Zinc in PDB 3n2c: Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline

The structure of Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline, PDB code: 3n2c was solved by Y.Patskovsky, C.Xu, J.M.Sauder, S.K.Burley, F.M.Raushel, 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)	40.00 / 2.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	113.186, 108.035, 170.772, 81.32, 80.47, 73.76
R / Rfree (%)	22 / 27.3

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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline (pdb code 3n2c). 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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline, PDB code: 3n2c:
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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn425 b:86.5 occ:1.00 OQ2 A:KCX188 2.0 0.6 1.0 NE2 A:HIS63 2.2 79.7 1.0 NE2 A:HIS65 2.2 77.4 1.0 O2 A:LWY427 2.3 97.5 1.0 OD1 A:ASP321 2.4 93.3 1.0 CD2 A:HIS65 3.0 63.3 1.0 CX A:KCX188 3.0 0.0 1.0 CD2 A:HIS63 3.1 71.8 1.0 CE1 A:HIS63 3.2 68.7 1.0 CE1 A:HIS65 3.2 69.8 1.0 CG A:ASP321 3.3 88.0 1.0 C1 A:LWY427 3.4 0.1 1.0 P A:LWY427 3.5 95.4 1.0 OQ1 A:KCX188 3.6 0.0 1.0 OD2 A:ASP321 3.7 98.5 1.0 ZN A:ZN426 3.8 99.2 1.0 NZ A:KCX188 4.0 0.4 1.0 CB A:ALA106 4.0 52.2 1.0 CG A:HIS65 4.1 65.8 1.0 ND1 A:HIS65 4.2 72.5 1.0 CG A:HIS63 4.2 63.6 1.0 ND1 A:HIS63 4.3 55.8 1.0 NE2 A:HIS249 4.4 66.7 1.0 CB A:ASP321 4.5 74.1 1.0 CE1 A:HIS249 4.5 68.1 1.0 N A:LWY427 4.6 0.4 1.0 O1 A:LWY427 4.6 96.4 1.0

Zinc binding site 2 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn426 b:99.2 occ:1.00 OQ1 A:KCX188 2.1 0.0 1.0 O2 A:LWY427 2.4 97.5 1.0 ND1 A:HIS229 2.4 52.8 1.0 NE2 A:HIS249 2.7 66.7 1.0 CX A:KCX188 3.0 0.0 1.0 CE1 A:HIS229 3.2 62.7 1.0 CG A:HIS229 3.2 44.8 1.0 OQ2 A:KCX188 3.2 0.6 1.0 P A:LWY427 3.3 95.4 1.0 O1 A:LWY427 3.4 96.4 1.0 CD2 A:HIS249 3.5 71.8 1.0 CB A:HIS229 3.6 53.5 1.0 CE1 A:HIS249 3.6 68.1 1.0 ZN A:ZN425 3.8 86.5 1.0 NE2 A:HIS140 3.9 82.2 1.0 CD2 A:HIS140 3.9 82.8 1.0 CA A:LWY427 4.0 0.1 1.0 NE2 A:HIS229 4.0 66.7 1.0 CD2 A:HIS229 4.1 56.4 1.0 N A:LWY427 4.2 0.4 1.0 OXT A:LWY427 4.3 0.0 1.0 NZ A:KCX188 4.3 0.4 1.0 C A:LWY427 4.3 0.3 1.0 NE2 A:HIS63 4.6 79.7 1.0 SD A:MET190 4.6 83.7 1.0 CE1 A:HIS63 4.6 68.7 1.0 CG A:HIS249 4.7 72.6 1.0 C1 A:LWY427 4.7 0.1 1.0 ND1 A:HIS249 4.7 69.8 1.0 CA A:HIS229 4.8 55.5 1.0 CE A:KCX188 4.8 99.1 1.0 OD2 A:ASP321 4.9 98.5 1.0 CE A:MET190 5.0 86.1 1.0

