Nickel in PDB 7ula: Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex

The structure of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex, PDB code: 7ula was solved by A.A.Gheorghita, E.Y.Li, R.Pfoh, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 2.46
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.95, 169.95, 143.02, 90, 90, 90
R / Rfree (%)	21.5 / 25.4

The structure of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex (pdb code 7ula). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex, PDB code: 7ula:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:132.1 occ:1.00 CE1 B:HIS401 2.4 76.2 1.0 NE2 B:HIS401 2.9 92.9 1.0 ND1 B:HIS401 3.6 72.6 1.0 CD2 B:HIS401 4.2 81.7 1.0 OG A:SER234 4.3 74.0 1.0 O B:GLU399 4.4 72.7 1.0 CG B:HIS401 4.5 71.9 1.0

Nickel binding site 2 out of 6 in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:116.7 occ:1.00 OE1 B:GLU451 3.1 81.8 1.0 OD1 B:ASP390 3.5 90.6 1.0 CD1 B:LEU416 3.6 99.3 1.0 CB B:ALA382 3.9 79.0 1.0 CD B:GLU451 4.0 91.8 1.0 CG B:GLU451 4.1 91.6 1.0 C B:ALA382 4.1 81.1 1.0 N B:ARG383 4.2 78.3 1.0 O B:ALA382 4.3 82.4 1.0 CG B:ARG383 4.3 70.7 1.0 CG B:ASP390 4.4 97.8 1.0 OD2 B:ASP390 4.4 103.5 1.0 CA B:ARG383 4.5 77.0 1.0 CA B:ALA382 4.7 77.8 1.0 CG B:LEU416 4.8 102.6 1.0 CB B:LEU416 4.9 96.9 1.0 CD1 B:LEU379 5.0 77.7 1.0

Nickel binding site 3 out of 6 in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:121.4 occ:1.00 NE2 A:HIS411 2.2 85.4 1.0 OD2 A:ASP413 2.9 91.0 1.0 CE1 A:HIS411 3.1 78.0 1.0 CD2 A:HIS411 3.3 78.4 1.0 CG A:ASP413 4.0 81.2 1.0 ND1 A:HIS411 4.2 69.9 1.0 CG A:HIS411 4.4 73.3 1.0 OD1 A:ASP413 4.4 81.7 1.0

Nickel binding site 4 out of 6 in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:135.9 occ:1.00 ND1 A:HIS196 2.8 59.9 1.0 OD2 A:ASP193 3.3 97.1 1.0 CE1 A:HIS196 3.5 55.4 1.0 CG A:HIS196 3.9 62.5 1.0 CB A:HIS196 4.4 53.6 1.0 CG A:ASP193 4.5 80.1 1.0 CA A:ASP193 4.5 56.3 1.0 NE2 A:HIS196 4.7 58.3 1.0 O A:ALA192 4.7 57.1 1.0 N A:ASP193 4.8 52.5 1.0 CD2 A:HIS196 5.0 57.4 1.0 C A:ALA192 5.0 57.5 1.0

Nickel binding site 5 out of 6 in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni503 b:127.5 occ:1.00 O A:GLY148 2.5 64.2 1.0 NE2 A:HIS94 2.7 70.1 1.0 OE1 A:GLU103 3.0 64.6 1.0 OE2 A:GLU103 3.3 67.7 1.0 C A:GLY148 3.4 64.8 1.0 CE1 A:HIS94 3.4 55.0 1.0 CD A:GLU103 3.6 61.2 1.0 CA A:GLY148 3.7 63.0 1.0 CD2 A:HIS94 3.8 66.8 1.0 N A:TYR149 4.5 58.8 1.0 ND1 A:HIS94 4.6 58.5 1.0 ND2 A:ASN150 4.7 52.0 1.0 O A:HOH617 4.8 54.4 1.0 CG A:HIS94 4.8 68.3 1.0 CA A:TYR149 5.0 60.9 1.0

Nickel binding site 6 out of 6 in the Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of the Pseudomonas Putida Algkx Modification and Secretion Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:116.4 occ:1.00 OH A:TYR277 3.4 43.7 1.0 ND2 A:ASN276 3.5 63.2 1.0 CE1 A:HIS178 3.6 53.1 1.0 NE2 A:HIS178 4.0 51.5 1.0 NZ A:LYS219 4.1 58.7 1.0 ND1 A:HIS178 4.1 51.5 1.0 CB A:SER271 4.2 48.4 1.0 CZ A:TYR277 4.3 44.8 1.0 CE2 A:TYR277 4.3 46.0 1.0 OG A:SER271 4.7 45.5 1.0 CG A:ASN276 4.7 62.7 1.0 CD2 A:HIS178 4.8 54.3 1.0 CG A:HIS178 4.8 52.9 1.0 O A:SER271 4.9 51.8 1.0

A.A.Gheorghita, Y.E.Li, E.N.Kitova, D.T.Bui, R.Pfoh, K.E.Low, G.B.Whitfield, M.T.C.Walvoort, Q.Zhang, J.D.C.Codee, J.S.Klassen, P.L.Howell. Structure of the Algkx Modification and Secretion Complex Required For Alginate Production and Biofilm Attachment in Pseudomonas Aeruginosa. Nat Commun V. 13 7631 2022.
ISSN: ESSN 2041-1723
PubMed: 36494359
DOI: 10.1038/S41467-022-35131-6