Zinc in PDB 4dlm: Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121

The structure of Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121, PDB code: 4dlm was solved by M.W.Vetting, R.Toro, R.Bhosle, R.D.Seidel, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, N.F.Al Obaidi, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.65 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.860, 63.200, 76.220, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 23.5

The binding sites of Zinc atom in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 (pdb code 4dlm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121, PDB code: 4dlm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.3 occ:1.00 OD1 A:ASP244 1.9 13.8 1.0 O A:HOH503 2.0 15.8 1.0 NE2 A:HIS11 2.1 10.2 1.0 O A:HOH538 2.1 26.9 1.0 NE2 A:HIS9 2.2 21.7 1.0 CD2 A:HIS11 3.0 10.0 1.0 CG A:ASP244 3.0 12.3 1.0 CE1 A:HIS11 3.1 13.3 1.0 CD2 A:HIS9 3.2 20.7 1.0 CE1 A:HIS9 3.2 20.7 1.0 NE2 A:HIS166 3.5 35.7 1.0 OD2 A:ASP244 3.5 15.6 1.0 O A:HOH646 3.8 45.8 1.0 CE1 A:HIS166 3.9 31.2 1.0 O A:HOH507 4.1 20.3 1.0 CG A:HIS11 4.2 10.7 1.0 ND1 A:HIS11 4.2 11.9 1.0 CB A:ASP244 4.3 12.1 1.0 ND1 A:HIS9 4.3 19.9 1.0 CG A:HIS9 4.4 20.7 1.0 NH2 A:ARG106 4.6 16.1 1.0 CA A:ASP244 4.6 16.1 1.0 CG2 A:VAL247 4.7 15.2 1.0 NH1 A:ARG106 4.8 20.4 1.0 CD2 A:HIS166 4.8 33.3 1.0 O A:ASP244 5.0 16.8 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:29.2 occ:1.00 NE2 A:HIS44 2.0 21.4 1.0 O A:HOH704 2.1 28.9 1.0 ND1 A:HIS40 2.1 25.2 1.0 O A:HOH536 2.1 25.2 1.0 O A:HOH513 2.2 16.9 1.0 CE1 A:HIS44 2.9 28.2 1.0 CE1 A:HIS40 3.0 25.6 1.0 CG A:HIS40 3.1 25.5 1.0 CD2 A:HIS44 3.1 19.2 1.0 CB A:HIS40 3.5 23.8 1.0 O A:HOH584 4.0 25.3 1.0 ND1 A:HIS44 4.1 28.5 1.0 NE2 A:HIS40 4.1 32.5 1.0 CD2 A:HIS40 4.2 26.0 1.0 O A:HOH642 4.2 35.9 1.0 CG A:HIS44 4.2 18.0 1.0 CA A:HIS40 4.4 19.0 1.0 C A:HIS40 4.6 13.0 1.0 O A:HIS40 4.7 16.3 1.0 NE A:ARG75 4.8 37.5 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:24.1 occ:1.00 NE2 A:HIS222 2.0 17.9 1.0 O A:HOH712 2.0 23.6 1.0 O A:HOH711 2.1 18.5 1.0 O A:HOH713 2.2 18.6 1.0 CE1 A:HIS222 3.0 14.5 1.0 CD2 A:HIS222 3.0 14.3 1.0 ND1 A:HIS222 4.1 14.7 1.0 CG A:HIS222 4.2 18.8 1.0 O A:PHE175 4.2 20.8 1.0 O A:HOH575 4.4 21.2 1.0 C A:PHE175 4.9 22.0 1.0 CA A:ASP176 5.0 35.0 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:41.3 occ:1.00 OD1 A:ASP135 2.0 37.2 1.0 O A:HOH701 2.1 37.5 1.0 O A:HOH598 2.1 50.4 1.0 O A:HOH702 2.1 39.4 1.0 O A:HOH643 2.2 30.9 1.0 O A:HOH569 3.0 35.3 1.0 CG A:ASP135 3.0 32.9 1.0 OD2 A:ASP135 3.4 38.5 1.0 O A:HOH674 3.9 43.1 1.0 O A:GLN132 4.0 23.8 1.0 ND1 A:HIS160 4.3 18.8 1.0 CB A:ASP135 4.4 26.9 1.0 O A:ALA159 4.5 32.0 1.0 CA A:ASP135 4.6 20.7 1.0 N A:ASP135 4.7 23.4 1.0 O A:ALA133 4.7 24.1 1.0 CE1 A:HIS160 4.9 18.0 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:70.9 occ:1.00 OD2 A:ASP158 2.1 37.5 1.0 CG A:ASP158 2.9 27.2 1.0 OD1 A:ASP158 3.0 29.9 1.0 CB A:ASP158 4.3 22.3 1.0 O A:ALA155 4.9 25.2 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:72.3 occ:1.00 OE1 A:GLU191 2.1 53.0 1.0 OE2 A:GLU191 2.1 56.0 1.0 CD A:GLU191 2.4 49.4 1.0 CG A:GLU191 3.8 38.0 1.0 O A:HOH559 4.2 24.9 1.0 CB A:GLU191 4.8 25.0 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:66.9 occ:1.00 OD2 A:ASP228 2.0 23.4 1.0 NH2 A:ARG268 2.1 16.8 0.4 OE2 A:GLU224 2.5 23.0 0.5 CG A:ASP228 3.0 16.9 1.0 CD A:GLU224 3.0 23.9 0.5 CZ A:ARG268 3.0 17.2 0.4 OD1 A:ASP228 3.3 15.7 1.0 NE A:ARG268 3.4 13.1 0.4 CG A:GLU224 3.4 22.8 0.5 OE1 A:GLU224 3.7 24.4 0.5 NH1 A:ARG268 4.1 14.6 0.4 CB A:ASP228 4.3 12.2 1.0 O A:GLU224 4.4 16.3 0.5 O A:HOH693 4.5 39.2 1.0 O A:GLU224 4.6 15.0 0.5 CB A:GLU224 4.7 20.0 0.5 CD A:ARG268 4.8 20.7 0.4 CB A:GLU224 4.8 20.8 0.5 C A:GLU224 4.8 16.7 0.5 C A:GLU224 4.9 16.7 0.5

M.W.Vetting, R.Toro, R.Bhosle, R.D.Seidel, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, N.F.Al Obaidi, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 To Be Published.