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Magnesium in PDB 2xul: Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations

Protein crystallography data

The structure of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations, PDB code: 2xul was solved by K.Zeth, V.-R.Chellamuthu, K.Forchhammer, O.Fokina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.09 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.870, 87.987, 116.341, 90.00, 90.00, 90.00
R / Rfree (%) 17.929 / 22.488

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations (pdb code 2xul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations, PDB code: 2xul:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2xul

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Magnesium binding site 1 out of 6 in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:26.1
occ:1.00
 O3G A:ATP200 1.9 19.2 1.0
O1B A:ATP200 2.0 22.2 1.0
O5 A:AKG201 2.1 23.0 1.0
OE1 A:GLN39 2.1 25.5 1.0
O2 A:AKG201 2.1 20.5 1.0
O2A A:ATP200 2.3 21.3 1.0
C2 A:AKG201 2.9 26.6 1.0
C1 A:AKG201 2.9 23.1 1.0
PB A:ATP200 3.1 23.2 1.0
PG A:ATP200 3.1 23.0 1.0
CD A:GLN39 3.2 26.0 1.0
PA A:ATP200 3.3 21.4 1.0
O3B A:ATP200 3.5 24.1 1.0
O3A A:ATP200 3.5 22.6 1.0
O1G A:ATP200 3.7 22.3 1.0
NE2 A:GLN39 3.7 22.9 1.0
N A:GLY87 3.8 22.6 1.0
O1 A:AKG201 4.1 27.1 1.0
O1A A:ATP200 4.1 21.9 1.0
N A:ARG38 4.2 24.0 1.0
CA A:GLY87 4.2 21.6 1.0
N A:GLN39 4.2 24.9 1.0
CA A:GLY37 4.2 21.9 1.0
O A:HOH2039 4.3 17.6 1.0
O2G A:ATP200 4.3 24.9 1.0
C3 A:AKG201 4.3 28.0 1.0
CB A:ILE86 4.4 25.3 1.0
C A:GLY37 4.4 23.1 1.0
O2B A:ATP200 4.5 21.7 1.0
CG A:GLN39 4.5 24.9 1.0
O5' A:ATP200 4.5 23.3 1.0
CB A:GLN39 4.6 26.2 1.0
C A:ILE86 4.6 23.7 1.0
N A:GLY37 4.6 21.8 1.0
CG A:ARG38 4.8 30.8 1.0
CA A:ILE86 4.9 25.2 1.0
C4 A:AKG201 4.9 30.8 1.0
CA A:ARG38 4.9 25.7 1.0
CA A:GLN39 5.0 26.4 1.0

Magnesium binding site 2 out of 6 in 2xul

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Magnesium binding site 2 out of 6 in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:21.9
occ:1.00
 O1B B:ATP200 1.9 20.2 1.0
O2A B:ATP200 2.1 18.0 1.0
OE1 B:GLN39 2.1 22.2 1.0
O2 B:AKG201 2.1 22.2 1.0
O3G B:ATP200 2.1 23.4 1.0
O5 B:AKG201 2.3 21.6 1.0
C1 B:AKG201 2.9 24.9 1.0
C2 B:AKG201 3.0 23.6 1.0
PB B:ATP200 3.1 19.4 1.0
PA B:ATP200 3.3 21.2 1.0
CD B:GLN39 3.3 25.7 1.0
PG B:ATP200 3.3 24.3 1.0
O3B B:ATP200 3.5 18.1 1.0
O3A B:ATP200 3.6 20.8 1.0
N B:GLY87 3.7 20.6 1.0
O1G B:ATP200 3.8 21.9 1.0
N B:ARG38 3.9 23.2 1.0
NE2 B:GLN39 3.9 23.1 1.0
O B:HOH2049 4.0 20.7 1.0
N B:GLN39 4.1 26.5 1.0
O1A B:ATP200 4.1 17.9 1.0
CA B:GLY87 4.1 20.0 1.0
O1 B:AKG201 4.1 26.0 1.0
CA B:GLY37 4.1 20.4 1.0
C B:GLY37 4.3 22.7 1.0
CB B:ILE86 4.3 22.7 1.0
O2B B:ATP200 4.4 18.1 1.0
N B:GLY37 4.5 20.9 1.0
O5' B:ATP200 4.5 19.8 1.0
O2G B:ATP200 4.5 25.2 1.0
CG B:GLN39 4.5 26.4 1.0
CB B:GLN39 4.5 27.5 1.0
C3 B:AKG201 4.5 23.6 1.0
C B:ILE86 4.6 21.2 1.0
CA B:ARG38 4.8 25.4 1.0
CA B:GLN39 4.8 27.6 1.0
CA B:ILE86 4.9 21.4 1.0
C B:ARG38 4.9 25.7 1.0
CB B:ARG38 5.0 25.6 1.0

