Calcium in PDB 3n4e: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222, PDB code: 3n4e was solved by V.N.Malashkevich, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, 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)	19.93 / 2.40
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.711, 137.711, 80.363, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 21.3

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 (pdb code 3n4e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222, PDB code: 3n4e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:24.3 occ:1.00 OD2 A:ASP197 2.2 18.8 1.0 OE2 A:GLU223 2.3 21.2 1.0 O A:HOH419 2.3 15.1 1.0 OE2 A:GLU249 2.3 31.8 1.0 O A:HOH418 2.7 24.0 1.0 O A:HOH556 2.8 11.7 1.0 OE1 A:GLU249 3.0 32.2 1.0 CD A:GLU249 3.0 19.3 1.0 CG A:ASP197 3.3 25.8 1.0 CD A:GLU223 3.4 21.3 1.0 OD1 A:ASP197 3.7 18.7 1.0 ND2 A:ASN199 3.9 15.3 1.0 CG A:GLU223 4.0 20.2 1.0 CD2 A:HIS298 4.1 20.8 1.0 CD A:ARG162 4.3 21.0 1.0 NZ A:LYS160 4.3 18.1 1.0 O A:HOH445 4.3 24.0 1.0 OE1 A:GLU223 4.4 20.0 1.0 CG A:GLU249 4.5 31.4 1.0 OE1 A:GLU224 4.5 25.6 1.0 NE2 A:HIS298 4.6 21.4 1.0 CB A:ASP197 4.6 18.9 1.0 CE A:LYS160 4.6 20.7 1.0 NE A:ARG162 4.9 21.1 1.0 CG A:ASN199 5.0 29.8 1.0 O A:HOH420 5.0 23.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:49.7 occ:1.00 O A:HOH495 2.4 19.8 1.0 O A:HOH497 2.5 30.1 1.0 OE2 A:GLU64 2.5 38.1 1.0 O A:HOH496 2.6 19.2 1.0 OE1 A:GLU64 2.6 39.1 1.0 CD A:GLU64 2.9 31.9 1.0 CG A:GLU64 4.5 38.0 1.0 CG A:LYS7 4.8 49.3 1.0 O A:VAL8 4.8 28.1 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:43.7 occ:0.50 O A:HOH580 2.3 29.9 1.0 O A:VAL359 2.4 32.2 1.0 OE1 A:GLU361 2.4 45.3 1.0 CD A:GLU361 3.5 35.3 1.0 C A:VAL359 3.6 32.0 1.0 OE2 A:GLU361 3.8 45.0 1.0 N A:GLU361 4.2 33.1 1.0 CA A:ASP360 4.2 32.4 1.0 N A:ASP360 4.3 32.1 1.0 N A:VAL359 4.7 31.3 1.0 CA A:VAL359 4.7 31.7 1.0 C A:ASP360 4.7 32.6 1.0 CG A:GLU361 4.8 44.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:28.4 occ:1.00 OE2 B:GLU223 2.3 24.4 1.0 O B:HOH415 2.4 28.6 1.0 OE1 B:GLU249 2.4 22.1 1.0 OD2 B:ASP197 2.4 18.4 1.0 O B:HOH416 2.5 15.5 1.0 O B:HOH414 2.6 25.5 1.0 OE2 B:GLU249 2.7 21.2 1.0 CD B:GLU249 2.9 20.5 1.0 CG B:ASP197 3.4 17.7 1.0 CD B:GLU223 3.5 19.5 1.0 OD1 B:ASP197 3.8 17.6 1.0 ND2 B:ASN199 3.9 20.2 1.0 ND1 B:HIS298 4.0 20.4 1.0 CG B:GLU223 4.2 23.8 1.0 O B:HOH420 4.2 24.8 1.0 NZ B:LYS160 4.2 20.1 1.0 CE1 B:HIS298 4.2 20.3 1.0 CG B:GLU249 4.4 21.1 1.0 OE1 B:GLU224 4.4 30.6 1.0 CD B:ARG162 4.4 22.8 1.0 OE1 B:GLU223 4.5 23.9 1.0 O B:HOH421 4.6 19.3 1.0 CB B:ASP197 4.7 17.9 1.0 CE B:LYS160 4.7 15.5 1.0 O B:HOH496 5.0 21.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:37.6 occ:0.50 O B:HOH471 2.3 21.3 1.0 O B:HOH413 2.5 27.6 1.0 OE1 B:GLU67 2.5 31.2 1.0 OE2 B:GLU67 2.9 31.0 1.0 CD B:GLU67 3.1 26.3 1.0 CB B:SER2 4.4 42.1 1.0 CG B:GLU67 4.6 30.9 1.0 OG B:SER2 4.6 56.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:40.0 occ:1.00 O B:HOH488 2.4 31.1 1.0 O B:HOH483 2.4 16.6 1.0 OE2 B:GLU64 2.6 33.1 1.0 O B:HOH484 2.6 21.2 1.0 OE1 B:GLU64 2.6 34.0 1.0 O B:HOH489 2.6 18.3 1.0 CD B:GLU64 3.0 25.9 1.0 CG B:GLU64 4.5 33.1 1.0 O B:HOH473 4.5 15.4 1.0 CG B:LYS7 4.5 46.4 1.0 O B:VAL8 4.7 23.6 1.0 N B:VAL8 5.0 24.6 1.0

V.N.Malashkevich, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 To Be Published.