Cadmium in PDB 4q9m: Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor

The structure of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor, PDB code: 4q9m was solved by S.Liu, X.Qiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.85 / 2.06
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.850, 91.850, 155.540, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.5

The structure of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor (pdb code 4q9m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor, PDB code: 4q9m:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:32.1 occ:1.00 O2B A:FPP302 2.2 28.5 1.0 O2A A:FPP302 2.2 22.8 1.0 OD1 A:ASP28 2.3 29.3 1.0 O A:HOH404 2.5 19.0 1.0 O A:HOH419 2.5 31.1 1.0 O A:HOH433 2.5 36.0 1.0 PA A:FPP302 3.4 28.0 1.0 CG A:ASP28 3.4 29.2 1.0 PB A:FPP302 3.4 30.6 1.0 O3A A:FPP302 3.5 31.2 1.0 OD2 A:ASP28 3.7 34.8 1.0 O3B A:FPP302 3.9 28.6 1.0 NH1 A:ARG32 4.0 26.6 1.0 O1 A:FPP302 4.2 25.1 1.0 NH2 A:ARG79 4.3 25.3 1.0 O A:HOH475 4.4 33.8 1.0 O1A A:FPP302 4.5 26.4 1.0 O A:HOH542 4.5 54.4 1.0 N A:GLY29 4.6 23.4 1.0 O1B A:FPP302 4.6 34.2 1.0 C1 A:FPP302 4.7 29.5 1.0 CB A:ASP28 4.7 22.8 1.0

Cadmium binding site 2 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:30.0 occ:1.00 OE1 A:GLU114 2.2 23.7 1.0 OD2 A:ASP116 2.3 31.6 1.0 OD1 A:ASP116 2.4 27.6 1.0 O A:HOH403 2.5 19.3 1.0 CG A:ASP116 2.7 27.6 1.0 CD A:GLU114 3.0 36.3 1.0 CG A:GLU114 3.2 26.8 1.0 CB A:ASP116 4.2 24.7 1.0 O A:HOH436 4.2 30.2 1.0 OE2 A:GLU114 4.2 28.5 1.0 CG A:ARG117 4.4 28.0 1.0 CD A:ARG117 4.6 29.1 1.0 CB A:GLU114 4.8 21.1 1.0

Cadmium binding site 3 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:33.2 occ:1.00 OE2 A:GLU176 2.3 23.4 1.0 OE1 A:GLU176 2.4 22.4 1.0 O A:HOH408 2.4 17.5 1.0 O B:HOH404 2.4 9.0 1.0 O A:HOH406 2.5 20.5 1.0 CD A:GLU176 2.7 25.7 1.0 CG A:GLU176 4.2 28.7 1.0 CB B:ARG150 4.4 15.9 1.0 OH A:TYR217 4.4 36.5 1.0 N B:ALA151 4.4 16.4 1.0 O A:HOH427 4.5 26.2 1.0 CB B:ALA151 4.5 17.6 1.0 ND2 B:ASN209 4.6 20.1 1.0 O A:HOH449 4.8 28.9 1.0 CA B:ALA151 4.9 16.6 1.0 OG1 B:THR74 4.9 29.2 1.0

Cadmium binding site 4 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:68.5 occ:1.00 O A:HOH459 2.6 27.4 1.0 O A:HOH478 2.7 30.8 1.0 O A:HOH451 2.8 34.5 1.0 O A:ASP191 2.9 24.3 1.0 O A:HOH481 3.4 40.0 1.0 C A:ASP191 4.0 25.4 1.0 O A:ASP194 4.0 20.3 1.0 OD1 A:ASP196 4.1 34.3 1.0 CA A:LEU192 4.6 19.2 1.0 OD2 A:ASP196 4.6 40.2 1.0 N A:LEU192 4.7 20.5 1.0 CG A:ASP196 4.8 33.8 1.0 CB A:ASP194 4.8 20.4 1.0 CA A:ASP191 4.9 21.6 1.0 N A:ASP194 4.9 18.0 1.0 C A:ASP194 5.0 20.8 1.0

Cadmium binding site 5 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:88.7 occ:1.00 O A:HOH596 2.2 55.4 1.0 O A:HOH599 2.5 43.0 1.0 OD2 A:ASP96 2.9 48.9 1.0 O A:HOH588 2.9 41.6 1.0 CG A:ASP96 3.8 40.9 1.0 OD1 A:ASP96 4.1 42.5 1.0 O A:HOH442 4.6 27.9 1.0 O A:HOH534 4.6 61.7 1.0

