Nickel in PDB 2xci: Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form

The structure of Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form, PDB code: 2xci was solved by H.Schmidt, G.Hansen, R.Hilgenfeld, U.Mamat, J.R.Mesters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	132.500, 45.820, 144.070, 90.00, 97.23, 90.00
R / Rfree (%)	20.7 / 25.4

The structure of Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Nickel atom in the Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form (pdb code 2xci). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form, PDB code: 2xci:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1358 b:64.8 occ:0.65 NE2 A:HIS213 2.6 65.2 1.0 CD2 A:HIS213 3.1 64.5 1.0 CE1 A:HIS213 3.8 71.2 1.0 CG A:HIS213 4.4 61.7 1.0 ND1 A:HIS213 4.7 66.7 1.0 NH2 A:ARG212 4.9 69.4 1.0 CD A:ARG212 4.9 67.2 1.0

Nickel binding site 2 out of 4 in the Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1354 b:61.0 occ:0.65 NE2 B:HIS213 2.5 58.0 1.0 CD2 B:HIS213 3.2 62.2 1.0 CE1 B:HIS213 3.6 66.1 1.0 CG B:HIS213 4.5 66.5 1.0 ND1 B:HIS213 4.6 70.2 1.0

Nickel binding site 3 out of 4 in the Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1357 b:60.8 occ:0.65 NE2 C:HIS213 2.5 55.3 1.0 CD2 C:HIS213 3.2 61.0 1.0 CE1 C:HIS213 3.7 62.5 1.0 CG C:HIS213 4.5 63.4 1.0 ND1 C:HIS213 4.7 66.4 1.0 CD C:ARG212 4.9 68.2 1.0

Nickel binding site 4 out of 4 in the Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Membrane-Embedded Monofunctional Glycosyltransferase Waaa of Aquifex Aeolicus, Substrate-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1358 b:59.9 occ:0.65 NE2 D:HIS213 2.6 68.8 1.0 CD2 D:HIS213 3.1 71.4 1.0 CE1 D:HIS213 3.8 74.6 1.0 O D:HOH2042 4.1 54.7 1.0 CG D:HIS213 4.4 71.4 1.0 ND1 D:HIS213 4.7 75.2 1.0

H.Schmidt, G.Hansen, S.Singh, A.Hanuszkiewicz, B.Lindner, K.Fukase, R.W.Woodard, O.Holst, R.Hilgenfeld, U.Mamat, J.R.Mesters. Structural and Mechanistic Analysis of the Membrane-Embedded Glycosyltransferase Waaa Required For Lipopolysaccharide Synthesis. Proc.Natl.Acad.Sci.Usa V. 109 6253 2012.
ISSN: ISSN 0027-8424
PubMed: 22474366
DOI: 10.1073/PNAS.1119894109