Sodium in PDB 5t1q: 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.

The structure of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus., PDB code: 5t1q was solved by G.Minasov, S.Nocadello, L.Shuvalova, O.Kiryukhina, I.Dubrovska, F.Bagnoli, G.Grandi, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.570, 66.838, 102.737, 108.70, 104.72, 90.25
R / Rfree (%)	17.3 / 21.9

The binding sites of Sodium atom in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. (pdb code 5t1q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus., PDB code: 5t1q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:25.8 occ:1.00 O A:HIS536 2.2 20.0 1.0 O A:HOH968 2.3 32.7 1.0 OD1 A:ASN540 2.3 22.6 1.0 OD1 A:ASN539 2.5 19.3 1.0 O A:HOH804 2.6 36.1 1.0 OE1 A:GLU562 2.6 26.8 1.0 OE2 A:GLU562 3.2 27.6 1.0 CD A:GLU562 3.3 26.1 1.0 C A:HIS536 3.4 20.0 1.0 CG A:ASN539 3.5 18.8 1.0 CG A:ASN540 3.5 21.9 1.0 ND2 A:ASN539 3.8 19.0 1.0 CA A:ASN537 4.1 20.1 1.0 N A:ASN537 4.2 19.5 1.0 N A:ASN540 4.3 19.6 1.0 CB A:ASN540 4.3 21.4 1.0 ND2 A:ASN540 4.4 22.3 1.0 CA A:HIS536 4.4 19.5 1.0 O A:HOH912 4.4 28.0 1.0 C A:ASN537 4.6 19.2 1.0 CB A:HIS536 4.6 20.7 1.0 ND1 A:HIS536 4.7 23.8 1.0 CG A:GLU562 4.8 24.5 1.0 N A:ASN539 4.8 18.2 1.0 CB A:ASN539 4.8 18.4 1.0 OD1 A:ASN537 4.9 24.2 1.0 CA A:ASN540 4.9 20.6 1.0 O A:ASN537 5.0 19.1 1.0

Sodium binding site 2 out of 6 in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:50.0 occ:1.00 O A:HOH1000 2.4 58.9 1.0 O A:PHE566 2.7 27.4 1.0 O A:HOH982 2.8 45.4 1.0 O A:HOH942 3.1 31.1 1.0 NH2 A:ARG603 3.6 28.8 1.0 N A:ALA568 3.6 28.3 1.0 C A:GLY567 3.7 29.0 1.0 C A:PHE566 3.7 26.9 1.0 NH1 A:ARG603 3.7 28.7 1.0 CA A:GLY567 4.1 29.4 1.0 CZ A:ARG603 4.1 27.0 1.0 O A:GLY567 4.1 30.9 1.0 CA A:ALA568 4.1 27.2 1.0 CE2 A:PHE561 4.3 19.2 1.0 N A:GLY567 4.3 28.7 1.0 CD2 A:PHE561 4.5 19.0 1.0 O A:GLN565 4.5 22.7 1.0 CB A:ALA568 4.6 25.6 1.0 CB A:PHE566 4.8 23.9 1.0 CA A:PHE566 4.9 25.4 1.0 CZ A:PHE561 4.9 18.5 1.0

Sodium binding site 3 out of 6 in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:27.1 occ:1.00 O B:HIS536 2.2 22.7 1.0 OD1 B:ASN540 2.4 23.6 1.0 OD1 B:ASN539 2.4 20.5 1.0 O B:HOH964 2.4 37.7 1.0 OE1 B:GLU562 2.9 37.3 1.0 OE2 B:GLU562 3.0 39.6 1.0 CG B:ASN539 3.4 20.6 1.0 CD B:GLU562 3.4 33.4 1.0 C B:HIS536 3.4 22.3 1.0 CG B:ASN540 3.5 23.3 1.0 ND2 B:ASN539 3.7 22.4 1.0 N B:ASN540 4.2 20.2 1.0 CA B:ASN537 4.2 23.0 1.0 N B:ASN537 4.3 22.2 1.0 ND2 B:ASN540 4.4 24.6 1.0 CA B:HIS536 4.4 21.9 1.0 CB B:ASN540 4.4 22.3 1.0 C B:ASN537 4.6 21.6 1.0 CB B:HIS536 4.7 24.2 1.0 CB B:ASN539 4.7 19.6 1.0 N B:ASN539 4.8 19.2 1.0 CG B:GLU562 4.9 30.2 1.0 CA B:ASN540 4.9 21.5 1.0 O B:ASN537 5.0 21.8 1.0 ND1 B:HIS536 5.0 28.2 1.0 O B:HOH943 5.0 42.4 1.0

