmore, S.Chang, K.Bain, S.Wasserman, J.Koss, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Arylsulfatase From Escherichia Coli To Be Published.