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Sodium in PDB 3oi7: Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate

Enzymatic activity of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate

All present enzymatic activity of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate:
3.1.3.11;

Protein crystallography data

The structure of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate, PDB code: 3oi7 was solved by A.U.Singer, X.Xu, A.Dong, H.Cui, M.F.Clasquin, A.A.Caudy, A.M.Edwards, A.Savchenko, A.Joachimiak, A.F.Yakunin, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.50 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.559, 74.945, 83.615, 90.04, 89.92, 77.22
R / Rfree (%) 22.8 / 26

Other elements in 3oi7:

The structure of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate (pdb code 3oi7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate, PDB code: 3oi7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3oi7

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Sodium binding site 1 out of 5 in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na272

b:29.4
occ:1.00
 O A:ARG154 2.8 17.2 1.0
O A:PRO214 2.9 19.7 1.0
ND2 A:ASN157 3.0 16.6 1.0
CB A:ASN157 3.5 18.9 1.0
CD A:PRO214 3.5 20.2 1.0
C A:ARG154 3.6 17.0 1.0
CA A:ARG154 3.6 17.0 1.0
N A:PRO214 3.7 19.8 1.0
CG A:ASN157 3.7 20.2 1.0
CG A:LEU158 3.7 19.3 1.0
CB A:PRO214 3.8 18.9 1.0
C A:PRO214 3.8 20.0 1.0
N A:LEU158 3.8 19.8 1.0
CG A:PRO214 4.0 19.3 1.0
CG1 A:VAL213 4.0 15.3 1.0
CA A:PRO214 4.0 19.6 1.0
CB A:ARG154 4.0 17.4 1.0
C A:VAL213 4.3 19.8 1.0
CG2 A:VAL216 4.4 20.2 1.0
C A:ASN157 4.4 19.8 1.0
CD1 A:LEU158 4.4 18.1 1.0
CG A:ARG154 4.4 17.2 1.0
CB A:LEU158 4.5 19.8 1.0
CA A:ASN157 4.5 19.1 1.0
CA A:LEU158 4.5 20.2 1.0
CD2 A:LEU158 4.5 13.6 1.0
CA A:VAL213 4.7 19.3 1.0
O A:ALA153 4.7 16.4 1.0
N A:ARG154 4.9 16.4 1.0
N A:ILE155 4.9 17.2 1.0
OD1 A:ASN157 4.9 20.8 1.0
N A:ASN157 5.0 18.6 1.0
CB A:VAL213 5.0 19.4 1.0

Sodium binding site 2 out of 5 in 3oi7

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Sodium binding site 2 out of 5 in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na272

b:24.9
occ:1.00
 O1P B:OI7301 2.2 25.7 1.0
O B:GLY14 3.0 16.3 1.0
O2P B:OI7301 3.2 24.1 1.0
O B:ALA13 3.2 15.1 1.0
P1 B:OI7301 3.3 21.8 1.0
CB B:SER19 3.4 22.3 1.0
OG B:SER19 3.5 21.5 1.0
NE B:ARG12 3.8 16.7 1.0
C B:GLY14 3.9 15.5 1.0
C B:ALA13 3.9 14.3 1.0
NH2 B:ARG12 4.1 15.7 1.0
CB B:ALA234 4.1 17.6 1.0
CB B:ALA13 4.2 13.5 1.0
MG B:MG311 4.2 30.1 1.0
O3P B:OI7301 4.3 24.2 1.0
CZ B:ARG12 4.3 17.1 1.0
O1 B:OI7301 4.5 30.6 1.0
CA B:ALA234 4.5 18.3 1.0
CG B:ARG12 4.5 12.8 1.0
CG2 B:THR16 4.5 17.9 1.0
CA B:ALA13 4.6 13.9 1.0
N B:THR16 4.6 18.0 1.0
CA B:GLN15 4.6 16.2 1.0
OG1 B:THR16 4.6 20.2 1.0
N B:GLN15 4.6 16.0 1.0
N B:GLY14 4.7 14.6 1.0
C1 B:OI7301 4.7 36.5 1.0
CD B:ARG12 4.7 12.4 1.0
C B:GLN15 4.8 17.1 1.0
CA B:GLY14 4.8 14.7 1.0
O B:HOH281 4.9 25.8 1.0
CA B:SER19 4.9 22.4 1.0
N B:ALA13 5.0 14.0 1.0

Sodium binding site 3 out of 5 in 3oi7

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Sodium binding site 3 out of 5 in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na272