Zinc binding site 3 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn425 b:78.9 occ:1.00 O2 B:LWY427 1.8 83.5 1.0 NE2 B:HIS65 2.1 72.0 1.0 NE2 B:HIS63 2.2 66.1 1.0 OQ2 B:KCX188 2.2 89.9 1.0 OD1 B:ASP321 2.6 77.7 1.0 CD2 B:HIS65 3.0 60.1 1.0 CD2 B:HIS63 3.0 54.8 1.0 CE1 B:HIS65 3.1 67.5 1.0 CX B:KCX188 3.3 82.2 1.0 P B:LWY427 3.3 81.6 1.0 CE1 B:HIS63 3.3 52.4 1.0 CG B:ASP321 3.4 72.5 1.0 OD2 B:ASP321 3.6 78.1 1.0 C1 B:LWY427 3.8 74.7 1.0 ZN B:ZN426 3.9 84.9 1.0 OQ1 B:KCX188 3.9 88.0 1.0 CB B:ALA106 4.1 48.7 1.0 NZ B:KCX188 4.1 73.1 1.0 CG B:HIS65 4.2 49.8 1.0 O1 B:LWY427 4.2 79.2 1.0 ND1 B:HIS65 4.2 65.3 1.0 CG B:HIS63 4.2 40.8 1.0 ND1 B:HIS63 4.3 46.9 1.0 N B:LWY427 4.4 78.4 1.0 NE2 B:HIS249 4.5 62.1 1.0 CB B:ASP321 4.6 64.1 1.0 CE1 B:HIS249 4.6 64.7 1.0 CD B:LWY427 4.9 77.8 1.0 O B:ALA106 4.9 62.5 1.0

Zinc binding site 4 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn426 b:84.9 occ:1.00 O1 B:LWY427 2.1 79.2 1.0 ND1 B:HIS229 2.2 65.5 1.0 OQ1 B:KCX188 2.3 88.0 1.0 NE2 B:HIS249 2.3 62.1 1.0 O2 B:LWY427 3.0 83.5 1.0 P B:LWY427 3.0 81.6 1.0 CE1 B:HIS229 3.0 66.2 1.0 CX B:KCX188 3.1 82.2 1.0 CG B:HIS229 3.1 65.5 1.0 CD2 B:HIS249 3.2 57.0 1.0 CE1 B:HIS249 3.4 64.7 1.0 OQ2 B:KCX188 3.4 89.9 1.0 CB B:HIS229 3.5 45.9 1.0 ZN B:ZN425 3.9 78.9 1.0 N B:LWY427 4.1 78.4 1.0 NE2 B:HIS229 4.1 76.5 1.0 NZ B:KCX188 4.2 73.1 1.0 CD2 B:HIS229 4.2 74.4 1.0 CA B:LWY427 4.2 75.8 1.0 C1 B:LWY427 4.3 74.7 1.0 NE2 B:HIS140 4.3 63.0 1.0 CG B:HIS249 4.4 60.9 1.0 CE1 B:HIS63 4.4 52.4 1.0 NE2 B:HIS63 4.4 66.1 1.0 ND1 B:HIS249 4.4 67.8 1.0 CD2 B:HIS140 4.4 57.8 1.0 CA B:HIS229 4.6 47.0 1.0 CE B:KCX188 4.6 68.2 1.0 C B:LWY427 4.7 76.8 1.0 SD B:MET190 4.7 74.3 1.0 OD2 B:ASP321 4.9 78.1 1.0 OXT B:LWY427 4.9 73.5 1.0

Zinc binding site 5 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn425 b:90.8 occ:1.00 O2 C:LWY427 2.2 0.9 1.0 OQ2 C:KCX188 2.2 85.5 1.0 NE2 C:HIS63 2.2 65.3 1.0 NE2 C:HIS65 2.5 75.3 1.0 OD1 C:ASP321 2.5 61.7 1.0 CD2 C:HIS65 3.0 77.5 1.0 CD2 C:HIS63 3.1 59.4 1.0 CE1 C:HIS63 3.2 71.2 1.0 CX C:KCX188 3.2 75.6 1.0 CG C:ASP321 3.3 78.4 1.0 P C:LWY427 3.4 93.2 1.0 C1 C:LWY427 3.5 96.4 1.0 OD2 C:ASP321 3.6 92.4 1.0 CE1 C:HIS65 3.7 74.8 1.0 CB C:ALA106 3.9 58.8 1.0 OQ1 C:KCX188 3.9 78.6 1.0 ZN C:ZN426 3.9 91.7 1.0 NZ C:KCX188 4.1 63.9 1.0 ND1 C:HIS63 4.2 64.1 1.0 CG C:HIS63 4.2 52.6 1.0 CG C:HIS65 4.2 64.1 1.0 CE1 C:HIS249 4.4 76.6 1.0 N C:LWY427 4.5 94.7 1.0 O1 C:LWY427 4.5 97.5 1.0 NE2 C:HIS249 4.5 81.0 1.0 ND1 C:HIS65 4.5 72.4 1.0 CB C:ASP321 4.5 75.2 1.0

