Zinc in PDB 3dug: Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc

The structure of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc, PDB code: 3dug was solved by Y.Patskovsky, U.A.Ramagopal, R.Toro, A.J.Meyer, J.Freeman, M.Iizuka, K.Bain, L.Rodgers, F.Raushel, J.M.Sauder, S.K.Burley, S.C.Almo, New Yorksgx 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)	20.00 / 2.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.325, 146.040, 255.646, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 26.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc (pdb code 3dug). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc, PDB code: 3dug:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn425 b:92.8 occ:1.00 NE2 A:HIS62 2.1 69.0 1.0 NE2 A:HIS64 2.4 81.1 1.0 OD1 A:ASP315 2.7 85.0 1.0 OD2 A:ASP315 2.7 85.3 1.0 CG A:ASP315 2.9 83.8 1.0 CD2 A:HIS62 3.0 68.7 1.0 CD2 A:HIS64 3.2 78.4 1.0 OQ2 A:KCX182 3.2 0.3 1.0 CE1 A:HIS62 3.2 69.9 1.0 CE1 A:HIS64 3.5 79.8 1.0 N A:ARG429 3.7 83.3 1.0 CX A:KCX182 3.7 0.1 1.0 OQ1 A:KCX182 3.8 98.1 1.0 ZN A:ZN428 3.8 0.3 0.8 CG A:HIS62 4.2 68.1 1.0 CG1 A:VAL105 4.2 67.8 1.0 ND1 A:HIS62 4.2 68.0 1.0 CB A:ASP315 4.3 82.7 1.0 CG A:HIS64 4.4 76.5 1.0 NE2 A:HIS243 4.4 78.7 1.0 CE1 A:HIS243 4.5 78.2 1.0 ND1 A:HIS64 4.5 79.0 1.0 NZ A:KCX182 4.6 95.5 1.0 CA A:ARG429 4.7 84.2 1.0 CA A:ASP315 4.7 82.2 1.0

Zinc binding site 2 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn426 b:0.5 occ:1.00 NE2 A:HIS304 2.3 95.2 1.0 OE2 A:GLU340 2.4 76.2 1.0 OE1 A:GLU340 2.5 74.0 1.0 CD A:GLU340 2.8 77.1 1.0 CE1 A:HIS304 3.2 92.0 1.0 CD2 A:HIS304 3.3 92.5 1.0 O A:GLY335 3.9 84.0 1.0 ND1 A:HIS304 4.3 94.8 1.0 CG A:GLU340 4.3 72.7 1.0 CG A:HIS304 4.3 92.2 1.0 CG2 A:THR337 4.6 77.3 1.0 N A:THR337 4.7 79.0 1.0 CA A:MET336 4.8 79.4 1.0 C A:GLY335 5.0 82.7 1.0

Zinc binding site 3 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn427 b:0.9 occ:1.00 OG1 A:THR128 2.4 68.5 1.0 OE2 A:GLU392 2.6 76.9 1.0 CB A:THR128 3.3 58.9 1.0 CD A:GLU392 3.5 75.1 1.0 CG A:GLU392 3.8 72.4 1.0 OD2 A:ASP368 3.9 68.4 1.0 CG2 A:THR128 4.0 51.4 1.0 OG1 A:THR101 4.2 67.0 1.0 OD1 A:ASP368 4.4 75.4 1.0 O A:THR100 4.4 63.7 1.0 CG A:ASP368 4.6 71.1 1.0 CA A:THR128 4.6 58.3 1.0 CE A:LYS391 4.6 63.7 1.0 OE1 A:GLU392 4.7 80.3 1.0 OD1 A:ASP366 4.7 75.2 1.0 N A:THR128 4.7 56.8 1.0 CG A:LYS391 4.8 73.2 1.0 CD A:LYS391 4.8 68.6 1.0