b:25.9
occ:1.00
 O1P C:OI7301 2.2 25.7 1.0
O C:GLY14 3.0 16.4 1.0
O2P C:OI7301 3.3 23.9 1.0
O C:ALA13 3.3 15.3 1.0
P1 C:OI7301 3.3 21.5 1.0
CB C:SER19 3.4 22.3 1.0
OG C:SER19 3.5 21.5 1.0
C C:GLY14 3.9 15.4 1.0
C C:ALA13 3.9 14.3 1.0
NE C:ARG12 3.9 16.8 1.0
MG C:MG311 4.0 30.0 1.0
CB C:ALA234 4.1 17.5 1.0
NH2 C:ARG12 4.1 15.8 1.0
CB C:ALA13 4.2 13.5 1.0
O3P C:OI7301 4.3 24.2 1.0
CZ C:ARG12 4.4 17.2 1.0
CG2 C:THR16 4.5 18.1 1.0
N C:THR16 4.5 18.0 1.0
CA C:ALA234 4.5 18.3 1.0
O1 C:OI7301 4.5 30.5 1.0
CA C:GLN15 4.5 16.4 1.0
OG1 C:THR16 4.6 20.2 1.0
N C:GLN15 4.6 15.9 1.0
CA C:ALA13 4.6 13.9 1.0
CG C:ARG12 4.6 12.7 1.0
N C:GLY14 4.7 14.7 1.0
C C:GLN15 4.7 17.1 1.0
CA C:GLY14 4.8 14.8 1.0
C1 C:OI7301 4.8 36.6 1.0
CD C:ARG12 4.9 12.3 1.0
CA C:SER19 4.9 22.4 1.0
N C:ALA13 5.0 13.9 1.0

Sodium binding site 4 out of 5 in 3oi7

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Sodium binding site 4 out of 5 in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na273

b:27.4
occ:1.00
 O C:PRO31 2.7 20.7 1.0
CG C:GLU17 2.8 32.2 1.0
N C:GLU17 2.9 22.4 1.0
CB C:GLU17 3.5 25.8 1.0
CA C:THR16 3.8 19.4 1.0
CB C:THR16 3.8 18.8 1.0
CA C:GLU17 3.8 24.5 1.0
C C:THR16 3.8 20.7 1.0
C C:PRO31 3.8 21.1 1.0
CD C:PRO31 4.0 20.9 1.0
N C:THR33 4.0 20.4 1.0
CG2 C:THR33 4.0 18.5 1.0
CD C:GLU17 4.1 41.8 1.0
CG C:PRO31 4.2 20.7 1.0
C C:LEU32 4.2 20.4 1.0
N C:PRO31 4.3 21.1 1.0
CB C:LEU30 4.4 21.2 1.0
OE2 C:GLU17 4.4 46.4 1.0
CA C:THR33 4.5 20.5 1.0
CG2 C:THR16 4.5 18.1 1.0
O C:LEU32 4.6 20.5 1.0
CA C:PRO31 4.6 20.8 1.0
N C:LEU32 4.7 21.0 1.0
CD1 C:LEU30 4.7 22.7 1.0
CA C:LEU32 4.8 20.5 1.0
OG1 C:THR16 4.8 20.2 1.0
CB C:THR33 4.9 20.3 1.0
C C:LEU30 4.9 21.1 1.0
CB C:PRO31 4.9 21.1 1.0
CG C:LEU30 4.9 22.6 1.0
O C:THR16 5.0 21.1 1.0
CD2 C:LEU30 5.0 24.0 1.0

Sodium binding site 5 out of 5 in 3oi7

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Sodium binding site 5 out of 5 in the Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Structure of the H13A Mutant of YKR043C in Complex with Sedoheptulose-1,7-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na272

b:25.8
occ:1.00
 O1P D:OI7301 2.2 25.9 1.0
O D:GLY14 3.0 16.4 1.0
O D:ALA13 3.3 15.3 1.0
O2P D:OI7301 3.3 24.0 1.0
P1 D:OI7301 3.4 21.9 1.0
CB D:SER19 3.4 22.3 1.0
OG D:SER19 3.4 21.4 1.0
C D:GLY14 3.9 15.5 1.0
NE D:ARG12 3.9 16.4 1.0
C D:ALA13 4.0 14.4 1.0
MG D:MG311 4.0 27.8 1.0
CB D:ALA234 4.1 17.5 1.0
NH2 D:ARG12 4.1 15.8 1.0
CB D:ALA13 4.2 13.5 1.0
O3P D:OI7301 4.4 24.4 1.0
CZ D:ARG12 4.4 17.0 1.0
N D:THR16 4.5 17.8 1.0
CA D:GLN15 4.5 16.1 1.0
CG2 D:THR16 4.5 17.9 1.0
O1 D:OI7301 4.5 30.6 1.0
OG1 D:THR16 4.5 20.0 1.0
CA D:ALA234 4.5 18.3 1.0
N D:GLN15 4.6 15.9 1.0
CA D:ALA13 4.6 13.9 1.0
CG D:ARG12 4.6 12.8 1.0
N D:GLY14 4.7 14.7 1.0
C D:GLN15 4.7 16.9 1.0
C1 D:OI7301 4.8 36.6 1.0
CA D:GLY14 4.8 14.8 1.0
CD D:ARG12 4.8 12.2 1.0
O D:HOH336 4.9 29.5 1.0
CA D:SER19 4.9 22.4 1.0
N D:ALA13 5.0 13.8 1.0

Reference:

M.F.Clasquin, E.Melamud, A.Singer, J.R.Gooding, X.Xu, A.Dong, H.Cui, S.R.Campagna, A.Savchenko, A.F.Yakunin, J.D.Rabinowitz, A.A.Caudy. Riboneogenesis in Yeast. Cell(Cambridge,Mass.) V. 145 969 2011.
ISSN: ISSN 0092-8674
PubMed: 21663798
DOI: 10.1016/J.CELL.2011.05.022
Page generated: Mon Oct 7 12:02:33 2024

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