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Sodium in PDB 8eyp: Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal

Enzymatic activity of Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal

All present enzymatic activity of Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal:
4.2.1.20;

Protein crystallography data

The structure of Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal, PDB code: 8eyp was solved by V.N.Drago, A.Kovalevsky, M.P.Blakeley, V.T.Forsyth, T.C.Mueser, 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 C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.51, 61.86, 67.67, 90, 94.74, 90
R / Rfree (%) 22.4 / 28.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal (pdb code 8eyp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal, PDB code: 8eyp:

Sodium binding site 1 out of 1 in 8eyp

Go back to Sodium Binding Sites List in 8eyp
Sodium binding site 1 out of 1 in the Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Joint X-Ray/Neutron Structure of Salmonella Typhimurium Tryptophan Synthase Internal Aldimine From Microgravity-Grown Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2001

b:37.2
occ:1.00
O B:SER1308 2.4 33.2 1.0
O B:DOD2140 2.4 44.5 1.0
O B:GLY1232 2.4 33.2 1.0
O B:DOD2185 2.5 33.1 1.0
O B:PHE1306 2.5 44.2 1.0
D1 B:DOD2185 2.9 31.6 1.0
DB3 B:PHE1306 2.9 46.3 0.9
HB3 B:PHE1306 2.9 46.3 0.1
D2 B:DOD2140 3.0 44.0 1.0
D1 B:DOD2140 3.1 44.8 1.0
D2 B:DOD2185 3.3 34.2 1.0
DD2 B:PHE1306 3.3 45.2 0.5
HD2 B:PHE1306 3.3 45.2 0.5
HG3 B:PRO1270 3.4 33.8 0.4
DG3 B:PRO1270 3.4 33.8 0.6
DD2 B:PRO1270 3.4 34.2 0.6
HD2 B:PRO1270 3.4 34.2 0.4
C B:GLY1232 3.5 33.2 1.0
C B:PHE1306 3.5 45.6 1.0
DA2 B:GLY1232 3.6 31.4 1.0
C B:SER1308 3.6 35.7 1.0
D B:SER1308 3.6 35.1 1.0
HG2 B:PRO1270 3.6 34.0 0.1
DG2 B:PRO1270 3.6 34.0 0.9
CG B:PRO1270 3.8 33.9 1.0
DB B:VAL1309 3.8 33.3 1.0
CB B:PHE1306 3.8 46.7 1.0
H B:PHE1306 3.9 48.3 0.4
D B:PHE1306 3.9 48.3 0.6
CD B:PRO1270 3.9 33.0 1.0
DD3 B:PRO1270 3.9 34.0 1.0
HD3 B:PRO1270 3.9 34.0 0.0
N B:SER1308 3.9 36.9 1.0
HA B:VAL1309 4.1 34.1 0.1
DA B:VAL1309 4.1 34.1 0.9
CA B:GLY1232 4.1 33.0 1.0
CA B:PHE1306 4.1 46.4 1.0
CD2 B:PHE1306 4.1 45.1 1.0
HA2 B:GLY1233 4.2 30.8 0.2
DA2 B:GLY1233 4.2 30.8 0.8
O B:GLY1268 4.3 36.1 1.0
N B:PHE1306 4.3 48.3 1.0
CA B:SER1308 4.4 34.7 1.0
DG12 B:VAL1231 4.4 33.6 0.8
HG12 B:VAL1231 4.4 33.6 0.1
CG B:PHE1306 4.4 45.2 1.0
HG21 B:VAL1309 4.4 34.7 0.1
DG21 B:VAL1309 4.4 34.7 0.9
DA B:PRO1307 4.5 40.9 1.0
O B:VAL1231 4.5 34.1 1.0
C B:PRO1307 4.5 39.7 1.0
N B:VAL1309 4.5 33.5 1.0
O B:LEU1304 4.6 42.1 1.0
N B:PRO1307 4.6 44.6 1.0
CA B:VAL1309 4.6 33.8 1.0
N B:GLY1233 4.6 30.3 1.0
CB B:VAL1309 4.6 33.9 1.0
DB2 B:PHE1306 4.6 46.2 0.4
HB2 B:PHE1306 4.6 46.2 0.6
DA B:SER1308 4.7 35.0 0.7
HA B:SER1308 4.7 35.0 0.3
CA B:PRO1307 4.7 41.3 1.0
HA3 B:GLY1232 4.8 32.7 0.2
DA3 B:GLY1232 4.8 32.7 0.8
DD2 B:PRO1257 4.8 32.1 0.9
HD2 B:PRO1257 4.8 32.1 0.1
OE2 B:GLU1256 4.9 31.1 1.0
CA B:GLY1233 5.0 30.1 1.0
N B:GLY1232 5.0 32.6 1.0
HG B:SER1297 5.0 54.0 0.4
DG B:SER1297 5.0 54.0 0.6

Reference:

V.N.Drago, J.M.Devos, M.P.Blakeley, V.T.Forsyth, J.M.Parks, A.Kovalevsky, T.C.Mueser. Microgravity-Assisted Neutron Crystallography Reveals Functional Hydrogen Atoms in the Resting State of Tryptophan Synthase Cell Rep Phys Sci 2024.
ISSN: ESSN 2666-3864
DOI: 10.1016/J.XCRP.2024.101827
Page generated: Wed Oct 9 11:45:12 2024

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