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Nickel in PDB 4qdw: Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose

Enzymatic activity of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose

All present enzymatic activity of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose:
5.3.1.5;

Protein crystallography data

The structure of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose, PDB code: 4qdw was solved by A.Y.Kovalevsky, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.190, 99.670, 102.940, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 17.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose (pdb code 4qdw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose, PDB code: 4qdw:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 4qdw

Go back to Nickel Binding Sites List in 4qdw
Nickel binding site 1 out of 3 in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:21.2
occ:0.50
 NI A:NI402 1.9 19.1 0.5
O A:DOD1001 2.0 26.7 1.0
NE2 A:HIS220 2.0 22.8 1.0
OE2 A:GLU217 2.4 24.4 1.0
O18 A:LAI404 2.4 39.5 1.0
O20 A:LAI404 2.4 36.3 1.0
D1 A:DOD1001 2.5 29.2 1.0
CE1 A:HIS220 2.7 22.8 1.0
D2 A:DOD1001 2.7 30.1 1.0
HE1 A:HIS220 2.8 23.4 1.0
OE1 A:GLU217 2.8 24.6 1.0
CD A:GLU217 2.9 20.5 1.0
HO18 A:LAI404 2.9 44.1 1.0
C10 A:LAI404 3.0 41.0 1.0
CD2 A:HIS220 3.2 22.6 1.0
OD2 A:ASP255 3.2 33.3 1.0
C8 A:LAI404 3.3 41.5 1.0
NI A:NI403 3.6 26.7 1.0
HD2 A:HIS220 3.6 21.9 1.0
OD1 A:ASP257 3.8 23.3 1.0
ND1 A:HIS220 3.9 22.4 1.0
DZ1 A:LYS183 3.9 22.2 1.0
H10 A:LAI404 3.9 40.2 1.0
OD2 A:ASP287 4.0 24.2 1.0
H8 A:LAI404 4.0 41.7 1.0
HE3 A:LYS183 4.0 22.2 1.0
CG A:ASP255 4.0 31.5 1.0
HD2 A:LYS183 4.1 20.7 1.0
OD2 A:ASP257 4.1 25.6 1.0
OD1 A:ASP255 4.1 31.2 1.0
CG A:HIS220 4.1 17.9 1.0
OE2 A:GLU181 4.2 27.8 1.0
DD21 A:ASN247 4.3 20.4 0.7
HD21 A:ASN247 4.3 20.4 0.3
CG A:GLU217 4.3 18.6 1.0
CG A:ASP257 4.4 21.4 1.0
C6 A:LAI404 4.4 43.6 1.0
O16 A:LAI404 4.5 47.0 1.0
HG2 A:GLU217 4.6 19.0 1.0
HB3 A:GLU217 4.6 16.8 1.0
D2 A:DOD1118 4.7 43.7 1.0
CG A:ASP287 4.7 20.6 1.0
DD1 A:HIS220 4.7 22.8 1.0
CE A:LYS183 4.7 22.0 1.0
NZ A:LYS183 4.7 23.5 1.0
HB2 A:GLU217 4.8 17.8 1.0
DD22 A:ASN247 4.8 20.7 1.0
CB A:GLU217 4.8 17.2 1.0
CD A:LYS183 4.9 20.2 1.0
ND2 A:ASN247 4.9 20.0 1.0
O14 A:LAI404 4.9 42.5 1.0
HG3 A:GLU217 5.0 18.7 1.0

Nickel binding site 2 out of 3 in 4qdw

Go back to Nickel Binding Sites List in 4qdw
Nickel binding site 2 out of 3 in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:19.1
occ:0.50
 NI A:NI401 1.9 21.2 0.5
OD2 A:ASP255 2.1 33.3 1.0
OE2 A:GLU217 2.1 24.4 1.0
OD1 A:ASP257 2.3 23.3 1.0
OD1 A:ASP255 2.3 31.2 1.0
CG A:ASP255 2.5 31.5 1.0
O A:DOD1001 2.6 26.7 1.0
NE2 A:HIS220 2.6 22.8 1.0
D2 A:DOD1001 2.6 30.1 1.0
HD2 A:HIS220 2.8 21.9 1.0
CD2 A:HIS220 3.0 22.6 1.0
CG A:ASP257 3.2 21.4 1.0
CD A:GLU217 3.2 20.5 1.0
DD21 A:ASN247 3.3 20.4 0.7
HD21 A:ASN247 3.3 20.4 0.3
D1 A:DOD1001 3.3 29.2 1.0
OD2 A:ASP257 3.4 25.6 1.0
D2 A:DOD1042 3.5 29.4 1.0
O20 A:LAI404 3.6 36.3 1.0
OE1 A:GLU217 3.8 24.6 1.0
HE3 A:LYS183 3.8 22.2 1.0
CE1 A:HIS220 3.8 22.8 1.0
ND2 A:ASN247 3.9 20.0 1.0
DD22 A:ASN247 4.0 20.7 1.0
CB A:ASP255 4.0 24.2 1.0
D2 A:DOD1118 4.0 43.7 1.0
DZ1 A:LYS183 4.2 22.2 1.0
O A:DOD1042 4.2 24.6 1.0
HG2 A:GLU217 4.3 19.0 1.0
O18 A:LAI404 4.3 39.5 1.0
HE1 A:HIS220 4.3 23.4 1.0
CG A:HIS220 4.3 17.9 1.0
CG A:GLU217 4.4 18.6 1.0
HB2 A:ASP255 4.4 26.2 1.0
HB3 A:ASP255 4.4 27.6 1.0
C10 A:LAI404 4.5 41.0 1.0
O A:DOD1118 4.6 45.6 1.0
HA A:ASP257 4.6 20.8 1.0
CB A:ASP257 4.6 19.9 1.0
H A:ASP257 4.6 20.0 0.3
D A:ASP257 4.6 20.0 0.7
ND1 A:HIS220 4.7 22.4 1.0
CE A:LYS183 4.7 22.0 1.0
HA3 A:GLY219 4.8 17.7 1.0
NZ A:LYS183 4.8 23.5 1.0
HO18 A:LAI404 4.8 44.1 1.0
DZ2 A:LYS183 4.8 24.1 1.0
HD2 A:LYS183 4.9 20.7 1.0
D A:HIS220 4.9 26.5 1.0
HA A:ASP255 4.9 21.8 1.0
D1 A:DOD1042 5.0 25.8 1.0
DZ2 A:LYS289 5.0 46.1 1.0
CA A:ASP255 5.0 20.7 1.0
D1 A:DOD1118 5.0 45.8 1.0
CA A:ASP257 5.0 20.3 1.0

