Zinc in PDB 2rag: Crystal Structure of Aminohydrolase From Caulobacter Crescentus

The structure of Crystal Structure of Aminohydrolase From Caulobacter Crescentus, PDB code: 2rag was solved by A.A.Fedorov, E.V.Fedorov, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.672, 129.238, 99.226, 90.00, 104.76, 90.00
R / Rfree (%)	23.8 / 25

The structure of Crystal Structure of Aminohydrolase From Caulobacter Crescentus also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus (pdb code 2rag). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus, PDB code: 2rag:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn418 b:36.7 occ:1.00 OE1 A:GLU159 2.1 26.1 1.0 NE2 A:HIS53 2.2 31.5 1.0 OD2 A:ASP55 2.4 29.2 1.0 O A:HOH421 2.4 30.5 1.0 OD1 A:ASP55 2.6 24.8 1.0 CG A:ASP55 2.8 32.9 1.0 CD A:GLU159 2.9 26.2 1.0 OE2 A:GLU159 3.0 28.9 1.0 CE1 A:HIS53 3.1 30.1 1.0 CD2 A:HIS53 3.3 31.0 1.0 ZN A:ZN419 3.6 36.1 1.0 O A:HOH595 3.7 49.4 1.0 OD1 A:ASP360 4.0 36.1 1.0 CG A:GLU159 4.3 26.0 1.0 ND1 A:HIS53 4.3 31.2 1.0 CB A:ASP55 4.3 28.2 1.0 NE2 A:HIS250 4.4 27.7 1.0 CG A:HIS53 4.4 29.8 1.0 CG A:TYR98 4.6 27.8 1.0 CG1 A:VAL96 4.6 22.8 1.0 CD1 A:TYR98 4.6 28.2 1.0 CB A:TYR98 4.6 26.5 1.0 CB A:GLU159 4.6 24.6 1.0 CE1 A:HIS250 4.8 27.7 1.0 O A:HOH467 4.8 26.5 1.0 CA A:GLY363 4.9 34.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn419 b:36.1 occ:1.00 NE2 A:HIS250 2.2 27.7 1.0 OE2 A:GLU159 2.3 28.9 1.0 NE2 A:HIS229 2.3 34.1 1.0 CL A:CL420 2.9 52.4 1.0 CD2 A:HIS250 3.1 28.7 1.0 CE1 A:HIS250 3.2 27.7 1.0 CD2 A:HIS229 3.3 32.3 1.0 CE1 A:HIS229 3.3 33.0 1.0 CD A:GLU159 3.5 26.2 1.0 ZN A:ZN418 3.6 36.7 1.0 NH2 A:ARG261 3.7 37.2 1.0 O A:HOH595 3.9 49.4 1.0 NE2 A:HIS53 4.0 31.5 1.0 OE1 A:GLU159 4.0 26.1 1.0 NE2 A:HIS186 4.1 30.7 1.0 OD1 A:ASP360 4.2 36.1 1.0 CG A:HIS250 4.3 30.0 1.0 OD2 A:ASP360 4.3 40.2 1.0 ND1 A:HIS250 4.3 28.1 1.0 CD2 A:HIS186 4.4 28.8 1.0 ND1 A:HIS229 4.4 33.3 1.0 CG A:HIS229 4.4 32.6 1.0 CE1 A:HIS53 4.5 30.1 1.0 CD2 A:HIS53 4.6 31.0 1.0 CG A:ASP360 4.6 37.9 1.0 CG A:GLU159 4.6 26.0 1.0 CZ A:ARG261 4.7 38.1 1.0 O A:HOH421 4.7 30.5 1.0 NE A:ARG261 4.8 37.