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Nickel in PDB 4dvo: Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9

Enzymatic activity of Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9

All present enzymatic activity of Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9:
5.3.1.5;

Protein crystallography data

The structure of Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9, PDB code: 4dvo was solved by A.Y.Kovalevsky, L.Hanson, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.061, 99.428, 102.798, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9 (pdb code 4dvo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9, PDB code: 4dvo:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 4dvo

Go back to Nickel Binding Sites List in 4dvo
Nickel binding site 1 out of 3 in the Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:21.7
occ:0.50
NI A:NI402 1.8 17.5 0.5
O A:DOD1001 2.0 28.7 1.0
NE2 A:HIS220 2.1 21.1 1.0
O2 A:SOR404 2.2 31.2 1.0
OE2 A:GLU217 2.3 25.6 1.0
DO2 A:SOR404 2.3 36.5 1.0
DO1 A:SOR404 2.4 31.9 1.0
O1 A:SOR404 2.4 31.2 1.0
D1 A:DOD1001 2.5 28.7 1.0
D2 A:DOD1001 2.6 29.0 1.0
CD A:GLU217 2.9 20.7 1.0
OE1 A:GLU217 2.9 24.2 1.0
CE1 A:HIS220 2.9 20.2 1.0
C1 A:SOR404 3.0 32.1 1.0
D11 A:SOR404 3.0 31.7 1.0
OD2 A:ASP255 3.0 31.9 1.0
C2 A:SOR404 3.1 31.5 1.0
HE1 A:HIS220 3.1 21.3 1.0
CD2 A:HIS220 3.2 21.4 1.0
O A:DOD1247 3.4 41.3 1.0
D2 A:SOR404 3.5 30.8 1.0
OD1 A:ASP257 3.5 24.9 1.0
HD2 A:HIS220 3.6 18.4 1.0
NI A:NI403 3.6 32.3 1.0
D1 A:DOD1247 3.8 40.6 1.0
D12 A:SOR404 4.0 32.4 1.0
D2 A:DOD1247 4.0 40.8 1.0
DD22 A:ASN247 4.0 18.4 0.8
HD22 A:ASN247 4.0 18.4 0.2
DZ1 A:LYS183 4.0 20.4 1.0
CG A:ASP255 4.0 32.0 1.0
ND1 A:HIS220 4.1 20.5 1.0
HD2 A:LYS183 4.1 18.4 1.0
OD2 A:ASP287 4.2 23.7 1.0
OD1 A:ASP255 4.2 33.6 1.0
DO3 A:SOR404 4.2 26.1 1.0
HE3 A:LYS183 4.2 19.5 1.0
OE2 A:GLU181 4.2 27.3 1.0
CG A:GLU217 4.2 18.6 1.0
CG A:HIS220 4.3 18.1 1.0
C3 A:SOR404 4.3 29.5 1.0
O3 A:SOR404 4.4 29.3 1.0
CG A:ASP257 4.4 22.5 1.0
OD2 A:ASP257 4.4 29.9 1.0
DD21 A:ASN247 4.5 18.6 1.0
HD21 A:ASN247 4.5 18.6 0.0
HG2 A:GLU217 4.5 19.4 1.0
DZ2 A:LYS183 4.5 21.3 1.0
ND2 A:ASN247 4.6 19.5 1.0
D2 A:DOD1227 4.6 33.6 0.5
NZ A:LYS183 4.6 21.8 1.0
CG A:ASP287 4.6 19.0 1.0
HB3 A:GLU217 4.7 18.3 1.0
HB3 A:ASP287 4.8 16.6 1.0
HB2 A:GLU217 4.8 17.9 1.0
CE A:LYS183 4.8 19.7 1.0
CB A:GLU217 4.9 18.2 1.0
DD1 A:HIS220 4.9 18.6 1.0
O4 A:SOR404 4.9 31.1 1.0
HG3 A:GLU217 4.9 18.5 1.0
OD1 A:ASP287 4.9 21.6 1.0
CD A:LYS183 5.0 16.8 1.0

