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Calcium in PDB 1gw9: Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus

Enzymatic activity of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus

All present enzymatic activity of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus:
5.3.1.5;

Protein crystallography data

The structure of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus, PDB code: 1gw9 was solved by G.Evans, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.05 / 1.55
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.354, 98.540, 102.507, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.8

Other elements in 1gw9:

The structure of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus also contains other interesting chemical elements:

Iodine (I) 29 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus (pdb code 1gw9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus, PDB code: 1gw9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1gw9

Go back to Calcium Binding Sites List in 1gw9
Calcium binding site 1 out of 2 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1387

b:9.6
occ:0.73
OE1 A:GLU217 2.0 22.1 1.0
OD2 A:ASP287 2.1 21.8 1.0
OE2 A:GLU181 2.1 15.4 1.0
OD2 A:ASP245 2.1 17.4 1.0
O3 A:LXC1390 2.3 19.2 1.0
O2 A:LXC1390 2.4 18.2 1.0
C2 A:LXC1390 3.0 21.8 1.0
CD A:GLU181 3.0 17.6 1.0
CD A:GLU217 3.1 18.2 1.0
C3 A:LXC1390 3.2 21.6 1.0
CG A:ASP287 3.2 13.7 1.0
OE1 A:GLU181 3.3 12.9 1.0
CG A:ASP245 3.3 13.4 1.0
CB A:ASP287 3.7 8.8 1.0
O A:HOH2245 3.8 18.9 1.0
O A:HOH2345 3.8 18.9 1.0
CB A:ASP245 3.9 9.3 1.0
OE2 A:GLU217 4.0 18.8 1.0
CE1 A:HIS220 4.1 11.5 1.0
CG A:GLU217 4.1 8.7 1.0
OD1 A:ASP287 4.2 11.7 1.0
CB A:GLU217 4.2 7.4 1.0
OD1 A:ASP245 4.3 12.8 1.0
CG A:GLU181 4.3 10.4 1.0
C4 A:LXC1390 4.5 23.4 1.0
NE2 A:HIS220 4.5 11.9 1.0
C1 A:LXC1390 4.5 27.7 1.0
ND1 A:HIS220 4.8 11.5 1.0
CA A:CA1388 4.9 10.6 0.6
ND2 A:ASN215 4.9 10.9 1.0
O A:HOH2346 5.0 20.9 1.0

Calcium binding site 2 out of 2 in 1gw9

Go back to Calcium Binding Sites List in 1gw9
Calcium binding site 2 out of 2 in the Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tri-Iodide Derivative of Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1388

b:10.6
occ:0.58
OE2 A:GLU217 2.0 18.8 1.0
OD2 A:ASP255 2.0 29.6 1.0
OD1 A:ASP257 2.3 17.0 1.0
OD1 A:ASP255 2.4 25.4 1.0
O A:HOH2245 2.4 18.9 1.0
CG A:ASP255 2.5 25.1 1.0
O A:HOH2243 2.6 24.4 1.0
NE2 A:HIS220 2.6 11.9 1.0
CD A:GLU217 3.1 18.2 1.0
CD2 A:HIS220 3.2 11.4 1.0
CG A:ASP257 3.2 16.9 1.0
O A:HOH2346 3.4 20.9 1.0
OD2 A:ASP257 3.5 23.8 1.0
OE1 A:GLU217 3.6 22.1 1.0
CE1 A:HIS220 3.8 11.5 1.0
ND2 A:ASN247 3.9 9.2 1.0
O2 A:LXC1390 4.1 18.2 1.0
CB A:ASP255 4.1 12.8 1.0
CG A:GLU217 4.4 8.7 1.0
O A:HOH2235 4.4 11.0 1.0
O A:HOH2246 4.4 28.8 1.0
CG A:HIS220 4.5 9.7 1.0
CB A:ASP257 4.7 9.8 1.0
ND1 A:HIS220 4.7 11.5 1.0
OD2 A:ASP287 4.7 21.8 1.0
NZ A:LYS183 4.8 14.1 1.0
CE A:LYS183 4.8 10.4 1.0
CA A:CA1387 4.9 9.6 0.7
O1 A:LXC1390 4.9 30.2 1.0

Reference:

G.Evans, G.Bricogne. Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods For Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Acta Crystallogr.,Sect.D V. 58 976 2002.
ISSN: ISSN 0907-4449
PubMed: 12037300
DOI: 10.1107/S0907444902005486
Page generated: Sat Dec 12 02:58:24 2020

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