Nickel binding site 3 out of 3 in 4qdw

Go back to Nickel Binding Sites List in 4qdw
Nickel binding site 3 out of 3 in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two NI2+ Ions and Linear L-Arabinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:26.7
occ:1.00
 HO18 A:LAI404 2.1 44.1 1.0
OE2 A:GLU181 2.1 27.8 1.0
OE1 A:GLU217 2.1 24.6 1.0
OD2 A:ASP287 2.1 24.2 1.0
OD2 A:ASP245 2.2 23.6 1.0
O14 A:LAI404 2.2 42.5 1.0
O18 A:LAI404 2.3 39.5 1.0
HO14 A:LAI404 2.7 45.9 1.0
D2 A:DOD1062 3.0 48.3 1.0
CD A:GLU181 3.0 25.0 1.0
CG A:ASP287 3.2 20.6 1.0
OE1 A:GLU181 3.3 27.0 1.0
CD A:GLU217 3.3 20.5 1.0
CG A:ASP245 3.3 22.6 1.0
C4 A:LAI404 3.3 43.8 1.0
C8 A:LAI404 3.4 41.5 1.0
D1 A:DOD1001 3.4 29.2 1.0
HB2 A:GLU217 3.5 17.8 1.0
HB3 A:ASP287 3.5 19.4 1.0
NI A:NI401 3.6 21.2 0.5
HB2 A:ASP287 3.6 20.0 1.0
HB3 A:ASP245 3.6 20.1 1.0
HE1 A:HIS220 3.7 23.4 1.0
CB A:ASP287 3.7 20.3 1.0
H4 A:LAI404 3.7 43.1 1.0
C6 A:LAI404 3.7 43.6 1.0
H8 A:LAI404 3.9 41.7 1.0
CB A:ASP245 3.9 19.7 1.0
O A:DOD1062 3.9 47.1 1.0
HB2 A:ASP245 3.9 20.6 1.0
O A:DOD1001 3.9 26.7 1.0
OE2 A:GLU217 4.1 24.4 1.0
O16 A:LAI404 4.1 47.0 1.0
CE1 A:HIS220 4.2 22.8 1.0
D1 A:DOD1062 4.2 49.0 1.0
CG A:GLU217 4.2 18.6 1.0
OD1 A:ASP287 4.3 23.4 1.0
CB A:GLU217 4.3 17.2 1.0
CG A:GLU181 4.3 21.8 1.0
OD1 A:ASP245 4.4 23.0 1.0
H2A A:LAI404 4.4 44.4 1.0
HG3 A:GLU217 4.4 18.7 1.0
HD21 A:ASN215 4.4 19.5 0.1
DD21 A:ASN215 4.4 19.5 0.9
C2 A:LAI404 4.5 42.5 1.0
HZ2 A:TRP16 4.5 24.7 1.0
HG3 A:GLU181 4.5 22.6 1.0
NE2 A:HIS220 4.6 22.8 1.0
C10 A:LAI404 4.6 41.0 1.0
HB3 A:GLU217 4.6 16.8 1.0
HG2 A:GLU181 4.6 22.7 1.0
H6 A:LAI404 4.7 43.7 1.0
D2 A:DOD1001 4.8 30.1 1.0
HD22 A:ASN215 4.9 21.2 0.1
DD22 A:ASN215 4.9 21.2 0.9
H2 A:LAI404 4.9 44.4 1.0
ND2 A:ASN215 4.9 21.6 1.0
O20 A:LAI404 5.0 36.3 1.0

Reference:

P.Langan, A.K.Sangha, T.Wymore, J.M.Parks, Z.K.Yang, B.L.Hanson, Z.Fisher, S.A.Mason, M.P.Blakeley, V.T.Forsyth, J.P.Glusker, H.L.Carrell, J.C.Smith, D.A.Keen, D.E.Graham, A.Kovalevsky. L-Arabinose Binding, Isomerization, and Epimerization By D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Structure V. 22 1287 2014.
ISSN: ISSN 0969-2126
PubMed: 25132082
DOI: 10.1016/J.STR.2014.07.002
Page generated: Wed Oct 9 18:39:38 2024

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