Zinc in PDB 3mkv: Crystal Structure of Amidohydrolase EAJ56179

The structure of Crystal Structure of Amidohydrolase EAJ56179, PDB code: 3mkv was solved by Y.Patskovsky, J.Bonanno, S.Ozyurt, J.M.Sauder, J.Freeman, B.Wu, D.Smith, K.Bain, L.Rodgers, S.R.Wasserman, F.M.Raushel, 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)	40.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.022, 198.599, 104.294, 90.00, 107.76, 90.00
R / Rfree (%)	17.1 / 22.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Amidohydrolase EAJ56179 (pdb code 3mkv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Amidohydrolase EAJ56179, PDB code: 3mkv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn425 b:59.7 occ:1.00 NE2 A:HIS63 2.1 37.3 1.0 NE2 A:HIS65 2.1 54.4 1.0 OQ2 A:KCX191 2.3 66.2 1.0 OD1 A:ASP324 2.4 64.4 1.0 CD2 A:HIS63 3.0 44.4 1.0 CD2 A:HIS65 3.0 53.2 1.0 CG A:ASP324 3.0 53.1 1.0 CE1 A:HIS63 3.1 43.9 1.0 CE1 A:HIS65 3.1 45.4 1.0 CX A:KCX191 3.2 57.7 1.0 OD2 A:ASP324 3.3 55.9 1.0 ZN A:ZN426 3.3 66.3 1.0 OQ1 A:KCX191 3.5 61.7 1.0 O A:HOH559 3.8 87.0 1.0 O A:HOH435 4.1 63.9 1.0 CG A:HIS63 4.1 42.4 1.0 CB A:ASP324 4.2 46.4 1.0 ND1 A:HIS63 4.2 49.4 1.0 CG A:HIS65 4.2 44.8 1.0 ND1 A:HIS65 4.2 43.9 1.0 CB A:ALA106 4.3 52.0 1.0 NZ A:KCX191 4.3 51.4 1.0 NE2 A:HIS252 4.4 52.4 1.0 CE1 A:HIS252 4.6 54.9 1.0 CA A:ASP324 4.8 46.5 1.0 O4 A:SO4427 4.9 57.6 0.5

Zinc binding site 2 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn426 b:66.3 occ:1.00 OQ1 A:KCX191 2.2 61.7 1.0 ND1 A:HIS232 2.4 57.5 1.0 NE2 A:HIS252 2.4 52.4 1.0 CX A:KCX191 3.0 57.7 1.0 OQ2 A:KCX191 3.1 66.2 1.0 O4 A:SO4427 3.2 57.6 0.5 CD2 A:HIS252 3.3 51.7 1.0 ZN A:ZN425 3.3 59.7 1.0 CE1 A:HIS232 3.3 48.4 1.0 CG A:HIS232 3.4 50.0 1.0 O A:HOH435 3.5 63.9 1.0 CE1 A:HIS252 3.5 54.9 1.0 CB A:HIS232 3.7 49.8 1.0 CE1 A:HIS63 3.9 43.9 1.0 NE2 A:HIS63 3.9 37.3 1.0 OD2 A:ASP324 4.0 55.9 1.0 NZ A:KCX191 4.3 51.4 1.0 NE2 A:HIS140 4.4 66.7 1.0 NE2 A:HIS232 4.5 57.3 1.0 CG A:HIS252 4.5 55.0 1.0 CD2 A:HIS232 4.5 51.9 1.0 ND1 A:HIS252 4.6 65.0 1.0 CD2 A:HIS140 4.6 63.7 1.0 S A:SO4427 4.6 64.1 0.5 CG A:ASP324 4.7 53.1 1.0 O A:HOH559 4.8 87.0 1.0 CA A:HIS232 4.8 54.6 1.0 OD1 A:ASP324 4.8 64.4 1.0 CE A:KCX191 4.8 41.6 1.0 SD A:MET193 4.9 43.1 1.0 O2 A:SO4427 5.0 64.1 0.5