Cadmium binding site 6 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd308 b:0.1 occ:1.00 OE2 A:GLU50 2.5 64.0 1.0 OE1 A:GLU50 2.8 71.5 1.0 CD A:GLU50 3.0 67.2 1.0 CD A:CD310 3.9 0.0 1.0 CG A:GLU50 4.5 37.8 1.0 CE1 A:TYR98 4.7 28.8 1.0

Cadmium binding site 7 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd309 b:0.3 occ:1.00 OE1 A:GLU204 2.2 66.2 1.0 O A:HOH552 2.6 44.8 1.0 CD A:GLU204 3.0 63.7 1.0 OE2 A:GLU204 3.1 52.3 1.0 NH2 A:ARG206 3.8 74.1 1.0 NH1 A:ARG206 4.2 73.0 1.0 O A:HOH569 4.2 76.0 1.0 O B:HOH603 4.4 82.8 1.0 CG A:GLU204 4.4 45.8 1.0 CZ A:ARG206 4.5 86.1 1.0 O B:HOH583 4.6 65.1 1.0 O A:HOH576 4.8 44.8 1.0 NH2 A:ARG32 4.9 42.2 1.0

Cadmium binding site 8 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd310 b:0.0 occ:1.00 OE1 A:GLU101 2.6 39.9 1.0 CD A:GLU101 3.3 43.5 1.0 OE2 A:GLU101 3.4 42.8 1.0 O A:HOH551 3.4 63.0 1.0 CD A:CD308 3.9 0.1 1.0 NZ A:LYS57 3.9 62.8 1.0 CG A:GLN53 4.6 25.8 1.0 CG A:GLU101 4.8 29.4 1.0 OE1 A:GLN53 4.8 30.9 1.0

Cadmium binding site 9 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd311 b:0.8 occ:1.00 O A:HOH561 2.3 60.7 1.0 O A:HOH541 2.6 59.8 1.0 OD1 A:ASP163 2.7 46.6 1.0 OD2 A:ASP163 2.9 44.1 1.0 CG A:ASP163 3.1 44.2 1.0 NZ A:LYS168 4.4 91.2 0.0 O A:LEU159 4.5 33.8 1.0 CE2 A:TYR182 4.6 27.0 1.0 CD2 A:LEU159 4.6 36.3 1.0 CB A:ASP163 4.7 36.4 1.0 CD A:LYS168 4.8 71.0 0.0 OH A:TYR182 5.0 30.8 1.0

Cadmium binding site 10 out of 15 in the Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Upps in Complex with Fpp and An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd303 b:32.6 occ:1.00 O B:HOH439 2.1 21.8 1.0 O2A B:FPP302 2.2 28.7 1.0 O2B B:FPP302 2.3 34.3 1.0 OD1 B:ASP28 2.3 27.0 1.0 O B:HOH436 2.3 30.0 1.0 O B:HOH420 2.6 26.3 1.0 CG B:ASP28 3.3 28.8 1.0 PB B:FPP302 3.4 34.6 1.0 PA B:FPP302 3.4 29.2 1.0 O3A B:FPP302 3.5 32.0 1.0 OD2 B:ASP28 3.6 31.2 1.0 O3B B:FPP302 4.0 36.7 1.0 O B:HOH507 4.1 51.5 1.0 NH1 B:ARG32 4.1 37.0 1.0 NH2 B:ARG79 4.1 25.7 1.0 O1 B:FPP302 4.2 25.8 1.0 O B:HOH512 4.3 42.1 1.0 O B:HOH445 4.4 32.5 1.0 O1A B:FPP302 4.5 28.1 1.0 O1B B:FPP302 4.6 37.1 1.0 C1 B:FPP302 4.6 26.8 1.0 N B:GLY29 4.6 25.1 1.0 CB B:ASP28 4.6 24.3 1.0 O B:HOH479 4.8 30.8 1.0 CA B:ASP28 5.0 23.3 1.0 O B:HOH462 5.0 39.5 1.0

D.E.Danley, E.T.Baima, M.Mansour, K.F.Fennell, B.A.Chrunyk, J.P.Mueller, S.Liu, X.Qiu. Discovery and Structural Characterization of An Allosteric Inhibitor of Bacterial Cis-Prenyltransferase. Protein Sci. 2014.
ISSN: ESSN 1469-896X
PubMed: 25287857
DOI: 10.1002/PRO.2579