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn418 b:39.1 occ:1.00 OE1 B:GLU159 2.1 26.4 1.0 NE2 B:HIS53 2.3 32.1 1.0 OD2 B:ASP55 2.3 32.4 1.0 O B:HOH421 2.4 38.5 1.0 OD1 B:ASP55 2.6 32.2 1.0 CG B:ASP55 2.8 35.3 1.0 CD B:GLU159 2.9 26.6 1.0 OE2 B:GLU159 3.0 30.3 1.0 CE1 B:HIS53 3.2 29.6 1.0 CD2 B:HIS53 3.3 30.0 1.0 ZN B:ZN419 3.6 47.2 1.0 O B:HOH576 3.9 52.1 1.0 OD1 B:ASP360 4.0 37.8 1.0 CG B:GLU159 4.3 26.9 1.0 CB B:ASP55 4.3 32.8 1.0 ND1 B:HIS53 4.3 30.8 1.0 CG B:HIS53 4.4 32.8 1.0 NE2 B:HIS250 4.4 33.6 1.0 CG1 B:VAL96 4.6 29.2 1.0 CG B:TYR98 4.6 32.9 1.0 CD1 B:TYR98 4.6 33.7 1.0 CB B:TYR98 4.6 30.3 1.0 CB B:GLU159 4.7 25.6 1.0 CE1 B:HIS250 4.8 33.7 1.0 CA B:GLY363 4.9 36.0 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn419 b:47.2 occ:1.00 NE2 B:HIS250 2.2 33.6 1.0 OE2 B:GLU159 2.3 30.3 1.0 NE2 B:HIS229 2.3 32.0 1.0 CL B:CL420 2.9 50.1 1.0 CD2 B:HIS250 3.1 33.0 1.0 CE1 B:HIS250 3.3 33.7 1.0 CD2 B:HIS229 3.3 30.5 1.0 CE1 B:HIS229 3.3 31.2 1.0 CD B:GLU159 3.4 26.6 1.0 ZN B:ZN418 3.6 39.1 1.0 NH2 B:ARG261 3.7 40.6 1.0 O B:HOH576 3.9 52.1 1.0 NE2 B:HIS53 3.9 32.1 1.0 OE1 B:GLU159 4.0 26.4 1.0 NE2 B:HIS186 4.1 33.6 1.0 OD1 B:ASP360 4.2 37.8 1.0 OD2 B:ASP360 4.3 41.6 1.0 CG B:HIS250 4.3 33.7 1.0 ND1 B:HIS250 4.3 32.0 1.0 CD2 B:HIS186 4.4 32.5 1.0 ND1 B:HIS229 4.4 31.0 1.0 CG B:HIS229 4.4 30.4 1.0 CE1 B:HIS53 4.5 29.6 1.0 CD2 B:HIS53 4.6 30.0 1.0 CG B:ASP360 4.6 38.6 1.0 CG B:GLU159 4.7 26.9 1.0 CZ B:ARG261 4.7 41.3 1.0 NE B:ARG261 4.8 39.0 1.0 O B:HOH421 4.9 38.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn418 b:52.3 occ:1.00 OE1 C:GLU159 2.1 34.5 1.0 NE2 C:HIS53 2.2 35.5 1.0 OD2 C:ASP55 2.4 41.9 1.0 O C:HOH421 2.4 43.0 1.0 OD1 C:ASP55 2.5 39.0 1.0 CG C:ASP55 2.8 42.5 1.0 CD C:GLU159 2.9 36.1 1.0 OE2 C:GLU159 3.0 36.0 1.0 CE1 C:HIS53 3.1 36.9 1.0 CD2 C:HIS53 3.3 36.8 1.0 ZN C:ZN419 3.6 59.7 1.0 O C:HOH518 3.8 58.3 1.0 OD1 C:ASP360 4.0 46.6 1.0 CG C:GLU159 4.3 33.7 1.0 ND1 C:HIS53 4.3 37.7 1.0 CB C:ASP55 4.3 40.0 1.0 CG C:HIS53 4.4 37.7 1.0 NE2 C:HIS250 4.4 39.3 1.0 CG1 C:VAL96 4.6 33.2 1.0 CG C:TYR98 4.6 37.9 1.0 CD1 C:TYR98 4.6 37.6 1.0 CB C:TYR98 4.6 37.1 1.0 CB C:GLU159 4.6 33.8 1.0 CE1 C:HIS250 4.8 39.9 1.0 O C:HOH486 4.9 37.9 1.0 CA C:GLY363 4.9 44.