Zinc binding site 3 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn425 b:62.8 occ:1.00 OQ2 B:KCX191 2.1 63.9 1.0 NE2 B:HIS65 2.1 46.6 1.0 NE2 B:HIS63 2.1 42.1 1.0 OD1 B:ASP324 2.2 54.6 1.0 O B:HOH546 2.4 58.1 1.0 CG B:ASP324 2.9 52.0 1.0 CE1 B:HIS65 3.0 42.3 1.0 CX B:KCX191 3.1 67.4 1.0 CD2 B:HIS63 3.1 43.4 1.0 CD2 B:HIS65 3.1 39.3 1.0 CE1 B:HIS63 3.1 51.0 1.0 OD2 B:ASP324 3.3 49.3 1.0 OQ1 B:KCX191 3.3 64.6 1.0 ZN B:ZN426 3.5 66.6 1.0 CB B:ASP324 4.1 48.8 1.0 ND1 B:HIS65 4.2 50.3 1.0 CB B:ALA106 4.2 40.6 1.0 O B:HOH513 4.2 68.2 1.0 NZ B:KCX191 4.2 55.8 1.0 ND1 B:HIS63 4.2 46.7 1.0 CG B:HIS65 4.2 49.7 1.0 CG B:HIS63 4.2 44.1 1.0 NE2 B:HIS252 4.4 53.4 1.0 CE1 B:HIS252 4.4 50.3 1.0 O3 B:SO4427 4.8 64.5 0.5 CA B:ASP324 4.9 45.3 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn426 b:66.6 occ:1.00 O B:HOH546 2.1 58.1 1.0 OQ1 B:KCX191 2.2 64.6 1.0 NE2 B:HIS252 2.2 53.4 1.0 ND1 B:HIS232 2.3 50.1 1.0 CX B:KCX191 3.0 67.4 1.0 CD2 B:HIS252 3.1 44.6 1.0 O3 B:SO4427 3.2 64.5 0.5 CE1 B:HIS232 3.2 51.5 1.0 CE1 B:HIS252 3.2 50.3 1.0 OQ2 B:KCX191 3.3 63.9 1.0 CG B:HIS232 3.3 55.0 1.0 ZN B:ZN425 3.5 62.8 1.0 CB B:HIS232 3.6 45.7 1.0 CE1 B:HIS63 4.0 51.0 1.0 NE2 B:HIS63 4.1 42.1 1.0 NZ B:KCX191 4.2 55.8 1.0 O B:HOH513 4.2 68.2 1.0 CG B:HIS252 4.3 56.4 1.0 ND1 B:HIS252 4.3 53.1 1.0 NE2 B:HIS232 4.3 57.4 1.0 CD2 B:HIS232 4.4 49.9 1.0 OD2 B:ASP324 4.4 49.3 1.0 S B:SO4427 4.4 77.2 0.5 CA B:HIS232 4.5 46.0 1.0 NE2 B:HIS140 4.6 72.0 1.0 CE B:KCX191 4.7 42.0 1.0 CD2 B:HIS140 4.7 72.1 1.0 SD B:MET193 4.8 44.0 1.0 O4 B:SO4427 4.8 66.7 0.5 O1 B:SO4427 4.9 73.6 0.5 CB B:GLU251 4.9 41.2 1.0 CG B:ASP324 5.0 52.0 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn425 b:63.5 occ:1.00 NE2 C:HIS63 2.0 50.6 1.0 NE2 C:HIS65 2.2 55.7 1.0 OD1 C:ASP324 2.3 59.2 1.0 OQ2 C:KCX191 2.4 65.4 1.0 CE1 C:HIS63 2.9 47.8 1.0 CD2 C:HIS63 3.0 40.5 1.0 CG C:ASP324 3.1 55.1 1.0 CX C:KCX191 3.1 60.0 1.0 CE1 C:HIS65 3.2 57.0 1.0 CD2 C:HIS65 3.2 59.2 1.0 O C:HOH557 3.3 70.1 1.0 ZN C:ZN426 3.3 66.2 1.0 OQ1 C:KCX191 3.3 61.3 1.0 OD2 C:ASP324 3.5 58.7 1.0 O C:HOH535 3.9 90.0 1.0 ND1 C:HIS63 4.1 49.9 1.0 CG C:HIS63 4.1 52.6 1.0 NE2 C:HIS252 4.2 43.2 1.0 NZ C:KCX191 4.2 50.4 1.0 CE1 C:HIS252 4.3 41.6 1.0 ND1 C:HIS65 4.3 60.2 1.0 CB C:ASP324 4.3 52.3 1.0 CB C:ALA106 4.3 50.3 1.0 CG C:HIS65 4.4 60.6 1.0 O4 C:SO4427 4.9 49.6 0.5

