Zinc in PDB 4pe3: Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure, PDB code: 4pe3 was solved by M.W.Vetting, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, M.Stead, J.D.Attonito, A.Scott Glenn, S.Chowdhury, B.Evans, B.Hillerich, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative(Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.61 / 1.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.072, 97.938, 35.788, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.6

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure (pdb code 4pe3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure, PDB code: 4pe3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:15.2 occ:0.86 OD1 A:ASP231 2.0 12.1 1.0 O A:HOH707 2.0 15.4 1.0 OE1 A:GLU173 2.1 14.3 1.0 O A:HOH710 2.1 26.9 1.0 OE2 A:GLU173 2.1 22.6 1.0 O A:TYR232 2.4 19.1 1.0 CD A:GLU173 2.4 13.4 1.0 CG A:ASP231 2.8 14.2 1.0 OD2 A:ASP231 3.1 13.6 1.0 C A:TYR232 3.5 13.0 1.0 HG A:SER257 3.7 12.7 1.0 O A:HOH861 3.9 35.2 1.0 CG A:GLU173 3.9 9.2 1.0 HA A:SER233 4.0 8.9 1.0 N A:TYR232 4.1 9.7 1.0 O A:HOH729 4.1 23.0 1.0 H A:TYR232 4.1 11.6 1.0 HA A:TYR232 4.2 13.8 1.0 O A:HOH838 4.2 43.2 1.0 O A:HOH682 4.2 14.2 1.0 CA A:TYR232 4.2 11.5 1.0 CB A:ASP231 4.2 10.5 1.0 HG3 A:GLU173 4.3 11.0 1.0 HG2 A:GLU173 4.3 11.0 1.0 C A:ASP231 4.4 11.2 1.0 HG2 A:PRO195 4.4 16.4 1.0 N A:SER233 4.4 7.4 1.0 HB3 A:SER257 4.4 11.3 1.0 HB3 A:GLU173 4.5 9.8 1.0 OG A:SER257 4.5 10.6 1.0 HE2 A:HIS256 4.5 14.8 1.0 HB3 A:ASP231 4.6 12.6 1.0 HA A:ASP231 4.7 10.9 1.0 CA A:SER233 4.7 7.4 1.0 CA A:ASP231 4.7 9.1 1.0 HH12 A:ARG193 4.7 21.3 1.0 CB A:GLU173 4.7 8.2 1.0 O A:HOH789 4.7 23.9 1.0 HD13 A:ILE199 4.7 13.5 1.0 HB2 A:SER257 4.8 11.3 1.0 CB A:SER257 4.8 9.4 1.0 HB2 A:GLU173 4.8 9.8 1.0 HB2 A:ASP231 4.8 12.6 1.0 O A:ASP231 4.9 10.8 1.0 HG3 A:PRO195 5.0 16.4 1.0

Zinc binding site 2 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:49.6 occ:0.70 NE2 A:HIS49 2.0 33.2 1.0 O A:HOH848 2.1 36.3 1.0 O A:HOH882 2.1 32.6 1.0 CE1 A:HIS49 2.9 36.5 1.0 HE1 A:HIS49 3.0 43.8 1.0 CD2 A:HIS49 3.1 34.3 1.0 HD2 A:HIS49 3.4 41.2 1.0 HD12 A:LEU277 4.0 40.5 1.0 HD11 A:LEU277 4.0 40.5 1.0 ND1 A:HIS49 4.0 35.3 1.0 HD23 A:LEU273 4.1 40.9 1.0 OE2 A:GLU81 4.2 42.5 1.0 CG A:HIS49 4.2 33.4 1.0 CD1 A:LEU277 4.3 33.8 1.0 HD13 A:LEU277 4.3 40.5 1.0 OE1 A:GLU81 4.5 51.8 1.0 CD A:GLU81 4.7 47.7 1.0 HA A:LEU273 4.7 37.8 1.0 HD1 A:HIS49 4.8 42.3 1.0 HD22 A:LEU273 4.8 40.9 1.0 CD2 A:LEU273 4.9 34.1 1.0

Zinc binding site 3 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:10.8 occ:0.96 OD2 A:ASP240 2.0 10.5 1.0 N1 A:IMD402 2.0 11.4 1.0 CG A:ASP240 2.8 9.4 1.0 OD1 A:ASP240 3.0 12.1 1.0 C2 A:IMD402 3.0 12.4 1.0 C5 A:IMD402 3.0 12.3 1.0 H2 A:IMD402 3.2 14.9 1.0 H5 A:IMD402 3.3 14.8 1.0 O A:HOH533 3.9 15.4 1.0 N3 A:IMD402 4.2 14.8 1.0 C4 A:IMD402 4.2 14.0 1.0 CB A:ASP240 4.2 9.3 1.0 HB3 A:ASP240 4.4 11.1 1.0 HB2 A:ASP240 4.5 11.1 1.0

