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Magnesium 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:

Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3oi7

Go back to Magnesium Binding Sites List in 3oi7
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg311

b:30.9
occ:1.00
 OG1 A:THR16 2.2 20.3 1.0
O1P A:OI7301 2.9 25.7 1.0
CG2 A:THR16 3.0 18.0 1.0
CB A:THR16 3.1 18.8 1.0
OG1 A:THR25 3.2 17.5 1.0
CD A:ARG69 3.4 15.2 1.0
NE A:ARG69 3.5 15.1 1.0
CB A:THR25 3.6 17.0 1.0
CG2 A:THR25 3.7 14.3 1.0
CB A:SER19 3.9 22.3 1.0
P1 A:OI7301 4.0 21.7 1.0
O3P A:OI7301 4.1 24.2 1.0
N A:SER19 4.1 22.5 1.0
O A:HOH282 4.2 15.8 1.0
CZ A:ARG69 4.3 16.4 1.0
CA A:THR16 4.4 19.5 1.0
CD1 A:LEU30 4.5 22.6 1.0
CA A:SER19 4.5 22.4 1.0
CB A:TRP18 4.6 23.8 1.0
OG A:SER19 4.6 21.4 1.0
N A:THR16 4.6 17.9 1.0
CB A:LEU30 4.7 21.1 1.0
O1 A:OI7301 4.7 30.4 1.0
CG A:ARG69 4.8 14.7 1.0
NH2 A:ARG69 4.9 14.3 1.0
C A:TRP18 4.9 22.5 1.0
NH1 A:ARG69 5.0 16.5 1.0

Magnesium binding site 2 out of 4 in 3oi7

Go back to Magnesium Binding Sites List in 3oi7
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg311

b:30.1
occ:1.00
 OG1 B:THR16 2.2 20.2 1.0
CG2 B:THR16 2.9 17.9 1.0
CB B:THR16 2.9 18.9 1.0
OG1 B:THR25 3.2 17.5 1.0
O1P B:OI7301 3.2 25.7 1.0
CD B:ARG69 3.3 15.2 1.0
NE B:ARG69 3.5 15.1 1.0
CB B:THR25 3.6 16.9 1.0
CG2 B:THR25 3.6 14.3 1.0
O B:HOH281 3.8 25.8 1.0
CB B:SER19 4.1 22.3 1.0
CD1 B:LEU30 4.2 22.8 1.0
N B:SER19 4.2 22.4 1.0
O3P B:OI7301 4.2 24.2 1.0
NA B:NA272 4.2 24.9 1.0
CZ B:ARG69 4.2 16.6 1.0
P1 B:OI7301 4.3 21.8 1.0
CA B:THR16 4.3 19.4 1.0
CB B:LEU30 4.4 21.2 1.0
CB B:TRP18 4.5 23.8 1.0
N B:THR16 4.6 18.0 1.0
CA B:SER19 4.7 22.4 1.0
CG B:ARG69 4.8 14.8 1.0
OG B:SER19 4.8 21.5 1.0
CG B:LEU30 4.8 22.6 1.0
NH1 B:ARG69 4.9 16.5 1.0
NH2 B:ARG69 4.9 14.3 1.0
N B:TRP18 5.0 23.0 1.0
C B:THR16 5.0 20.7 1.0
O1 B:OI7301 5.0 30.6 1.0

Magnesium binding site 3 out of 4 in 3oi7

Go back to Magnesium Binding Sites List in 3oi7
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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:Mg311

b:30.0
occ:1.00
 OG1 C:THR16 2.2 20.2 1.0
O1P C:OI7301 2.9 25.7 1.0
CG2 C:THR16 3.0 18.1 1.0
CB C:THR16 3.0 18.8 1.0
OG1 C:THR25 3.2 17.6 1.0
CD C:ARG69 3.4 15.3 1.0
NE C:ARG69 3.5 15.1 1.0
CB C:THR25 3.6 17.0 1.0
CG2 C:THR25 3.7 14.3 1.0
CB C:SER19 4.0 22.3 1.0
O C:HOH341 4.0 25.5 1.0
NA C:NA272 4.0 25.9 1.0
P1 C:OI7301 4.0 21.5 1.0
O3P C:OI7301 4.1 24.2 1.0
N C:SER19 4.2 22.5 1.0
CZ C:ARG69 4.3 16.4 1.0
CA C:THR16 4.4 19.4 1.0
CD1 C:LEU30 4.4 22.7 1.0
CB C:TRP18 4.6 23.8 1.0
CB C:LEU30 4.6 21.2 1.0
OG C:SER19 4.6 21.5 1.0
CA C:SER19 4.6 22.4 1.0
N C:THR16 4.6 18.0 1.0
O1 C:OI7301 4.7 30.5 1.0
CG C:ARG69 4.8 14.8 1.0
NH2 C:ARG69 4.8 14.4 1.0
NH1 C:ARG69 4.9 16.7 1.0

Magnesium binding site 4 out of 4 in 3oi7

Go back to Magnesium Binding Sites List in 3oi7
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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
D:Mg311

b:27.8
occ:1.00
 OG1 D:THR16 2.2 20.0 1.0
O1P D:OI7301 2.9 25.9 1.0
CG2 D:THR16 3.0 17.9 1.0
CB D:THR16 3.0 18.8 1.0
OG1 D:THR25 3.1 17.5 1.0
CD D:ARG69 3.5 15.3 1.0
NE D:ARG69 3.6 15.1 1.0
CB D:THR25 3.6 17.0 1.0
O D:HOH336 3.6 29.5 1.0
CG2 D:THR25 3.7 14.1 1.0
CB D:SER19 3.9 22.3 1.0
NA D:NA272 4.0 25.8 1.0
P1 D:OI7301 4.1 21.9 1.0
N D:SER19 4.1 22.4 1.0
O3P D:OI7301 4.2 24.4 1.0
CZ D:ARG69 4.3 16.6 1.0
CA D:THR16 4.4 19.4 1.0
CD1 D:LEU30 4.4 22.6 1.0
CA D:SER19 4.5 22.4 1.0
OG D:SER19 4.6 21.4 1.0
CB D:TRP18 4.6 23.8 1.0
N D:THR16 4.6 17.8 1.0
CB D:LEU30 4.7 21.2 1.0
O1 D:OI7301 4.7 30.6 1.0
CG D:ARG69 4.9 14.6 1.0
NH2 D:ARG69 4.9 14.3 1.0
C D:TRP18 4.9 22.4 1.0
NH1 D:ARG69 5.0 16.5 1.0
N D:TRP18 5.0 22.9 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 Dec 14 08:35:05 2020

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