Zinc binding site 6 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn426 b:66.2 occ:1.00 OQ1 C:KCX191 2.2 61.3 1.0 NE2 C:HIS252 2.2 43.2 1.0 O C:HOH557 2.3 70.1 1.0 ND1 C:HIS232 2.4 55.6 1.0 CD2 C:HIS252 3.1 45.6 1.0 CX C:KCX191 3.1 60.0 1.0 CE1 C:HIS252 3.2 41.6 1.0 CE1 C:HIS232 3.3 50.9 1.0 ZN C:ZN425 3.3 63.5 1.0 CG C:HIS232 3.3 55.0 1.0 OQ2 C:KCX191 3.3 65.4 1.0 O4 C:SO4427 3.6 49.6 0.5 CB C:HIS232 3.6 47.4 1.0 CE1 C:HIS63 3.9 47.8 1.0 NE2 C:HIS63 4.1 50.6 1.0 CG C:HIS252 4.2 43.0 1.0 ND1 C:HIS252 4.3 45.4 1.0 NZ C:KCX191 4.3 50.4 1.0 NE2 C:HIS140 4.4 74.7 1.0 NE2 C:HIS232 4.4 55.6 1.0 CD2 C:HIS232 4.5 47.9 1.0 OD2 C:ASP324 4.5 58.7 1.0 CA C:HIS232 4.6 46.5 1.0 S C:SO4427 4.6 59.9 0.5 CD2 C:HIS140 4.6 70.5 1.0 O C:HOH535 4.7 90.0 1.0 O3 C:SO4427 4.7 48.0 0.5 CE C:KCX191 4.7 46.1 1.0 O2 C:SO4427 4.8 52.6 0.5 SD C:MET193 4.8 47.3 1.0 CB C:GLU251 4.9 46.2 1.0 OD1 C:ASP324 5.0 59.2 1.0 CG C:ASP324 5.0 55.1 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn425 b:63.8 occ:1.00 NE2 D:HIS65 1.8 52.5 1.0 OQ2 D:KCX191 2.2 63.5 1.0 NE2 D:HIS63 2.2 45.6 1.0 OD1 D:ASP324 2.3 58.0 1.0 CE1 D:HIS65 2.7 53.9 1.0 CD2 D:HIS65 2.9 53.5 1.0 CG D:ASP324 3.1 66.6 1.0 CD2 D:HIS63 3.1 56.2 1.0 CX D:KCX191 3.2 63.0 1.0 CE1 D:HIS63 3.2 48.8 1.0 OD2 D:ASP324 3.3 71.8 1.0 O D:HOH483 3.4 69.3 1.0 ZN D:ZN426 3.4 73.2 1.0 OQ1 D:KCX191 3.5 60.7 1.0 ND1 D:HIS65 3.8 59.4 1.0 CG D:HIS65 3.9 55.9 1.0 NZ D:KCX191 4.3 57.3 1.0 ND1 D:HIS63 4.3 40.1 1.0 CG D:HIS63 4.3 51.7 1.0 CE1 D:HIS252 4.3 69.1 1.0 CB D:ASP324 4.3 57.6 1.0 O D:HOH522 4.3 82.0 1.0 CB D:ALA106 4.4 50.3 1.0 NE2 D:HIS252 4.4 61.1 1.0 CA D:ASP324 4.9 56.8 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn426 b:73.2 occ:1.00 OQ1 D:KCX191 2.1 60.7 1.0 NE2 D:HIS252 2.2 61.1 1.0 ND1 D:HIS232 2.3 57.9 1.0 CX D:KCX191 3.0 63.0 1.0 CE1 D:HIS252 3.1 69.1 1.0 OQ2 D:KCX191 3.1 63.5 1.0 O D:HOH483 3.2 69.3 1.0 CD2 D:HIS252 