Magnesium binding site 3 out of 6 in 2xul

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Magnesium binding site 3 out of 6 in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:21.1
occ:1.00
 O3G C:ATP200 2.0 13.8 1.0
O2 C:AKG201 2.0 20.1 1.0
O2A C:ATP200 2.0 22.0 1.0
O5 C:AKG201 2.1 17.6 1.0
OE1 C:GLN39 2.1 24.0 1.0
O1B C:ATP200 2.2 22.2 1.0
C1 C:AKG201 2.8 19.2 1.0
C2 C:AKG201 2.8 19.0 1.0
PA C:ATP200 3.2 19.5 1.0
CD C:GLN39 3.2 24.3 1.0
PG C:ATP200 3.2 20.5 1.0
PB C:ATP200 3.2 18.5 1.0
O3B C:ATP200 3.6 21.6 1.0
O3A C:ATP200 3.6 19.3 1.0
N C:GLY87 3.6 20.9 1.0
NE2 C:GLN39 3.8 19.6 1.0
O1G C:ATP200 3.9 17.7 1.0
O1 C:AKG201 4.0 17.7 1.0
N C:ARG38 4.0 23.0 1.0
O C:HOH2038 4.1 19.6 1.0
O1A C:ATP200 4.1 17.7 1.0
CA C:GLY87 4.1 20.6 1.0
CA C:GLY37 4.2 21.3 1.0
N C:GLN39 4.2 25.2 1.0
CB C:ILE86 4.3 23.7 1.0
C3 C:AKG201 4.3 22.4 1.0
C C:GLY37 4.4 22.3 1.0
O5' C:ATP200 4.4 19.9 1.0
C C:ILE86 4.4 22.4 1.0
CG C:GLN39 4.5 25.5 1.0
O2G C:ATP200 4.5 15.9 1.0
N C:GLY37 4.5 20.9 1.0
CB C:GLN39 4.6 25.7 1.0
O2B C:ATP200 4.7 17.6 1.0
CA C:ILE86 4.7 23.5 1.0
CB C:ARG38 4.7 26.4 1.0
CA C:ARG38 4.8 25.3 1.0
C4 C:AKG201 5.0 25.2 1.0

Magnesium binding site 4 out of 6 in 2xul

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Magnesium binding site 4 out of 6 in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:20.0
occ:1.00
 O3G D:ATP200 2.0 18.6 1.0
O2A D:ATP200 2.1 20.4 1.0
O1B D:ATP200 2.1 20.3 1.0
O2 D:AKG201 2.1 24.8 1.0
OE1 D:GLN39 2.1 25.3 1.0
O5 D:AKG201 2.2 23.5 1.0
C1 D:AKG201 2.9 25.1 1.0
C2 D:AKG201 3.0 25.1 1.0
PB D:ATP200 3.1 20.0 1.0
PG D:ATP200 3.2 21.8 1.0
PA D:ATP200 3.2 20.1 1.0
CD D:GLN39 3.3 26.7 1.0
O3B D:ATP200 3.5 19.1 1.0
O3A D:ATP200 3.5 22.5 1.0
N D:GLY87 3.6 20.2 1.0
O1G D:ATP200 3.7 21.1 1.0
NE2 D:GLN39 3.9 25.8 1.0
O1A D:ATP200 4.0 22.3 1.0
N D:ARG38 4.1 24.6 1.0
CA D:GLY87 4.1 20.4 1.0
O1 D:AKG201 4.1 27.7 1.0
O D:HOH2040 4.2 15.7 1.0
N D:GLN39 4.2 27.9 1.0
CA D:GLY37 4.3 21.9 1.0
CB D:ILE86 4.3 22.0 1.0
C D:GLY37 4.4 24.8 1.0
O2G D:ATP200 4.4 22.0 1.0
C3 D:AKG201 4.4 22.1 1.0
C D:ILE86 4.4 21.5 1.0
O5' D:ATP200 4.5 20.9 1.0
CG D:GLN39 4.5 25.9 1.0
CB D:GLN39 4.5 28.2 1.0
O2B D:ATP200 4.5 23.2 1.0
N D:GLY37 4.6 22.0 1.0
CA D:ILE86 4.7 21.4 1.0
CA D:GLN39 4.9 28.3 1.0
CA D:ARG38 5.0 25.9 1.0
C4 D:AKG201 5.0 22.8 1.0