Zinc binding site 4 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn428 b:0.3 occ:0.80 OQ1 A:KCX182 2.4 98.1 1.0 ND1 A:HIS223 2.4 86.0 1.0 NE2 A:HIS243 2.4 78.7 1.0 OQ2 A:KCX182 2.5 0.3 1.0 CX A:KCX182 2.7 0.1 1.0 CE1 A:HIS223 3.0 85.5 1.0 N A:ARG429 3.2 83.3 1.0 CA A:ARG429 3.2 84.2 1.0 CD2 A:HIS243 3.3 73.4 1.0 CE1 A:HIS243 3.3 78.2 1.0 CG A:HIS223 3.4 81.8 1.0 C A:ARG429 3.8 85.5 1.0 ZN A:ZN425 3.8 92.8 1.0 NE2 A:HIS142 3.8 84.2 1.0 CB A:HIS223 3.9 71.0 1.0 O A:ARG429 4.0 85.2 1.0 NZ A:KCX182 4.0 95.5 1.0 NE2 A:HIS223 4.2 87.4 1.0 CD2 A:HIS142 4.3 79.7 1.0 CE1 A:HIS62 4.3 69.9 1.0 NE2 A:HIS62 4.3 69.0 1.0 OD2 A:ASP315 4.4 85.3 1.0 ND1 A:HIS243 4.4 77.6 1.0 CD2 A:HIS223 4.4 83.9 1.0 CG A:HIS243 4.4 73.7 1.0 CB A:ARG429 4.6 85.0 1.0 OXT A:ARG429 4.6 86.5 1.0 CA A:HIS223 4.9 67.9 1.0 CE A:KCX182 4.9 87.3 1.0 CE1 A:HIS142 4.9 83.1 1.0

Zinc binding site 5 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn425 b:85.3 occ:1.00 NE2 B:HIS62 2.1 70.3 1.0 NE2 B:HIS64 2.6 79.2 1.0 OD2 B:ASP315 2.6 88.3 1.0 OD1 B:ASP315 2.8 87.6 1.0 OQ2 B:KCX182 3.0 0.7 1.0 CG B:ASP315 3.0 86.2 1.0 CD2 B:HIS62 3.1 66.3 1.0 CE1 B:HIS62 3.1 69.8 1.0 N B:ARG429 3.4 67.4 1.0 CD2 B:HIS64 3.4 77.3 1.0 CX B:KCX182 3.5 0.1 1.0 OQ1 B:KCX182 3.6 99.5 1.0 CE1 B:HIS64 3.6 79.1 1.0 ZN B:ZN428 3.7 87.2 0.8 NE2 B:HIS243 4.1 82.2 1.0 ND1 B:HIS62 4.2 68.0 1.0 CG B:HIS62 4.2 64.9 1.0 CB B:ASP315 4.3 82.2 1.0 CG1 B:VAL105 4.3 70.6 1.0 CE1 B:HIS243 4.3 75.2 1.0 CA B:ARG429 4.5 73.4 1.0 NZ B:KCX182 4.6 94.9 1.0 CG B:HIS64 4.6 74.1 1.0 ND1 B:HIS64 4.7 76.8 1.0 CA B:ASP315 4.8 80.8 1.0

Zinc binding site 6 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn426 b:77.5 occ:0.50 OE2 B:GLU340 2.4 69.3 1.0 NE2 B:HIS304 2.5 95.4 1.0 OE1 B:GLU340 2.7 68.1 1.0 CD B:GLU340 3.0 71.5 1.0 CE1 B:HIS304 3.4 94.0 1.0 CD2 B:HIS304 3.4 92.0 1.0 O B:GLY335 4.1 80.5 1.0 ND1 B:HIS304 4.4 92.6 1.0 CG B:GLU340 4.5 69.3 1.0 CG B:HIS304 4.5 90.5 1.0 CG2 B:THR337 4.7 75.5 1.0

Zinc binding site 7 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn427 b:80.9 occ:0.50 OG1 B:THR128 2.3 63.3 1.0 OE2 B:GLU392 2.5 73.0 1.0 CB B:THR128 3.2 57.2 1.0 CD B:GLU392 3.5 74.0 1.0 CG2 B:THR128 3.8 50.8 1.0 CG B:GLU392 3.8 74.1 1.0 OD2 B:ASP368 4.1 73.4 1.0 OG1 B:THR101 4.3 65.5 1.0 CA B:THR128 4.5 54.7 1.0 OE1 B:GLU392 4.6 79.0 1.0 OD1 B:ASP366 4.6 79.2 1.0 O B:THR100 4.6 67.0 1.0 OD1 B:ASP368 4.7 73.1 1.0 N B:THR128 4.8 54.3 1.0 CG B:ASP368 4.8 73.4 1.0 CE B:LYS391 4.8 67.2 1.0 CD B:LYS391 5.0 71.1 1.0

