Nickel in PDB 5xkt: Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel

The structure of Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel, PDB code: 5xkt was solved by Y.H.Fong, M.H.Yuen, Y.S.Nim, P.H.Lau, K.B.Wong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.43 / 1.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.553, 49.318, 129.708, 90.00, 103.16, 90.00
R / Rfree (%)	15.6 / 19.1

The binding sites of Nickel atom in the Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel (pdb code 5xkt). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel, PDB code: 5xkt:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:20.0 occ:1.00 O1G A:GNP301 2.0 13.0 1.0 O1B A:GNP301 2.1 11.3 1.0 OG1 A:THR21 2.1 10.2 1.0 OE2 A:GLU104 2.1 12.7 1.0 OD2 A:ASP49 2.1 14.2 1.0 O A:HOH447 2.2 12.2 1.0 CG A:ASP49 3.0 20.7 1.0 CD A:GLU104 3.1 16.2 1.0 PB A:GNP301 3.2 12.6 1.0 CB A:THR21 3.2 12.2 1.0 PG A:GNP301 3.2 14.0 1.0 N3B A:GNP301 3.3 9.4 1.0 OE1 A:GLU104 3.4 15.0 1.0 OD1 A:ASP49 3.4 17.4 1.0 O A:HOH503 3.7 18.9 1.0 N A:THR21 3.8 9.8 1.0 NZ B:LYS137 3.9 12.6 1.0 CA A:THR21 4.0 11.4 1.0 O3G A:GNP301 4.0 15.2 1.0 O A:HOH509 4.1 28.7 1.0 O2B A:GNP301 4.2 10.3 1.0 O2A A:GNP301 4.2 13.8 1.0 CB A:ASP49 4.2 17.2 1.0 O3A A:GNP301 4.3 11.5 1.0 O2G A:GNP301 4.4 12.3 1.0 CG2 A:THR21 4.4 15.3 1.0 CG A:GLU104 4.5 15.1 1.0 PA A:GNP301 4.6 12.9 1.0 CB A:LYS20 4.6 9.9 1.0 CE A:LYS20 4.8 12.7 1.0 C A:LYS20 4.8 10.8 1.0 O1A A:GNP301 4.8 14.4 1.0 NZ A:LYS20 5.0 11.6 1.0

Nickel binding site 2 out of 3 in the Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:22.6 occ:1.00 NE2 B:HIS74 2.0 16.8 1.0 NE2 A:HIS74 2.0 18.6 1.0 SG A:CYS72 2.3 20.2 1.0 SG B:CYS72 2.3 17.5 1.0 CE1 B:HIS74 2.9 19.6 1.0 CE1 A:HIS74 3.0 18.8 1.0 CD2 A:HIS74 3.0 16.0 1.0 CD2 B:HIS74 3.0 16.2 1.0 CB B:CYS72 3.3 16.6 1.0 CB A:CYS72 3.4 18.3 1.0 O B:HOH799 3.6 43.2 1.0 O A:HOH589 3.7 26.9 1.0 ND1 B:HIS74 4.1 18.3 1.0 ND1 A:HIS74 4.1 16.8 1.0 CG B:HIS74 4.1 17.2 1.0 CG A:HIS74 4.1 18.7 1.0 ND2 A:ASN109 4.2 12.5 1.0 ND2 B:ASN109 4.2 13.7 1.0 CA B:CYS72 4.7 16.7 1.0 CA A:CYS72 4.7 15.2 1.0

Nickel binding site 3 out of 3 in the Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Klebsiella Pneumoniae Ureg in Complex with Gmppnp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:20.6 occ:1.00 O2B B:GNP500 2.1 11.4 1.0 O2G B:GNP500 2.1 13.9 1.0 OG1 B:THR21 2.1 12.1 1.0 OD2 B:ASP49 2.1 12.3 1.0 OE2 B:GLU104 2.1 11.3 1.0 O B:HOH612 2.2 12.0 1.0 CG B:ASP49 3.0 15.1 1.0 CD B:GLU104 3.1 15.9 1.0 PB B:GNP500 3.2 11.4 1.0 CB B:THR21 3.2 11.3 1.0 PG B:GNP500 3.3 12.7 1.0 N3B B:GNP500 3.3 10.3 1.0 OE1 B:GLU104 3.3 14.2 1.0 OD1 B:ASP49 3.4 17.2 1.0 O B:HOH634 3.5 18.4 1.0 N B:THR21 3.7 12.6 1.0 NZ A:LYS137 3.9 14.2 1.0 CA B:THR21 4.0 10.1 1.0 O1G B:GNP500 4.1 15.1 1.0 O1A B:GNP500 4.2 9.2 1.0 O B:HOH690 4.2 31.4 1.0 O1B B:GNP500 4.2 9.5 1.0 CB B:ASP49 4.2 15.5 1.0 O3A B:GNP500 4.3 9.2 1.0 O3G B:GNP500 4.3 11.8 1.0 CG2 B:THR21 4.3 12.5 1.0 CG B:GLU104 4.4 10.6 1.0 PA B:GNP500 4.6 10.9 1.0 CB B:LYS20 4.6 9.1 1.0 CE B:LYS20 4.7 12.6 1.0 C B:LYS20 4.8 10.8 1.0 O2A B:GNP500 4.8 12.3 1.0 OD2 B:ASP43 5.0 21.3 1.0

M.H.Yuen, Y.H.Fong, Y.S.Nim, P.H.Lau, K.B.Wong. Structural Insights Into How Gtp-Dependent Conformational Changes in A Metallochaperone Ureg Facilitate Urease Maturation. Proc. Natl. Acad. Sci. V. 114 10890 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203664
DOI: 10.1073/PNAS.1712658114