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Nickel in PDB 2ixl: Rmlc S. Suis with Dtdp-Rhamnose

Enzymatic activity of Rmlc S. Suis with Dtdp-Rhamnose

All present enzymatic activity of Rmlc S. Suis with Dtdp-Rhamnose:
5.1.3.13;

Protein crystallography data

The structure of Rmlc S. Suis with Dtdp-Rhamnose, PDB code: 2ixl was solved by C.Dong, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.68 / 1.6
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.408, 141.526, 53.586, 90.00, 92.57, 90.00
R / Rfree (%) 16.7 / 21.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Rmlc S. Suis with Dtdp-Rhamnose (pdb code 2ixl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Rmlc S. Suis with Dtdp-Rhamnose, PDB code: 2ixl:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2ixl

Go back to Nickel Binding Sites List in 2ixl
Nickel binding site 1 out of 2 in the Rmlc S. Suis with Dtdp-Rhamnose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Rmlc S. Suis with Dtdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1199

b:16.6
occ:1.00
O A:HOH2142 1.9 10.7 1.0
O A:HOH2135 2.1 9.0 1.0
OE1 A:GLU52 2.2 13.0 1.0
CD A:GLU52 3.2 15.5 1.0
OE2 A:GLU52 3.4 14.7 1.0
O A:HOH2134 3.7 21.6 1.0
O A:HOH2128 4.0 19.9 1.0
O A:PHE50 4.3 10.8 1.0
O A:HOH2143 4.3 14.1 1.0
N A:GLU52 4.3 11.0 1.0
O A:LEU46 4.3 11.0 1.0
CG A:GLU52 4.6 13.3 1.0
CA A:PRO51 4.6 11.1 1.0
CB A:GLU52 4.9 11.4 1.0
O A:GLY49 4.9 12.5 1.0
C A:PRO51 5.0 11.1 1.0

Nickel binding site 2 out of 2 in 2ixl

Go back to Nickel Binding Sites List in 2ixl
Nickel binding site 2 out of 2 in the Rmlc S. Suis with Dtdp-Rhamnose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Rmlc S. Suis with Dtdp-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni1199

b:19.4
occ:1.00
OE2 C:GLU52 2.0 12.1 1.0
CD C:GLU52 3.0 14.0 1.0
OE1 C:GLU52 3.2 17.3 1.0
O C:HOH2158 4.0 9.0 1.0
O C:HOH2156 4.2 28.3 1.0
CG C:GLU52 4.3 12.9 1.0
O B:HOH2071 4.9 24.7 1.0

Reference:

C.Dong, L.L.Major, V.Srikannathasan, J.C.Errey, M.F.Giraud, J.S.Lam, M.Graninger, P.Messner, M.R.Mcneil, R.A.Field, C.Whitfield, J.H.Naismith. Rmlc, A C3' and C5' Carbohydrate Epimerase, Appears to Operate Via An Intermediate with An Unusual Twist Boat Conformation. J.Mol.Biol. V. 365 146 2007.
ISSN: ISSN 0022-2836
PubMed: 17046787
DOI: 10.1016/J.JMB.2006.09.063
Page generated: Fri Sep 25 08:11:24 2020
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