Zinc binding site 4 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:13.0 occ:0.52 OD2 A:ASP245 1.9 16.2 1.0 HB3 A:ASP245 2.9 12.1 1.0 CG A:ASP245 2.9 14.4 1.0 O A:HOH504 3.0 25.6 1.0 CB A:ASP245 3.2 10.1 1.0 HB2 A:ASP245 3.3 12.1 1.0 OD1 A:ASP245 4.0 15.9 1.0 CA A:ASP245 4.7 9.7 1.0 HA2 A:GLY242 4.8 13.0 1.0 HA A:ASP245 5.0 11.6 1.0

Zinc binding site 5 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:14.5 occ:0.99 ND1 A:HIS297 2.0 11.3 1.0 O A:HOH541 2.0 14.0 1.0 CE1 A:HIS297 2.9 11.8 1.0 HE1 A:HIS297 3.1 14.2 1.0 HB3 A:HIS297 3.1 11.3 1.0 CG A:HIS297 3.1 10.1 1.0 CB A:HIS297 3.5 9.4 1.0 HB2 A:HIS297 3.6 11.3 1.0 HA A:ASP294 3.6 12.5 1.0 HE21 A:GLN298 4.0 29.8 1.0 OD1 A:ASP294 4.0 18.0 1.0 NE2 A:HIS297 4.1 12.2 1.0 CD2 A:HIS297 4.2 11.0 1.0 O A:HOH634 4.2 17.5 1.0 CA A:ASP294 4.6 10.4 1.0 HB3 A:ASP294 4.6 15.3 1.0 CG A:ASP294 4.6 16.3 1.0 HD11 A:LEU301 4.8 16.8 1.0 NE2 A:GLN298 4.8 24.8 1.0 O A:ASP294 4.8 11.3 1.0 CB A:ASP294 4.8 12.7 1.0 HE2 A:HIS297 4.8 14.7 1.0 HG2 A:GLN298 4.9 20.5 1.0 CA A:HIS297 4.9 8.7 1.0

Zinc binding site 6 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:17.2 occ:0.41 OD1 A:ASP357 2.0 30.4 1.0 OD2 A:ASP357 2.0 31.7 1.0 O A:HOH585 2.1 31.9 1.0 CG A:ASP357 2.2 33.2 1.0 CB A:ASP357 3.7 29.0 1.0 HD3 A:LYS358 3.8 36.7 1.0 O A:ASP357 3.9 29.7 1.0 HB2 A:ASP357 4.1 34.8 1.0 HB3 A:ASP357 4.1 34.8 1.0 HE2 A:LYS358 4.2 38.9 1.0 O A:HOH792 4.2 29.9 1.0 C A:ASP357 4.3 25.7 1.0 CA A:ASP357 4.5 26.2 1.0 HA A:ASP357 4.5 31.5 1.0 CD A:LYS358 4.6 30.6 1.0 CE A:LYS358 4.8 32.4 1.0 HD2 A:LYS358 4.9 36.7 1.0

Zinc binding site 7 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn411 b:15.6 occ:0.84 OE1 A:GLU305 2.0 29.5 1.0 O A:HOH534 2.1 25.0 1.0 OE2 A:GLU305 2.2 39.2 1.0 CD A:GLU305 2.4 21.8 1.0 HA A:GLU302 3.7 13.3 1.0 HG2 A:GLU302 3.9 18.0 1.0 O A:HOH507 3.9 27.7 1.0 CG A:GLU305 3.9 22.4 1.0 HB3 A:GLU305 4.2 22.7 1.0 HG2 A:GLU305 4.3 26.8 1.0 HG3 A:GLU305 4.4 26.8 1.0 HB2 A:GLU305 4.5 22.7 1.0 CB A:GLU305 4.5 18.9 1.0 CA A:GLU302 4.6 11.1 1.0 CG A:GLU302 4.7 15.0 1.0 HG3 A:GLU302 4.8 18.0 1.0 O A:HOH521 5.0 32.0 1.0

