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Nickel in PDB 3kco: Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN)

Enzymatic activity of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN)

All present enzymatic activity of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN):
5.3.1.5;

Protein crystallography data

The structure of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN), PDB code: 3kco 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) N/A / 1.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.007, 99.669, 102.862, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 21.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN) (pdb code 3kco). 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 Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN), PDB code: 3kco:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3kco

Go back to Nickel Binding Sites List in 3kco
Nickel binding site 1 out of 3 in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni391

b:21.0
occ:0.50
O A:DOD1001 1.9 21.8 1.0
NI A:NI392 1.9 19.0 0.5
NE2 A:HIS220 2.0 17.3 1.0
O2 A:GLO401 2.0 25.2 1.0
DO2 A:GLO401 2.2 26.5 1.0
D2 A:DOD1001 2.2 25.2 1.0
OE2 A:GLU217 2.3 15.7 1.0
O1 A:GLO401 2.3 21.8 1.0
D1 A:DOD1001 2.5 24.1 1.0
CE1 A:HIS220 2.7 15.5 1.0
HE1 A:HIS220 2.8 15.8 1.0
C1 A:GLO401 2.9 27.5 1.0
CD A:GLU217 2.9 14.7 1.0
OE1 A:GLU217 2.9 16.3 1.0
C2 A:GLO401 3.0 25.5 1.0
CD2 A:HIS220 3.2 14.4 1.0
OD2 A:ASP255 3.2 13.5 0.5
D2 A:GLO401 3.5 26.0 1.0
HD2 A:HIS220 3.6 14.6 1.0
DZ2 A:LYS183 3.6 16.5 1.0
NI A:NI393 3.7 20.6 1.0
OD1 A:ASP257 3.7 14.5 1.0
D1 A:GLO401 3.8 26.5 1.0
ND1 A:HIS220 3.8 15.4 1.0
OD1 A:ASP255 3.9 9.4 0.5
CG A:ASP255 3.9 10.3 0.5
OD2 A:ASP257 4.0 16.6 1.0
HD2 A:LYS183 4.0 14.5 1.0
DO3 A:GLO401 4.0 29.2 1.0
HE3 A:LYS183 4.1 15.3 1.0
CG A:HIS220 4.1 12.0 1.0
OD2 A:ASP287 4.1 15.9 1.0
DD21 A:ASN247 4.2 12.9 0.9
OE2 A:GLU181 4.2 20.4 1.0
C3 A:GLO401 4.2 28.9 1.0
CG A:GLU217 4.3 12.2 1.0
CG A:ASP257 4.3 14.1 1.0
D1 A:DOD1110 4.3 37.8 1.0
O3 A:GLO401 4.4 29.6 1.0
D1 A:DOD1084 4.5 45.4 1.0
NZ A:LYS183 4.5 17.1 1.0
HG2 A:GLU217 4.5 12.5 1.0
HB3 A:GLU217 4.6 12.4 1.0
DD1 A:HIS220 4.6 15.5 1.0
DZ3 A:LYS183 4.6 16.9 1.0
CE A:LYS183 4.6 15.5 1.0
D3 A:GLO401 4.7 29.0 1.0
CG A:ASP287 4.7 14.4 1.0
DD22 A:ASN247 4.8 12.6 1.0
CD A:LYS183 4.8 13.2 1.0
HB2 A:GLU217 4.8 12.9 1.0
ND2 A:ASN247 4.8 13.1 1.0
CB A:GLU217 4.9 11.7 1.0
D2 A:DOD1110 4.9 39.1 1.0
O A:DOD1110 5.0 37.8 1.0
HB3 A:ASP287 5.0 14.4 1.0
HG3 A:LYS183 5.0 13.2 1.0
HG3 A:GLU217 5.0 13.0 1.0

Nickel binding site 2 out of 3 in 3kco

Go back to Nickel Binding Sites List in 3kco
Nickel binding site 2 out of 3 in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni392

b:19.0
occ:0.50
NI A:NI391 1.9 21.0 0.5
OD2 A:ASP255 2.1 13.5 0.5
OE2 A:GLU217 2.2 15.7 1.0
OD1 A:ASP255 2.2 9.4 0.5
OD1 A:ASP257 2.2 14.5 1.0
CG A:ASP255 2.4 10.3 0.5
NE2 A:HIS220 2.6 17.3 1.0
O A:DOD1001 2.7 21.8 1.0
D2 A:DOD1001 2.7 25.2 1.0
D1 A:DOD1001 2.8 24.1 1.0
HD2 A:HIS220 2.9 14.6 1.0
CD2 A:HIS220 3.0 14.4 1.0
CG A:ASP257 3.1 14.1 1.0
D1 A:DOD1017 3.3 21.4 1.0
OD2 A:ASP257 3.3 16.6 1.0
DD21 A:ASN247 3.3 12.9 0.9
CD A:GLU217 3.3 14.7 1.0
O1 A:GLO401 3.4 21.8 1.0
D1 A:DOD1084 3.5 45.4 1.0
HE3 A:LYS183 3.8 15.3 1.0
CE1 A:HIS220 3.8 15.5 1.0
DO2 A:GLO401 3.8 26.5 1.0
O2 A:GLO401 3.9 25.2 1.0
DZ2 A:LYS183 3.9 16.5 1.0
CB A:ASP255 3.9 6.7 0.5
OE1 A:GLU217 4.0 16.3 1.0
ND2 A:ASN247 4.0 13.1 1.0
O A:DOD1017 4.0 19.2 1.0
DD22 A:ASN247 4.1 12.6 1.0
DZ3 A:LYS183 4.2 16.9 1.0
HG2 A:GLU217 4.3 12.5 1.0
HE1 A:HIS220 4.3 15.8 1.0
CG A:HIS220 4.3 12.0 1.0
HB2 A:ASP255 4.3 10.0 1.0
C1 A:GLO401 4.4 27.5 1.0
HB3 A:ASP255 4.4 8.8 1.0
O A:DOD1084 4.4 44.1 1.0
NZ A:LYS183 4.4 17.1 1.0
CG A:GLU217 4.5 12.2 1.0
CB A:ASP257 4.5 13.0 1.0
CE A:LYS183 4.6 15.5 1.0
HA A:ASP257 4.6 13.0 1.0
D A:ASP257 4.7 12.1 0.6
ND1 A:HIS220 4.7 15.4 1.0
D2 A:DOD1017 4.7 23.1 1.0
HD2 A:LYS183 4.8 14.5 1.0
HA3 A:GLY219 4.8 11.0 1.0
C2 A:GLO401 4.8 25.5 1.0
HA A:ASP255 4.8 7.5 1.0
CA A:ASP255 4.8 6.4 0.5
DZ3 A:LYS289 4.8 37.1 1.0
D A:HIS220 4.9 16.9 1.0
CA A:ASP257 5.0 12.9 1.0
N A:ASP257 5.0 11.7 1.0