Zinc binding site 6 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn426 b:91.7 occ:1.00 ND1 C:HIS229 2.1 70.0 1.0 OQ1 C:KCX188 2.3 78.6 1.0 NE2 C:HIS249 2.3 81.0 1.0 O2 C:LWY427 2.7 0.9 1.0 CE1 C:HIS229 3.0 73.4 1.0 CG C:HIS229 3.1 70.7 1.0 CX C:KCX188 3.1 75.6 1.0 O1 C:LWY427 3.1 97.5 1.0 CD2 C:HIS249 3.2 77.3 1.0 CE1 C:HIS249 3.4 76.6 1.0 CB C:HIS229 3.4 57.4 1.0 P C:LWY427 3.4 93.2 1.0 OQ2 C:KCX188 3.4 85.5 1.0 ZN C:ZN425 3.9 90.8 1.0 NZ C:KCX188 4.1 63.9 1.0 NE2 C:HIS229 4.1 78.9 1.0 CD2 C:HIS229 4.1 81.7 1.0 NE2 C:HIS63 4.3 65.3 1.0 CA C:HIS229 4.4 56.0 1.0 CG C:HIS249 4.4 80.0 1.0 CE1 C:HIS63 4.4 71.2 1.0 ND1 C:HIS249 4.5 85.2 1.0 N C:LWY427 4.5 94.7 1.0 CE C:KCX188 4.5 64.5 1.0 CA C:LWY427 4.5 93.7 1.0 NE2 C:HIS140 4.5 70.2 1.0 CD2 C:HIS140 4.6 76.6 1.0 CB C:GLU248 4.7 67.3 1.0 C1 C:LWY427 4.7 96.4 1.0 C C:LWY427 4.8 97.3 1.0 SD C:MET190 4.8 89.9 1.0 OXT C:LWY427 4.9 97.3 1.0

Zinc binding site 7 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn425 b:73.1 occ:1.00 NE2 D:HIS65 2.0 57.5 1.0 NE2 D:HIS63 2.2 56.0 1.0 OD1 D:ASP321 2.2 79.9 1.0 O2 D:LWY427 2.3 75.8 1.0 OQ2 D:KCX188 2.3 82.0 1.0 CD2 D:HIS65 2.9 46.3 1.0 CD2 D:HIS63 2.9 35.0 1.0 CE1 D:HIS65 3.1 57.5 1.0 CG D:ASP321 3.1 76.9 1.0 C1 D:LWY427 3.2 82.0 1.0 P D:LWY427 3.3 77.2 1.0 CE1 D:HIS63 3.3 43.9 1.0 CX D:KCX188 3.3 72.8 1.0 OD2 D:ASP321 3.6 88.8 1.0 ZN D:ZN426 3.8 72.2 1.0 OQ1 D:KCX188 3.9 59.9 1.0 CB D:ALA106 4.1 38.2 1.0 CG D:HIS65 4.1 42.1 1.0 CG D:HIS63 4.2 42.4 1.0 ND1 D:HIS65 4.2 56.2 1.0 ND1 D:HIS63 4.3 44.5 1.0 NZ D:KCX188 4.3 54.9 1.0 CB D:ASP321 4.3 65.8 1.0 N D:LWY427 4.4 73.1 1.0 O1 D:LWY427 4.4 80.2 1.0 NE2 D:HIS249 4.4 65.4 1.0 CE1 D:HIS249 4.5 62.8 1.0 CA D:ASP321 4.9 57.8 1.0 O D:ALA106 5.0 59.7 1.0

Zinc binding site 8 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn426 b:72.2 occ:1.00 OQ1 D:KCX188 2.1 59.9 1.0 ND1 D:HIS229 2.2 56.5 1.0 NE2 D:HIS249 2.2 65.4 1.0 O2 D:LWY427 2.3 75.8 1.0 CX D:KCX188 3.0 72.8 1.0 CE1 D:HIS229 3.0 41.4 1.0 CD2 D:HIS249 3.1 44.9 1.0 P D:LWY427 3.2 77.2 1.0 O1 D:LWY427 3.2 80.2 1.0 CE1 D:HIS249 3.2 62.8 1.0 OQ2 D:KCX188 3.2 82.0 1.0 CG D:HIS229 3.3 40.8 1.0 CB D:HIS229 3.7 47.3 1.0 ZN D:ZN425 3.8 73.1 1.0 CA D:LWY427 4.0 70.2 1.0 N D:LWY427 4.1 73.1 1.0 NE2 D:HIS63 4.2 56.0 1.0 NE2 D:HIS229 4.2 42.1 1.0 NZ D:KCX188 4.2 54.9 1.0 CG D:HIS249 4.2 49.0 1.0 ND1 D:HIS249 4.3 50.5 1.0 NE2 D:HIS140 4.3 52.6 1.0 CE1 D:HIS63 4.3 43.9 1.0 CD2 D:HIS229 4.3 34.9 1.0 CD2 D:HIS140 4.4 47.9 1.0 C D:LWY427 4.4 71.8 1.0 OXT D:LWY427 4.4 67.3 1.0 C1 D:LWY427 4.6 82.0 1.0 OD2 D:ASP321 4.7 88.8 1.0 CA D:HIS229 4.7 47.8 1.0 CE D:KCX188 4.8 56.6 1.0 SD D:MET190 5.0 59.3 1.0

