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Nickel in PDB 2f9m: 3D Structure of Active Human RAB11B Gtpase

Enzymatic activity of 3D Structure of Active Human RAB11B Gtpase

All present enzymatic activity of 3D Structure of Active Human RAB11B Gtpase:
3.6.5.2;

Protein crystallography data

The structure of 3D Structure of Active Human RAB11B Gtpase, PDB code: 2f9m was solved by S.M.N.Scapin, B.G.Guimaraes, N.I.T.Zanchin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.95
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.611, 85.409, 86.886, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.5

Other elements in 2f9m:

The structure of 3D Structure of Active Human RAB11B Gtpase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the 3D Structure of Active Human RAB11B Gtpase (pdb code 2f9m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 3D Structure of Active Human RAB11B Gtpase, PDB code: 2f9m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2f9m

Go back to Nickel Binding Sites List in 2f9m
Nickel binding site 1 out of 2 in the 3D Structure of Active Human RAB11B Gtpase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 3D Structure of Active Human RAB11B Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1202

b:22.9
occ:1.00
NE2 A:HIS112 2.0 17.6 1.0
OE1 A:GLU108 2.1 16.8 1.0
O A:HOH1348 2.2 13.7 1.0
O A:HOH1300 2.2 16.5 1.0
O A:HOH1281 2.2 25.9 1.0
O A:HOH1264 2.3 19.0 1.0
CD2 A:HIS112 2.9 18.0 1.0
CD A:GLU108 3.0 17.4 1.0
CE1 A:HIS112 3.1 17.8 1.0
OE2 A:GLU108 3.3 19.1 1.0
O A:HOH1261 3.9 26.3 1.0
O A:ILE76 4.0 13.6 1.0
O A:HOH1210 4.0 14.3 1.0
CG A:HIS112 4.1 17.9 1.0
O A:HOH1302 4.1 23.4 1.0
ND1 A:HIS112 4.1 18.9 1.0
O A:HOH1440 4.1 38.0 1.0
O A:HOH1295 4.3 31.2 1.0
OE2 A:GLU71 4.4 14.9 1.0
CG A:GLU108 4.4 15.5 1.0
OD2 A:ASP111 4.4 23.4 1.0
CB A:ASP111 4.8 18.9 1.0
CB A:GLU108 4.8 14.6 1.0
CA A:GLU108 4.9 14.8 1.0

Nickel binding site 2 out of 2 in 2f9m

Go back to Nickel Binding Sites List in 2f9m
Nickel binding site 2 out of 2 in the 3D Structure of Active Human RAB11B Gtpase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 3D Structure of Active Human RAB11B Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1203

b:27.6
occ:1.00
NE2 A:HIS187 2.1 28.6 1.0
OD2 A:ASP183 2.1 19.7 1.0
O A:HOH1247 2.2 20.6 1.0
CG A:ASP183 3.0 20.0 1.0
CD2 A:HIS187 3.0 28.9 1.0
CE1 A:HIS187 3.1 28.5 1.0
OD1 A:ASP183 3.2 19.2 1.0
O A:HOH1218 3.8 17.0 1.0
CG A:HIS187 4.2 29.9 1.0
ND1 A:HIS187 4.2 29.2 1.0
CB A:ASP183 4.4 19.8 1.0
O A:ASP183 4.9 19.9 1.0

Reference:

S.M.Scapin, F.R.Carneiro, A.C.Alves, F.J.Medrano, B.G.Guimaraes, N.I.Zanchin. The Crystal Structure of the Small Gtpase RAB11B Reveals Critical Differences Relative to the RAB11A Isoform. J.Struct.Biol. V. 154 260 2006.
ISSN: ISSN 1047-8477
PubMed: 16545962
DOI: 10.1016/J.JSB.2006.01.007
Page generated: Wed Dec 16 01:18:07 2020

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