Magnesium in PDB 3nzg: Crystal Structure of A Putative Racemase with Mg Ion

The structure of Crystal Structure of A Putative Racemase with Mg Ion, PDB code: 3nzg was solved by S.Eswaramoorthy, E.Raparia, S.K.Burley, S.Swaminathan, New York Sgxresearch Center For Structural Genomics (Nysgxrc), 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	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	132.144, 165.408, 165.666, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.4

The binding sites of Magnesium atom in the Crystal Structure of A Putative Racemase with Mg Ion (pdb code 3nzg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of A Putative Racemase with Mg Ion, PDB code: 3nzg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:15.1 occ:1.00 OG A:SER247 2.3 8.7 1.0 O C:HOH494 2.3 17.4 1.0 O C:HOH461 2.4 19.3 1.0 O A:HOH427 2.5 19.5 1.0 O A:HOH408 2.6 17.4 1.0 CB A:SER247 3.4 12.4 1.0 N A:SER247 4.4 10.1 1.0 OE1 C:GLU273 4.5 22.9 1.0 OE2 C:GLU273 4.5 24.1 1.0 OD1 A:ASP245 4.5 13.8 1.0 CA A:SER247 4.5 10.7 1.0 CD C:GLU273 4.9 21.8 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:27.9 occ:1.00 O A:HOH469 2.0 24.4 1.0 O1 A:GOL601 2.0 34.9 1.0 OD2 A:ASP211 2.1 23.4 1.0 OE2 A:GLU264 2.1 28.8 1.0 OE2 A:GLU238 2.1 18.9 1.0 O2 A:GOL601 2.2 32.3 1.0 C2 A:GOL601 2.8 35.6 1.0 C1 A:GOL601 2.8 35.3 1.0 CD A:GLU264 2.9 28.7 1.0 OE1 A:GLU264 3.1 28.4 1.0 CG A:ASP211 3.2 22.3 1.0 CD A:GLU238 3.2 18.0 1.0 OD1 A:ASP211 3.6 23.9 1.0 OE1 A:GLU238 4.0 18.4 1.0 CG A:GLU238 4.0 15.1 1.0 NZ A:LYS177 4.1 20.3 1.0 C3 A:GOL601 4.2 36.2 1.0 CG A:GLU264 4.3 25.5 1.0 O A:HOH445 4.4 19.1 1.0 CB A:ASP211 4.4 19.9 1.0 ND1 A:HIS314 4.4 18.4 1.0 CE1 A:HIS314 4.5 17.2 1.0 O3 A:GOL601 4.6 37.2 1.0 CD2 A:LEU213 4.7 20.9 1.0 CE A:LYS177 4.8 18.3 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:17.4 occ:1.00 O D:HOH421 2.2 23.1 1.0 OG B:SER247 2.3 13.7 1.0 O B:HOH445 2.5 17.2 1.0 O B:HOH426 2.5 18.1 1.0 O D:HOH427 2.6 17.5 1.0 CB B:SER247 3.4 14.5 1.0 N B:SER247 4.4 11.1 1.0 OD1 B:ASP245 4.5 15.9 1.0 CA B:SER247 4.5 11.1 1.0 OE1 D:GLU273 4.5 27.1 1.0 OE2 D:GLU273 4.6 27.6 1.0 CE B:LYS278 4.8 25.1 1.0 NZ B:LYS278 5.0 27.9 1.0 CD D:GLU273 5.0 24.9 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:16.5 occ:1.00 O C:HOH418 2.3 18.1 1.0 O B:ALA306 2.3 13.5 1.0 O A:HOH407 2.3 23.2 1.0 O A:HOH465 2.3 25.1 1.0 OG C:SER247 2.4 10.6 1.0 O C:HOH410 2.6 13.8 1.0 CB C:SER247 3.4 10.7 1.0 C B:ALA306 3.4 11.2 1.0 CA B:ALA306 4.0 12.4 1.0 N C:SER247 4.4 11.0 1.0 OD1 C:ASP245 4.4 15.7 1.0 ND2 B:ASN308 4.4 13.7 1.0 OE1 A:GLU273 4.5 25.2 1.0 CA C:SER247 4.5 10.8 1.0 CB B:ALA306 4.5 14.2 1.0 N B:ASN307 4.6 10.8 1.0 OE2 A:GLU273 4.6 24.9 1.0 O C:HOH467 4.6 32.4 1.0 CE C:LYS278 4.7 28.5 1.0 NZ C:LYS278 4.8 29.5 1.0 CA B:ASN307 4.9 10.9 1.0 CD A:GLU273 5.0 23.4 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:36.0 occ:1.00 O1 B:GOL601 1.9 