Magnesium binding site 5 out of 6 in 2xul

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Magnesium binding site 5 out of 6 in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:18.1
occ:1.00
 O3G E:ATP200 2.0 21.2 1.0
OE1 E:GLN39 2.1 21.5 1.0
O2 E:AKG201 2.1 19.4 1.0
O1B E:ATP200 2.1 17.9 1.0
O5 E:AKG201 2.1 19.3 1.0
O2A E:ATP200 2.2 18.9 1.0
C1 E:AKG201 2.8 23.1 1.0
C2 E:AKG201 2.8 22.7 1.0
PB E:ATP200 3.2 20.6 1.0
CD E:GLN39 3.3 22.4 1.0
PG E:ATP200 3.3 22.9 1.0
PA E:ATP200 3.4 19.5 1.0
N E:GLY87 3.7 20.9 1.0
O3A E:ATP200 3.7 23.1 1.0
O3B E:ATP200 3.7 22.0 1.0
O1G E:ATP200 3.9 22.3 1.0
NE2 E:GLN39 4.0 20.8 1.0
O1 E:AKG201 4.0 24.4 1.0
O E:HOH2038 4.1 21.5 1.0
N E:ARG38 4.1 24.4 1.0
CA E:GLY87 4.1 20.5 1.0
N E:GLN39 4.1 25.0 1.0
O1A E:ATP200 4.2 23.0 1.0
CA E:GLY37 4.2 22.0 1.0
CB E:ILE86 4.3 22.0 1.0
C3 E:AKG201 4.3 17.9 1.0
C E:GLY37 4.4 23.1 1.0
CG E:GLN39 4.5 25.2 1.0
C E:ILE86 4.5 21.4 1.0
CB E:GLN39 4.5 24.9 1.0
N E:GLY37 4.5 21.5 1.0
O2G E:ATP200 4.5 20.5 1.0
O5' E:ATP200 4.6 23.5 1.0
O2B E:ATP200 4.6 23.7 1.0
CA E:ILE86 4.7 22.4 1.0
CB E:ARG38 4.8 25.6 1.0
CA E:GLN39 4.9 25.1 1.0
C4 E:AKG201 4.9 20.2 1.0
CA E:ARG38 4.9 25.8 1.0
CG2 E:ILE86 5.0 22.6 1.0

Magnesium binding site 6 out of 6 in 2xul

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Magnesium binding site 6 out of 6 in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at High 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:29.5
occ:1.00
 O2 F:AKG201 1.9 28.4 1.0
OE1 F:GLN39 2.0 27.9 1.0
O5 F:AKG201 2.1 25.7 1.0
O3G F:ATP200 2.1 22.4 1.0
O1B F:ATP200 2.1 23.6 1.0
O2A F:ATP200 2.2 23.5 1.0
C1 F:AKG201 2.8 27.0 1.0
C2 F:AKG201 2.8 28.2 1.0
CD F:GLN39 3.2 30.9 1.0
PB F:ATP200 3.2 23.0 1.0
PA F:ATP200 3.3 23.0 1.0
PG F:ATP200 3.3 27.1 1.0
O3A F:ATP200 3.6 26.1 1.0
O3B F:ATP200 3.7 27.1 1.0
N F:GLY87 3.8 23.9 1.0
NE2 F:GLN39 3.8 28.4 1.0
O1G F:ATP200 3.8 29.1 1.0
N F:ARG38 3.9 27.3 1.0
O1 F:AKG201 4.0 25.3 1.0
O F:HOH2038 4.0 19.3 1.0
CA F:GLY87 4.1 23.2 1.0
N F:GLN39 4.1 29.4 1.0
O1A F:ATP200 4.1 23.0 1.0
CA F:GLY37 4.2 23.8 1.0
C F:GLY37 4.3 25.9 1.0
C3 F:AKG201 4.3 28.6 1.0
CB F:ILE86 4.4 25.3 1.0
CG F:GLN39 4.4 29.9 1.0
CB F:GLN39 4.5 30.1 1.0
O5' F:ATP200 4.6 24.6 1.0
C F:ILE86 4.6 24.8 1.0
O2G F:ATP200 4.6 28.8 1.0
N F:GLY37 4.6 22.9 1.0
O2B F:ATP200 4.6 25.9 1.0
CA F:ARG38 4.8 29.6 1.0
C4 F:AKG201 4.8 29.1 1.0
CA F:ILE86 4.9 25.2 1.0
CA F:GLN39 4.9 30.5 1.0
CB F:ARG38 4.9 30.9 1.0
C F:ARG38 5.0 30.1 1.0

Reference:

O.Fokina, V.-R.Chellamuthu, K.Forchhammer, K.Zeth. Mechanism of 2-Oxoglutarate Signaling By the Synechococcus Elongatus Pii Signal Transduction Protein Proc.Natl.Acad.Sci.Usa V. 107 19760 2010.
ISSN: ISSN 0027-8424
PubMed: 21041661
DOI: 10.1073/PNAS.1007653107
Page generated: Wed Aug 14 07:18:43 2024

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