Nickel binding site 2 out of 3 in 4dvo

Go back to Nickel Binding Sites List in 4dvo
Nickel binding site 2 out of 3 in the Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:17.5
occ:0.50
NI A:NI401 1.8 21.7 0.5
OD2 A:ASP255 1.9 31.9 1.0
OE2 A:GLU217 2.1 25.6 1.0
OD1 A:ASP257 2.4 24.9 1.0
CG A:ASP255 2.5 32.0 1.0
OD1 A:ASP255 2.5 33.6 1.0
NE2 A:HIS220 2.7 21.1 1.0
O A:DOD1001 2.7 28.7 1.0
HD2 A:HIS220 2.8 18.4 1.0
D2 A:DOD1001 2.8 29.0 1.0
DO1 A:SOR404 2.9 31.9 1.0
CD2 A:HIS220 3.1 21.4 1.0
DD22 A:ASN247 3.1 18.4 0.8
HD22 A:ASN247 3.1 18.4 0.2
CD A:GLU217 3.3 20.7 1.0
O A:DOD1247 3.3 41.3 1.0
O1 A:SOR404 3.4 31.2 1.0
CG A:ASP257 3.4 22.5 1.0
D2 A:DOD1247 3.5 40.8 1.0
D1 A:DOD1247 3.5 40.6 1.0
D1 A:DOD1001 3.5 28.7 1.0
OD2 A:ASP257 3.7 29.9 1.0
ND2 A:ASN247 3.8 19.5 1.0
HE3 A:LYS183 3.8 19.5 1.0
DD21 A:ASN247 3.8 18.6 1.0
HD21 A:ASN247 3.8 18.6 0.0
OE1 A:GLU217 3.9 24.2 1.0
CE1 A:HIS220 3.9 20.2 1.0
O2 A:SOR404 4.0 31.2 1.0
CB A:ASP255 4.0 24.1 1.0
DO2 A:SOR404 4.0 36.5 1.0
O A:DOD1026 4.1 23.6 1.0
DZ2 A:LYS183 4.2 21.3 1.0
D11 A:SOR404 4.2 31.7 1.0
HG2 A:GLU217 4.3 19.4 1.0
HB3 A:ASP255 4.3 26.7 1.0
C1 A:SOR404 4.3 32.1 1.0
DZ1 A:LYS183 4.3 20.4 1.0
CG A:HIS220 4.4 18.1 1.0
CG A:GLU217 4.4 18.6 1.0
HE1 A:HIS220 4.4 21.3 1.0
HB2 A:ASP255 4.5 25.9 1.0
HA A:ASP257 4.5 18.7 1.0
D2 A:DOD1026 4.5 26.4 1.0
NZ A:LYS183 4.6 21.8 1.0
HA3 A:GLY219 4.6 16.8 1.0
D A:ASP257 4.6 17.7 0.8
H A:ASP257 4.6 17.7 0.2
CE A:LYS183 4.7 19.7 1.0
CB A:ASP257 4.7 20.1 1.0
ND1 A:HIS220 4.7 20.5 1.0
C2 A:SOR404 4.8 31.5 1.0
HD2 A:LYS183 4.8 18.4 1.0
D1 A:DOD1026 4.9 24.6 1.0
H A:HIS220 4.9 15.6 0.9
D A:HIS220 4.9 15.6 0.1
HA A:ASP255 5.0 20.9 1.0
CA A:ASP255 5.0 19.7 1.0