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn419 b:59.7 occ:1.00 NE2 C:HIS250 2.2 39.3 1.0 OE2 C:GLU159 2.3 36.0 1.0 NE2 C:HIS229 2.3 42.7 1.0 CL C:CL420 3.0 52.6 1.0 CD2 C:HIS250 3.1 39.4 1.0 CE1 C:HIS250 3.2 39.9 1.0 CD2 C:HIS229 3.2 41.9 1.0 CE1 C:HIS229 3.3 40.8 1.0 CD C:GLU159 3.4 36.1 1.0 O C:HOH518 3.5 58.3 1.0 ZN C:ZN418 3.6 52.3 1.0 NH2 C:ARG261 3.7 43.2 1.0 NE2 C:HIS53 3.9 35.5 1.0 OE1 C:GLU159 4.0 34.5 1.0 NE2 C:HIS186 4.1 42.2 1.0 OD1 C:ASP360 4.2 46.6 1.0 CG C:HIS250 4.3 39.5 1.0 OD2 C:ASP360 4.3 48.1 1.0 ND1 C:HIS250 4.3 39.4 1.0 CD2 C:HIS186 4.4 41.5 1.0 ND1 C:HIS229 4.4 39.3 1.0 CG C:HIS229 4.4 38.9 1.0 CE1 C:HIS53 4.5 36.9 1.0 CD2 C:HIS53 4.6 36.8 1.0 CG C:GLU159 4.6 33.7 1.0 CG C:ASP360 4.6 44.2 1.0 O C:HOH421 4.7 43.0 1.0 CZ C:ARG261 4.7 43.7 1.0 NE C:ARG261 4.8 43.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn418 b:51.8 occ:1.00 O D:HOH421 2.0 46.6 1.0 OE1 D:GLU159 2.1 39.2 1.0 NE2 D:HIS53 2.2 38.3 1.0 OD2 D:ASP55 2.4 43.0 1.0 OD1 D:ASP55 2.6 41.5 1.0 CG D:ASP55 2.8 43.5 1.0 CD D:GLU159 2.9 35.6 1.0 OE2 D:GLU159 3.0 36.6 1.0 CE1 D:HIS53 3.2 37.6 1.0 CD2 D:HIS53 3.3 38.9 1.0 O D:HOH515 3.6 55.4 1.0 ZN D:ZN419 3.6 62.7 1.0 OD1 D:ASP360 4.0 47.4 1.0 CG D:GLU159 4.3 35.3 1.0 ND1 D:HIS53 4.3 37.9 1.0 CB D:ASP55 4.3 41.0 1.0 CG D:HIS53 4.4 38.3 1.0 NE2 D:HIS250 4.4 40.9 1.0 CG1 D:VAL96 4.6 37.4 1.0 CG D:TYR98 4.6 35.9 1.0 CD1 D:TYR98 4.6 35.8 1.0 CB D:TYR98 4.6 35.6 1.0 CB D:GLU159 4.7 34.9 1.0 CE1 D:HIS250 4.8 38.9 1.0 O D:HOH463 4.9 33.9 1.0 CA D:GLY363 4.9 45.3 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Aminohydrolase From Caulobacter Crescentus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Aminohydrolase From Caulobacter Crescentus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn419 b:62.7 occ:1.00 NE2 D:HIS250 2.2 40.9 1.0 OE2 D:GLU159 2.3 36.6 1.0 NE2 D:HIS229 2.3 40.2 1.0 CL D:CL420 2.8 50.8 1.0 CD2 D:HIS250 3.1 39.5 1.0 O D:HOH515 3.2 55.4 1.0 CE1 D:HIS250 3.3 38.9 1.0 CD2 D:HIS229 3.3 36.9 1.0 CE1 D:HIS229 3.3 35.5 1.0 CD D:GLU159 3.5 35.6 1.0 ZN D:ZN418 3.6 51.8 1.0 NH2 D:ARG261 3.7 41.8 1.0 NE2 D:HIS53 4.0 38.3 1.0 OE1 D:GLU159 4.0 39.2 1.0 NE2 D:HIS186 4.1 37.5 1.0 OD1 D:ASP360 4.2 47.4 1.0 OD2 D:ASP360 4.3 47.8 1.0 CG D:HIS250 4.3 39.7 1.0 ND1 D:HIS250 4.3 40.4 1.0 CD2 D:HIS186 4.4 36.9 1.0 ND1 D:HIS229 4.4 37.6 1.0 CG D:HIS229 4.4 37.2 1.0 O D:HOH421 4.5 46.6 1.0 CE1 D:HIS53 4.5 37.6 1.0 CG D:ASP360 4.6 46.8 1.0 CD2 D:HIS53 4.6 38.9 1.0 CG D:GLU159 4.7 35.3 1.0 CZ D:ARG261 4.7 43.3 1.0 NE D:ARG261 4.8 43.3 1.0

A.A.Fedorov, E.V.Fedorov, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Aminohydrolase From Caulobacter Crescentus. To Be Published.