Nickel binding site 3 out of 3 in 3kco

Go back to Nickel Binding Sites List in 3kco
Nickel binding site 3 out of 3 in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two NI2+ Cations and D12-D-Glucose in the Linear Form (Refined Jointly with X-Ray Structure 3KBN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni393

b:20.6
occ:1.00
OE1 A:GLU217 2.0 16.3 1.0
OE2 A:GLU181 2.0 20.4 1.0
OD2 A:ASP287 2.1 15.9 1.0
O2 A:GLO401 2.2 25.2 1.0
DO2 A:GLO401 2.2 26.5 1.0
OD2 A:ASP245 2.2 15.3 1.0
O4 A:GLO401 2.4 28.0 1.0
DO4 A:GLO401 2.8 26.6 1.0
CD A:GLU181 3.0 17.7 1.0
C2 A:GLO401 3.1 25.5 1.0
CG A:ASP287 3.2 14.4 1.0
OE1 A:GLU181 3.2 18.4 1.0
D2 A:GLO401 3.2 26.0 1.0
CD A:GLU217 3.2 14.7 1.0
CG A:ASP245 3.3 13.5 1.0
O3 A:GLO401 3.4 29.6 1.0
C3 A:GLO401 3.4 28.9 1.0
HB3 A:ASP287 3.4 14.4 1.0
D2 A:DOD1096 3.4 33.5 1.0
C4 A:GLO401 3.4 29.2 1.0
HB2 A:GLU217 3.5 12.9 1.0
HB3 A:ASP245 3.6 12.6 1.0
HB2 A:ASP287 3.6 15.0 1.0
CB A:ASP287 3.6 13.8 1.0
NI A:NI391 3.7 21.0 0.5
HE1 A:HIS220 3.7 15.8 1.0
O A:DOD1096 3.8 32.8 1.0
DO3 A:GLO401 3.8 29.2 1.0
CB A:ASP245 3.8 12.1 1.0
O A:DOD1001 3.9 21.8 1.0
D4 A:GLO401 3.9 20.3 1.0
HB2 A:ASP245 3.9 12.8 1.0
OE2 A:GLU217 4.0 15.7 1.0
D1 A:DOD1096 4.1 34.4 1.0
CE1 A:HIS220 4.2 15.5 1.0
CG A:GLU217 4.2 12.2 1.0
OD1 A:ASP287 4.3 15.2 1.0
D1 A:DOD1001 4.3 24.1 1.0
CB A:GLU217 4.3 11.7 1.0
CG A:GLU181 4.3 15.4 1.0
D3 A:GLO401 4.4 29.0 1.0
DD21 A:ASN215 4.4 15.5 1.0
OD1 A:ASP245 4.4 15.3 1.0
C1 A:GLO401 4.4 27.5 1.0
HG3 A:GLU217 4.5 13.0 1.0
D5 A:GLO401 4.5 29.5 1.0
C5 A:GLO401 4.5 21.8 1.0
D62 A:GLO401 4.6 24.7 1.0
HG3 A:GLU181 4.6 15.5 1.0
HG2 A:GLU181 4.6 16.1 1.0
HZ2 A:TRP16 4.6 15.7 1.0
HB3 A:GLU217 4.6 12.4 1.0
NE2 A:HIS220 4.7 17.3 1.0
D2 A:DOD1001 4.7 25.2 1.0
DD22 A:ASN215 4.8 14.4 1.0
DO6 A:GLO401 4.8 24.8 1.0
ND2 A:ASN215 4.9 13.8 1.0
O1 A:GLO401 4.9 21.8 1.0
ND1 A:HIS220 5.0 15.4 1.0

Reference:

A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, P.Langan. Metal Ion Roles and the Movement of Hydrogen During Reaction Catalyzed By D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study. Structure V. 18 688 2010.
ISSN: ISSN 0969-2126
PubMed: 20541506
DOI: 10.1016/J.STR.2010.03.011
Page generated: Fri Sep 25 08:26:15 2020
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