Nickel binding site 3 out of 3 in 4dvo

Go back to Nickel Binding Sites List in 4dvo
Nickel binding site 3 out of 3 in the Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Room-Temperature Joint X-Ray/Neutron Structure of D-Xylose Isomerase in Complex with 2NI2+ and Per-Deuterated D-Sorbitol at pH 5.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:32.3
occ:1.00
O4 A:SOR404 2.0 31.1 1.0
OE1 A:GLU217 2.1 24.2 1.0
DO2 A:SOR404 2.1 36.5 1.0
OD2 A:ASP287 2.1 23.7 1.0
OE2 A:GLU181 2.2 27.3 1.0
OD2 A:ASP245 2.2 21.4 1.0
O2 A:SOR404 2.2 31.2 1.0
DO4 A:SOR404 2.4 29.5 1.0
DO3 A:SOR404 2.9 26.1 1.0
CD A:GLU181 3.0 23.6 1.0
CG A:ASP287 3.2 19.0 1.0
C4 A:SOR404 3.2 30.5 1.0
D2 A:DOD1163 3.2 45.1 1.0
OE1 A:GLU181 3.3 25.4 1.0
CD A:GLU217 3.3 20.7 1.0
C2 A:SOR404 3.3 31.5 1.0
CG A:ASP245 3.3 20.2 1.0
D1 A:DOD1001 3.4 28.7 1.0
HB2 A:GLU217 3.5 17.9 1.0
HB3 A:ASP287 3.5 16.6 1.0
D4 A:SOR404 3.5 30.8 1.0
C3 A:SOR404 3.5 29.5 1.0
O A:DOD1163 3.6 45.0 1.0
HB3 A:ASP245 3.6 18.5 1.0
O3 A:SOR404 3.6 29.3 1.0
NI A:NI401 3.6 21.7 0.5
HB2 A:ASP287 3.6 16.9 1.0
HE1 A:HIS220 3.6 21.3 1.0
D2 A:SOR404 3.7 30.8 1.0
CB A:ASP287 3.7 16.6 1.0
O A:DOD1001 3.8 28.7 1.0
CB A:ASP245 3.9 17.7 1.0
HB2 A:ASP245 3.9 17.7 1.0
OE2 A:GLU217 4.0 25.6 1.0
CE1 A:HIS220 4.1 20.2 1.0
OD1 A:ASP287 4.2 21.6 1.0
D1 A:DOD1163 4.2 46.1 1.0
CG A:GLU217 4.2 18.6 1.0
CB A:GLU217 4.3 18.2 1.0
OD1 A:ASP245 4.3 20.4 1.0
CG A:GLU181 4.4 22.7 1.0
C5 A:SOR404 4.4 30.9 1.0
D5 A:SOR404 4.4 30.2 1.0
HG3 A:GLU217 4.4 18.5 1.0
NE2 A:HIS220 4.5 21.1 1.0
DD22 A:ASN215 4.5 20.4 1.0
D3 A:SOR404 4.5 30.1 1.0
C1 A:SOR404 4.6 32.1 1.0
HG3 A:GLU181 4.6 21.5 1.0
HZ2 A:TRP16 4.6 20.1 1.0
D62 A:SOR404 4.6 31.8 1.0
D11 A:SOR404 4.6 31.7 1.0
HB3 A:GLU217 4.6 18.3 1.0
HG2 A:GLU181 4.7 22.1 1.0
D2 A:DOD1001 4.7 29.0 1.0
DO6 A:SOR404 4.8 36.3 1.0
HD21 A:ASN215 4.8 19.8 0.1
DD21 A:ASN215 4.8 19.8 0.9
C6 A:SOR404 4.9 31.5 1.0
ND2 A:ASN215 4.9 19.8 1.0
ND1 A:HIS220 5.0 20.5 1.0
O1 A:SOR404 5.0 31.2 1.0

Reference:

A.Kovalevsky, B.L.Hanson, S.A.Mason, V.T.Forsyth, Z.Fisher, M.Mustyakimov, M.P.Blakeley, D.A.Keen, P.Langan. Inhibition of D-Xylose Isomerase By Polyols: Atomic Details By Joint X-Ray/Neutron Crystallography. Acta Crystallogr.,Sect.D V. 68 1201 2012.
ISSN: ISSN 0907-4449
PubMed: 22948921
DOI: 10.1107/S0907444912024808
Page generated: Wed Dec 16 01:29:38 2020

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