39.4 1.0 O B:HOH470 2.0 20.1 1.0 OD2 B:ASP211 2.0 22.6 1.0 O2 B:GOL601 2.1 37.4 1.0 OE2 B:GLU264 2.1 28.5 1.0 OE2 B:GLU238 2.3 19.9 1.0 C2 B:GOL601 2.8 40.0 1.0 C1 B:GOL601 2.8 39.8 1.0 CD B:GLU264 3.0 26.4 1.0 CG B:ASP211 3.1 20.5 1.0 OE1 B:GLU264 3.2 28.2 1.0 CD B:GLU238 3.2 18.3 1.0 OD1 B:ASP211 3.5 17.9 1.0 OE1 B:GLU238 4.0 16.8 1.0 CG B:GLU238 4.1 14.9 1.0 NZ B:LYS177 4.2 16.1 1.0 C3 B:GOL601 4.2 40.1 1.0 CB B:ASP211 4.4 18.2 1.0 CG B:GLU264 4.4 23.2 1.0 CD2 B:HIS314 4.4 18.6 1.0 O B:HOH480 4.4 25.0 1.0 O3 B:GOL601 4.5 41.3 1.0 NE2 B:HIS314 4.6 20.0 1.0 CD2 B:LEU213 4.7 24.1 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg508 b:29.6 occ:1.00 O C:HOH484 2.0 21.1 1.0 O1 C:GOL601 2.0 36.9 1.0 OD2 C:ASP211 2.1 21.2 1.0 O2 C:GOL601 2.1 31.7 1.0 OE2 C:GLU238 2.1 21.9 1.0 OE2 C:GLU264 2.2 24.5 1.0 C2 C:GOL601 2.8 35.3 1.0 C1 C:GOL601 2.9 34.9 1.0 CD C:GLU264 3.1 23.8 1.0 CG C:ASP211 3.1 21.0 1.0 OE1 C:GLU264 3.3 25.2 1.0 CD C:GLU238 3.3 20.1 1.0 OD1 C:ASP211 3.5 22.0 1.0 NZ C:LYS177 4.0 18.3 1.0 OE1 C:GLU238 4.1 19.5 1.0 C3 C:GOL601 4.2 35.0 1.0 CG C:GLU238 4.3 16.6 1.0 CD2 C:HIS314 4.4 19.6 1.0 O C:HOH444 4.4 21.9 1.0 CB C:ASP211 4.4 18.8 1.0 CG C:GLU264 4.5 22.7 1.0 O3 C:GOL601 4.6 37.2 1.0 CD2 C:LEU213 4.6 20.6 1.0 CE C:LYS177 4.7 17.1 1.0 NE2 C:HIS314 4.8 20.3 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:17.6 occ:1.00 O B:HOH427 2.3 19.9 1.0 OG D:SER247 2.4 12.4 1.0 O D:HOH431 2.4 17.2 1.0 O B:HOH438 2.5 20.7 1.0 O D:HOH428 2.5 15.3 1.0 O A:ALA306 2.5 11.8 1.0 CB D:SER247 3.4 12.2 1.0 C A:ALA306 3.6 11.3 1.0 CA A:ALA306 4.2 10.8 1.0 N D:SER247 4.4 12.8 1.0 OE2 B:GLU273 4.4 28.3 1.0 OE1 B:GLU273 4.4 28.6 1.0 CA D:SER247 4.5 12.1 1.0 OD1 D:ASP245 4.6 15.7 1.0 ND2 A:ASN308 4.6 9.5 1.0 CE D:LYS278 4.6 27.8 1.0 N A:ASN307 4.7 11.9 1.0 CB A:ALA306 4.7 11.2 1.0 NZ D:LYS278 4.8 30.9 1.0 O B:HOH465 4.9 27.1 1.0 CD B:GLU273 4.9 26.5 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of A Putative Racemase with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Putative Racemase with Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg505 b:29.4 occ:1.00 O D:HOH466 1.9 17.8 1.0 O1 D:GOL601 2.0 31.8 1.0 O2 D:GOL601 2.1 34.7 1.0 OE2 D:GLU238 2.1 18.9 1.0 OE2 D:GLU264 2.2 26.7 1.0 OD2 D:ASP211 2.2 22.4 1.0 C2 D:GOL601 2.8 35.6 1.0 CD D:GLU264 2.9 23.8 1.0 C1 D:GOL601 2.9 33.9 1.0 OE1 D:GLU264 3.0 25.2 1.0 CG D:ASP211 3.2 20.3 1.0 CD D:GLU238 3.3 19.0 1.0 OD1 D:ASP211 3.5 18.6 1.0 NZ D:LYS177 4.1 18.9 1.0 OE1 D:GLU238 4.2 17.7 1.0 CG D:GLU238 4.2 16.5 1.0 C3 D:GOL601 4.2 35.5 1.0 CG D:GLU264 4.3 21.9 1.0 CD2 D:HIS314 4.3 18.1 1.0 NE2 D:HIS314 4.5 20.2 1.0 O D:HOH460 4.5 25.5 1.0 CB D:ASP211 4.6 20.6 1.0 O3 D:GOL601 4.6 35.2 1.0 CD2 D:LEU213 4.7 21.0 1.0 CB D:ALA239 5.0 12.8 1.0

S.Eswaramoorthy, E.Raparia, S.K.Burley, S.Swaminathan. Crystal Structure of A Putative Racemase with Mg Ion To Be Published.