Zinc binding site 8 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn428 b:87.2 occ:0.80 ND1 B:HIS223 2.2 79.1 1.0 OQ1 B:KCX182 2.3 99.5 1.0 NE2 B:HIS243 2.4 82.2 1.0 OQ2 B:KCX182 2.6 0.7 1.0 CX B:KCX182 2.7 0.1 1.0 CE1 B:HIS223 3.0 83.1 1.0 CD2 B:HIS243 3.1 79.4 1.0 CG B:HIS223 3.2 77.1 1.0 N B:ARG429 3.3 67.4 1.0 CA B:ARG429 3.4 73.4 1.0 CE1 B:HIS243 3.5 75.2 1.0 CB B:HIS223 3.6 66.7 1.0 ZN B:ZN425 3.7 85.3 1.0 NE2 B:HIS142 3.9 84.8 1.0 NZ B:KCX182 4.0 94.9 1.0 C B:ARG429 4.1 69.6 1.0 NE2 B:HIS223 4.1 85.1 1.0 O B:ARG429 4.1 61.2 1.0 CD2 B:HIS223 4.2 81.8 1.0 CE1 B:HIS62 4.3 69.8 1.0 CD2 B:HIS142 4.3 79.5 1.0 CG B:HIS243 4.3 72.8 1.0 NE2 B:HIS62 4.4 70.3 1.0 ND1 B:HIS243 4.4 72.4 1.0 OD2 B:ASP315 4.5 88.3 1.0 CA B:HIS223 4.6 65.2 1.0 CE B:KCX182 4.7 83.4 1.0 CB B:ARG429 4.8 74.7 1.0 CE1 B:HIS142 5.0 83.6 1.0 OXT B:ARG429 5.0 66.7 1.0

Zinc binding site 9 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn425 b:93.2 occ:1.00 NE2 C:HIS62 2.1 70.1 1.0 NE2 C:HIS64 2.5 80.6 1.0 OD2 C:ASP315 2.8 87.3 1.0 OD1 C:ASP315 2.8 90.0 1.0 CD2 C:HIS62 3.0 69.4 1.0 CG C:ASP315 3.1 86.5 1.0 CE1 C:HIS62 3.1 73.0 1.0 OQ2 C:KCX182 3.1 0.7 1.0 CD2 C:HIS64 3.3 77.5 1.0 N C:ARG429 3.4 85.0 1.0 CE1 C:HIS64 3.5 78.8 1.0 CX C:KCX182 3.6 0.6 1.0 ZN C:ZN428 3.7 0.2 0.8 OQ1 C:KCX182 3.7 97.7 1.0 ND1 C:HIS62 4.2 73.4 1.0 CG C:HIS62 4.2 68.3 1.0 CG1 C:VAL105 4.3 67.7 1.0 NE2 C:HIS243 4.3 84.4 1.0 CE1 C:HIS243 4.4 82.1 1.0 CB C:ASP315 4.4 81.6 1.0 CG C:HIS64 4.5 73.4 1.0 NZ C:KCX182 4.6 95.8 1.0 ND1 C:HIS64 4.6 78.5 1.0 CA C:ASP315 4.8 81.0 1.0 CA C:ARG429 4.8 89.7 1.0

Zinc binding site 10 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn426 b:0.9 occ:1.00 NE2 C:HIS304 2.5 96.8 1.0 OE1 C:GLU340 2.6 75.2 1.0 OE2 C:GLU340 2.6 69.6 1.0 O C:HOH455 2.6 69.7 1.0 CD C:GLU340 2.9 75.0 1.0 CD2 C:HIS304 3.4 95.5 1.0 CE1 C:HIS304 3.5 92.8 1.0 O C:GLY335 3.9 86.4 1.0 CG C:GLU340 4.5 72.7 1.0 ND1 C:HIS304 4.5 92.5 1.0 CG2 C:THR337 4.5 77.0 1.0 CG C:HIS304 4.6 91.9 1.0 N C:THR337 4.8 78.8 1.0 CA C:MET336 4.8 78.9 1.0

D.F.Xiang, Y.Patskovsky, C.Xu, A.J.Meyer, J.M.Sauder, S.K.Burley, S.C.Almo, F.M.Raushel. Functional Identification of Incorrectly Annotated Prolidases From the Amidohydrolase Superfamily of Enzymes. Biochemistry V. 48 3730 2009.
ISSN: ISSN 0006-2960
PubMed: 19281183
DOI: 10.1021/BI900111Q