3.2 61.3 1.0 CE1 D:HIS232 3.3 58.2 1.0 CG D:HIS232 3.3 49.5 1.0 ZN D:ZN425 3.4 63.8 1.0 CB D:HIS232 3.6 50.3 1.0 NE2 D:HIS63 4.0 45.6 1.0 CE1 D:HIS63 4.1 48.8 1.0 OD2 D:ASP324 4.2 71.8 1.0 NZ D:KCX191 4.2 57.3 1.0 ND1 D:HIS252 4.2 73.2 1.0 NE2 D:HIS140 4.3 72.3 1.0 CG D:HIS252 4.3 66.4 1.0 NE2 D:HIS232 4.4 58.8 1.0 CD2 D:HIS232 4.4 56.8 1.0 CD2 D:HIS140 4.5 71.3 1.0 CA D:HIS232 4.6 53.2 1.0 CE D:KCX191 4.8 50.8 1.0 SD D:MET193 4.8 55.7 1.0 O D:HOH529 4.8 61.0 1.0 CG D:ASP324 4.9 66.6 1.0 OD1 D:ASP324 4.9 58.0 1.0 CE D:MET193 4.9 62.2 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn425 b:63.7 occ:1.00 OD1 E:ASP324 2.1 68.4 1.0 NE2 E:HIS63 2.1 50.6 1.0 NE2 E:HIS65 2.2 58.2 1.0 OQ2 E:KCX191 2.3 59.1 1.0 CG E:ASP324 2.9 57.4 1.0 CE1 E:HIS65 3.0 58.8 1.0 CE1 E:HIS63 3.1 52.6 1.0 CD2 E:HIS63 3.1 46.7 1.0 CX E:KCX191 3.2 63.4 1.0 CD2 E:HIS65 3.2 51.2 1.0 OD2 E:ASP324 3.2 63.2 1.0 ZN E:ZN426 3.3 68.2 1.0 OQ1 E:KCX191 3.5 58.8 1.0 O E:HOH489 3.6 65.8 1.0 ND1 E:HIS63 4.2 51.5 1.0 ND1 E:HIS65 4.2 56.4 1.0 CB E:ASP324 4.2 54.6 1.0 NE2 E:HIS252 4.2 67.9 1.0 CG E:HIS63 4.3 53.1 1.0 CE1 E:HIS252 4.3 66.8 1.0 CG E:HIS65 4.3 50.8 1.0 NZ E:KCX191 4.3 58.0 1.0 O4 E:SO4428 4.6 51.2 0.5 CB E:ALA106 4.6 54.9 1.0 CA E:ASP324 5.0 50.8 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn426 b:68.2 occ:1.00 NE2 E:HIS252 2.2 67.9 1.0 OQ1 E:KCX191 2.2 58.8 1.0 ND1 E:HIS232 2.2 61.7 1.0 O4 E:SO4428 2.9 51.2 0.5 CX E:KCX191 3.0 63.4 1.0 CE1 E:HIS232 3.0 63.4 1.0 OQ2 E:KCX191 3.1 59.1 1.0 CD2 E:HIS252 3.1 65.6 1.0 CE1 E:HIS252 3.2 66.8 1.0 ZN E:ZN425 3.3 63.7 1.0 CG E:HIS232 3.4 57.0 1.0 CB E:HIS232 3.8 54.1 1.0 CE1 E:HIS63 4.1 52.6 1.0 NE2 E:HIS63 4.1 50.6 1.0 O E:HOH489 4.1 65.8 1.0 NE2 E:HIS232 4.2 58.1 1.0 NZ E:KCX191 4.2 58.0 1.0 ND1 E:HIS252 4.3 70.1 1.0 S E:SO4428 4.3 69.2 0.5 CG E:HIS252 4.3 68.7 1.0 OD2 E:ASP324 4.4 63.2 1.0 CD2 E:HIS232 4.4 57.3 1.0 CA E:HIS232 4.5 55.1 1.0 NE2 E:HIS140 4.7 85.3 1.0 O1 E:SO4428 4.7 58.6 0.5 O3 E:SO4428 4.8 60.9 0.5 CD2 E:HIS140 4.8 81.2 1.0 OD1 E:ASP324 4.8 68.4 1.0 SD E:MET193 4.8 48.6 1.0 CE E:KCX191 4.8 52.7 1.0 CG E:ASP324 4.9 57.4 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