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Nickel in PDB 4avi: Structure of the Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution

Protein crystallography data

The structure of Structure of the Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution, PDB code: 4avi was solved by A.Wellens, M.Lahmann, M.Touaibia, J.Vaucher, S.Oscarson, R.Roy, H.Remaut, J.Bouckaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.640 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.620, 90.620, 79.700, 90.00, 90.00, 120.00
R / Rfree (%) 13.98 / 21.27

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution (pdb code 4avi). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of the Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution, PDB code: 4avi:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4avi

Go back to Nickel Binding Sites List in 4avi
Nickel binding site 1 out of 2 in the Structure of the Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution


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 Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1160

b:27.2
occ:1.00
OD1 A:ASP47 2.0 26.6 1.0
O A:HOH2077 2.0 25.1 1.0
NE2 A:HIS45 2.0 36.4 1.0
O A:HOH2076 2.0 30.2 1.0
O A:HOH2075 2.1 33.2 1.0
O A:HOH2079 2.4 26.3 1.0
CE1 A:HIS45 2.9 25.8 1.0
CG A:ASP47 3.0 21.8 1.0
HE1 A:HIS45 3.0 31.0 1.0
CD2 A:HIS45 3.1 20.1 1.0
O A:HOH2172 3.3 39.4 1.0
OD2 A:ASP47 3.3 22.3 1.0
HD2 A:HIS45 3.4 24.1 1.0
ND1 A:HIS45 4.1 27.4 1.0
HA A:ASP47 4.2 29.2 1.0
CG A:HIS45 4.2 14.9 1.0
CB A:ASP47 4.3 21.6 1.0
O A:HOH2141 4.3 39.3 1.0
HB1 A:ALA2 4.4 18.4 1.0
HB3 A:ASP47 4.5 25.9 1.0
CA A:ASP47 4.7 24.3 1.0
HD1 A:HIS45 4.8 32.9 1.0
HD12 A:ILE13 4.8 38.0 1.0
HB2 A:ASP47 5.0 25.9 1.0

Nickel binding site 2 out of 2 in 4avi

Go back to Nickel Binding Sites List in 4avi
Nickel binding site 2 out of 2 in the Structure of the Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution


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 Fimh Lectin Domain in the Trigonal Space Group, in Complex with A Methyl Ester Octyl Alpha-D- Mannoside at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1159

b:34.9
occ:1.00
O B:HOH2059 1.9 16.1 1.0
OD1 B:ASP47 2.0 25.1 1.0
O B:HOH2058 2.1 36.7 1.0
NE2 B:HIS45 2.1 27.9 1.0
O B:HOH2060 2.5 45.0 1.0
O B:HOH2137 2.7 40.7 1.0
CE1 B:HIS45 2.9 28.4 1.0
CG B:ASP47 3.0 19.7 1.0
HE1 B:HIS45 3.0 34.1 1.0
O B:HOH2138 3.2 38.4 1.0
CD2 B:HIS45 3.3 22.0 1.0
OD2 B:ASP47 3.3 27.6 1.0
HD2 B:HIS45 3.5 26.4 1.0
ND1 B:HIS45 4.1 24.9 1.0
HA B:ASP47 4.2 34.0 1.0
CB B:ASP47 4.3 17.5 1.0
CG B:HIS45 4.3 23.8 1.0
HB1 B:ALA2 4.4 12.3 1.0
HB3 B:ASP47 4.4 21.0 1.0
HD12 B:ILE13 4.5 25.3 1.0
CA B:ASP47 4.8 28.4 1.0
HD1 B:HIS45 4.9 29.9 1.0
HB2 B:ASP47 5.0 21.0 1.0

Reference:

A.Wellens, M.Lahmann, M.Touaibia, J.Vaucher, S.Oscarson, R.Roy, H.Remaut, J.Bouckaert. The Tyrosine Gate As A Potential Entropic Lever in the Receptor-Binding Site of the Bacterial Adhesin Fimh. Biochemistry V. 51 4790 2012.
ISSN: ISSN 0006-2960
PubMed: 22657089
DOI: 10.1021/BI300251R
Page generated: Thu Oct 29 06:22:53 2020
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