Zinc binding site 8 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn412 b:17.5 occ:0.44 OE2 A:GLU321 2.0 29.2 1.0 OE1 A:GLU321 2.1 45.4 1.0 O A:HOH616 2.1 46.1 1.0 OE2 A:GLU322 2.2 21.1 1.0 CD A:GLU321 2.3 34.8 1.0 HG2 A:GLU322 2.7 20.7 1.0 CD A:GLU322 3.1 21.6 1.0 CG A:GLU322 3.3 17.3 1.0 HG3 A:GLU322 3.5 20.7 1.0 HG22 A:THR183 3.7 22.7 1.0 O A:HOH522 3.8 31.3 1.0 O A:HOH778 3.8 42.1 1.0 CG A:GLU321 3.9 28.2 1.0 HZ2 A:LYS325 3.9 32.5 1.0 OG A:SER319 4.0 19.5 1.0 HG3 A:GLU321 4.2 33.8 1.0 HG2 A:GLU321 4.3 33.8 1.0 OE1 A:GLU322 4.3 18.1 1.0 HB2 A:GLU321 4.4 27.3 1.0 HG A:SER319 4.4 23.4 1.0 HG21 A:THR183 4.5 22.7 1.0 CG2 A:THR183 4.5 18.9 1.0 O A:HOH620 4.6 41.2 1.0 H A:GLU322 4.6 19.9 1.0 CB A:GLU322 4.7 16.1 1.0 NZ A:LYS325 4.7 27.1 1.0 HZ1 A:LYS325 4.7 32.5 1.0 CB A:GLU321 4.7 22.7 1.0 HD3 A:LYS325 4.8 27.1 1.0 N A:GLU322 4.8 16.5 1.0 HA A:GLU322 4.9 20.8 1.0

Zinc binding site 9 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn413 b:21.9 occ:0.47 ZN A:ZN413 0.0 21.9 0.5 OD1 A:ASP186 2.0 16.0 1.0 O A:HOH517 2.1 38.4 1.0 ZN A:ZN413 2.3 34.9 0.5 CG A:ASP186 3.1 13.3 1.0 OD2 A:ASP186 3.4 15.4 1.0 HG1 A:THR183 3.8 22.3 1.0 OG1 A:THR183 4.1 18.6 1.0 HA A:ASP186 4.3 17.7 1.0 CB A:ASP186 4.5 14.4 1.0 O A:HOH595 4.5 32.1 1.0 HG23 A:THR183 4.7 22.7 1.0 CA A:ASP186 4.7 14.7 1.0 HB2 A:GLU185 4.8 23.5 1.0 H A:ASP186 4.8 17.4 1.0 N A:ASP186 4.8 14.5 1.0 HG21 A:THR183 4.9 22.7 1.0 HB3 A:ASP186 4.9 17.3 1.0

Zinc binding site 10 out of 11 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure


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 A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn413 b:34.9 occ:0.53 ZN A:ZN413 0.0 34.9 0.5 ZN A:ZN413 2.3 21.9 0.5 OD2 A:ASP186 2.3 15.4 1.0 O A:HOH595 2.6 32.1 1.0 OD1 A:ASP186 2.7 16.0 1.0 CG A:ASP186 2.9 13.3 1.0 HB2 A:ASP182 3.4 20.5 1.0 H A:ASP182 3.5 16.7 1.0 HG23 A:THR183 3.8 22.7 1.0 H A:THR183 4.2 17.5 1.0 O A:HOH517 4.2 38.4 1.0 HG1 A:THR183 4.3 22.3 1.0 OG1 A:THR183 4.3 18.6 1.0 CB A:ASP182 4.3 17.1 1.0 N A:ASP182 4.3 13.9 1.0 CB A:ASP186 4.4 14.4 1.0 CG2 A:THR183 4.6 18.9 1.0 OD2 A:ASP182 4.6 20.7 1.0 HG21 A:THR183 4.6 22.7 1.0 N A:THR183 4.6 14.6 1.0 HB3 A:ASP186 4.7 17.3 1.0 O A:PRO180 4.7 14.8 1.0 HB2 A:ASP186 4.7 17.3 1.0 HA A:LEU181 4.8 12.2 1.0 CA A:ASP182 4.8 15.0 1.0 HB3 A:ASP182 4.9 20.5 1.0 CB A:THR183 5.0 18.4 1.0

M.W.Vetting, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, M.Stead, J.D.Attonito, A.Scott Glenn, S.Chowdhury, B.Evans, B.Hillerich, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Trap Periplasmic Solute Binding Protein From Rhodobacter Sphaeroides (RSPH17029_3620, Target Efi-510199), Apo Open Structure To Be Published.