Zinc binding site 9 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn425 b:79.7 occ:1.00 O2 E:LWY427 1.9 86.4 1.0 NE2 E:HIS65 2.1 72.1 1.0 OQ2 E:KCX188 2.1 86.8 1.0 NE2 E:HIS63 2.2 56.3 1.0 OD1 E:ASP321 2.9 86.9 1.0 CD2 E:HIS65 3.0 64.5 1.0 CX E:KCX188 3.0 76.4 1.0 CE1 E:HIS65 3.1 72.4 1.0 CD2 E:HIS63 3.1 50.6 1.0 CE1 E:HIS63 3.3 56.7 1.0 P E:LWY427 3.3 89.4 1.0 CG E:ASP321 3.5 75.7 1.0 OQ1 E:KCX188 3.5 78.0 1.0 OD2 E:ASP321 3.7 85.3 1.0 ZN E:ZN426 3.8 84.0 1.0 C1 E:LWY427 3.9 90.5 1.0 NZ E:KCX188 4.0 68.5 1.0 O1 E:LWY427 4.0 90.4 1.0 CG E:HIS65 4.1 60.0 1.0 ND1 E:HIS65 4.2 71.1 1.0 CB E:ALA106 4.2 59.3 1.0 CG E:HIS63 4.3 49.1 1.0 ND1 E:HIS63 4.3 43.9 1.0 N E:LWY427 4.4 89.6 1.0 NE2 E:HIS249 4.5 72.8 1.0 CE1 E:HIS249 4.6 71.6 1.0 CB E:ASP321 4.6 67.0 1.0 O E:ALA106 4.8 62.7 1.0 CD E:LWY427 5.0 89.5 1.0

Zinc binding site 10 out of 32 in the Crystal Structure of Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline


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 Prolidase EAH89906 Complexed with N- Methylphosphonate-L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn426 b:84.0 occ:1.00 O1 E:LWY427 1.9 90.4 1.0 OQ1 E:KCX188 2.1 78.0 1.0 ND1 E:HIS229 2.3 56.0 1.0 NE2 E:HIS249 2.5 72.8 1.0 P E:LWY427 3.0 89.4 1.0 CX E:KCX188 3.1 76.4 1.0 CE1 E:HIS229 3.1 66.1 1.0 CG E:HIS229 3.1 58.8 1.0 O2 E:LWY427 3.2 86.4 1.0 OQ2 E:KCX188 3.3 86.8 1.0 CD2 E:HIS249 3.3 54.9 1.0 CE1 E:HIS249 3.5 71.6 1.0 CB E:HIS229 3.6 47.4 1.0 ZN E:ZN425 3.8 79.7 1.0 NE2 E:HIS229 4.0 63.6 1.0 NE2 E:HIS140 4.1 74.0 1.0 CD2 E:HIS229 4.1 70.8 1.0 CD2 E:HIS140 4.1 74.0 1.0 C1 E:LWY427 4.2 90.5 1.0 N E:LWY427 4.2 89.6 1.0 NZ E:KCX188 4.3 68.5 1.0 CE1 E:HIS63 4.4 56.7 1.0 CA E:LWY427 4.4 88.8 1.0 NE2 E:HIS63 4.4 56.3 1.0 CG E:HIS249 4.5 61.9 1.0 CA E:HIS229 4.6 48.4 1.0 ND1 E:HIS249 4.6 73.3 1.0 SD E:MET190 4.7 70.5 1.0 CE E:KCX188 4.8 63.0 1.0 C E:LWY427 4.9 87.7 1.0 OD2 E:ASP321 4.9 85.3 1.0

D.F.Xiang, Y.Patskovsky, C.Xu, A.A.Fedorov, E.V.Fedorov, A.A.Sisco, J.M.Sauder, S.K.Burley, S.C.Almo, F.M.Raushel. Functional Identification and Structure Determination of Two Novel Prolidases From COG1228 in the Amidohydrolase Superfamily . Biochemistry V. 49 6791 2010.
ISSN: ISSN 0006-2960
PubMed: 20604542
DOI: 10.1021/BI100897U