Sodium binding site 4 out of 6 in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na701 b:22.6 occ:1.00 O C:HIS536 2.3 19.7 1.0 O C:HOH939 2.3 29.8 1.0 OD1 C:ASN540 2.3 21.2 1.0 O C:HOH912 2.4 32.0 1.0 OD1 C:ASN539 2.4 19.3 1.0 OE1 C:GLU562 2.7 31.3 1.0 OE2 C:GLU562 3.2 30.4 1.0 CD C:GLU562 3.4 29.0 1.0 CG C:ASN539 3.5 19.4 1.0 C C:HIS536 3.5 19.5 1.0 CG C:ASN540 3.5 21.5 1.0 ND2 C:ASN539 3.9 19.7 1.0 CA C:ASN537 4.2 19.7 1.0 N C:ASN540 4.2 19.5 1.0 N C:ASN537 4.3 19.3 1.0 CB C:ASN540 4.3 21.2 1.0 O C:HOH879 4.3 22.5 1.0 ND2 C:ASN540 4.4 21.8 1.0 CA C:HIS536 4.5 19.6 1.0 C C:ASN537 4.6 19.1 1.0 CB C:HIS536 4.8 20.9 1.0 OD1 C:ASN537 4.8 22.9 1.0 N C:ASN539 4.8 18.7 1.0 CB C:ASN539 4.8 19.0 1.0 CG C:GLU562 4.8 26.9 1.0 CA C:ASN540 4.9 20.3 1.0

Sodium binding site 5 out of 6 in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na702 b:54.9 occ:1.00 O C:HOH907 2.3 32.0 1.0 O C:HOH874 2.5 21.6 1.0 O C:VAL549 2.6 24.5 1.0 C C:VAL549 3.8 23.3 1.0 N C:VAL549 4.0 23.4 1.0 OE1 C:GLN543 4.1 27.4 1.0 O C:HOH914 4.5 49.1 1.0 CA C:VAL549 4.5 22.8 1.0 CB C:SER550 4.6 23.9 1.0 N C:SER550 4.7 22.7 1.0 CA C:SER550 4.8 23.1 1.0

Sodium binding site 6 out of 6 in the 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na701 b:27.0 occ:1.00 O D:HIS536 2.2 23.3 1.0 O D:HOH885 2.3 39.0 1.0 OD1 D:ASN540 2.4 26.6 1.0 OD1 D:ASN539 2.5 20.3 1.0 OE1 D:GLU562 2.7 35.6 1.0 OE2 D:GLU562 2.9 35.5 1.0 CD D:GLU562 3.2 32.3 1.0 CG D:ASN539 3.4 21.2 1.0 C D:HIS536 3.4 23.3 1.0 CG D:ASN540 3.6 25.4 1.0 ND2 D:ASN539 3.7 22.4 1.0 CA D:ASN537 4.2 22.6 1.0 N D:ASN537 4.3 22.6 1.0 N D:ASN540 4.4 21.0 1.0 CA D:HIS536 4.4 22.6 1.0 ND2 D:ASN540 4.5 26.6 1.0 CB D:ASN540 4.5 24.1 1.0 O D:HOH875 4.6 25.3 1.0 C D:ASN537 4.7 21.3 1.0 CB D:HIS536 4.7 26.1 1.0 CG D:GLU562 4.7 29.9 1.0 CB D:ASN539 4.8 20.4 1.0 ND1 D:HIS536 4.9 31.4 1.0 N D:ASN539 4.9 19.1 1.0

G.Minasov, S.Nocadello, L.Shuvalova, O.Kiryukhina, I.Dubrovska, F.Bagnoli, G.Grandi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.15 Angstrom Crystal Structure of N-Acetylmuramoyl-L-Alanine Amidase From Staphylococcus Aureus. To Be Published.