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

Protein crystallography data

The structure of Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at Low 2-Og Concentrations, PDB code: 2xzw 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) 47.89 / 1.95
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.334, 102.370, 135.774, 90.00, 90.00, 90.00
R / Rfree (%) 17.537 / 22.513

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Pii From Synechococcus Elongatus in Complex with 2-Oxoglutarate at Low 2-Og Concentrations (pdb code 2xzw). 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 Low 2-Og Concentrations, PDB code: 2xzw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2xzw

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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 Low 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 Low 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:29.5
occ:1.00
 O3G A:ATP200 2.0 26.9 1.0
O2A A:ATP200 2.1 24.3 1.0
O1B A:ATP200 2.1 24.2 1.0
O2 A:AKG201 2.1 29.2 1.0
OE1 A:GLN39 2.2 33.6 1.0
O5 A:AKG201 2.4 28.4 1.0
C1 A:AKG201 3.0 31.1 1.0
PB A:ATP200 3.1 26.8 1.0
C2 A:AKG201 3.1 31.3 1.0
PG A:ATP200 3.1 26.6 1.0
PA A:ATP200 3.2 27.4 1.0
CD A:GLN39 3.3 34.8 1.0
O3B A:ATP200 3.4 28.4 1.0
O3A A:ATP200 3.5 27.7 1.0
O1G A:ATP200 3.7 28.4 1.0
N A:GLY87 3.9 29.4 1.0
NE2 A:GLN39 4.0 32.3 1.0
N A:ARG38 4.0 29.8 1.0
O A:HOH2026 4.0 23.5 1.0
O1 A:AKG201 4.1 33.3 1.0
N A:GLN39 4.1 32.7 1.0
O1A A:ATP200 4.1 26.0 1.0
CA A:GLY87 4.2 28.3 1.0
CA A:GLY37 4.2 26.6 1.0
O2G A:ATP200 4.3 25.1 1.0
C A:GLY37 4.4 28.3 1.0
O5' A:ATP200 4.4 27.4 1.0
O2B A:ATP200 4.5 26.8 1.0
CB A:ILE86 4.5 31.8 1.0
CB A:GLN39 4.5 33.2 1.0
CG A:GLN39 4.5 33.7 1.0
C3 A:AKG201 4.6 31.5 1.0
CG A:ARG38 4.6 36.4 1.0
N A:GLY37 4.7 26.2 1.0
C A:ILE86 4.8 31.2 1.0
CA A:GLN39 4.9 33.5 1.0
CA A:ARG38 5.0 31.9 1.0
CA A:ILE86 5.0 31.8 1.0

Magnesium binding site 2 out of 6 in 2xzw

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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 Low 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 Low 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:18.1
occ:1.00
 O3G B:ATP200 1.9 20.2 1.0
O2A B:ATP200 2.0 18.9 1.0
O1B B:ATP200 2.1 16.8 1.0
OE1 B:GLN39 2.1 23.4 1.0
O2 B:AKG201 2.1 23.4 1.0
O5 B:AKG201 2.3 20.1 1.0
C1 B:AKG201 2.9 26.3 1.0
C2 B:AKG201 2.9 25.5 1.0
PB B:ATP200 3.0 20.3 1.0
PG B:ATP200 3.1 21.7 1.0
PA B:ATP200 3.2 20.2 1.0
CD B:GLN39 3.2 26.6 1.0
O3B B:ATP200 3.3 23.4 1.0
O3A B:ATP200 3.4 18.4 1.0
O1G B:ATP200 3.7 25.1 1.0
N B:GLY87 3.8 19.0 1.0
NE2 B:GLN39 3.8 24.9 1.0
N B:ARG38 3.9 22.6 1.0
O1A B:ATP200 4.0 21.8 1.0
N B:GLN39 4.1 22.5 1.0
O1 B:AKG201 4.2 22.4 1.0
CA B:GLY87 4.2 19.2 1.0
O B:HOH2045 4.3 19.6 1.0
O2G B:ATP200 4.3 18.7 1.0
CA B:GLY37 4.3 20.6 1.0
O2B B:ATP200 4.3 19.1 1.0
O5' B:ATP200 4.4 22.6 1.0
CB B:ILE86 4.4 23.4 1.0
C3 B:AKG201 4.4 26.2 1.0
C B:GLY37 4.4 21.9 1.0
CG B:GLN39 4.5 25.0 1.0
CB B:GLN39 4.5 21.4 1.0
C B:ILE86 4.6 21.8 1.0
N B:GLY37 4.6 21.5 1.0
CB B:ARG38 4.7 26.4 1.0
CA B:ARG38 4.7 24.6 1.0
CA B:ILE86 4.8 21.2 1.0
CA B:GLN39 4.9 21.6 1.0
C B:ARG38 4.9 24.2 1.0

Magnesium binding site 3 out of 6 in 2xzw

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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 Low 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 Low 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:17.9
occ:1.00
 O3G C:ATP200 2.0 21.1 1.0
O2A C:ATP200 2.0 21.5 1.0
O2 C:AKG201 2.1 18.8 1.0
OE1 C:GLN39 2.1 21.2 1.0
O1B C:ATP200 2.2 17.3 1.0
O5 C:AKG201 2.2 18.2 1.0
C1 C:AKG201 2.8 19.6 1.0
C2 C:AKG201 2.9 20.1 1.0
PB C:ATP200 3.2 20.5 1.0
PA C:ATP200 3.2 19.7 1.0
CD C:GLN39 3.3 24.0 1.0
PG C:ATP200 3.3 21.4 1.0
O3B C:ATP200 3.5 18.7 1.0
O3A C:ATP200 3.5 21.4 1.0
N C:GLY87 3.7 22.3 1.0
O1G C:ATP200 3.8 20.3 1.0
NE2 C:GLN39 3.9 21.6 1.0
O1 C:AKG201 4.0 20.5 1.0
O C:HOH2040 4.0 22.3 1.0
N C:ARG38 4.1 22.7 1.0
CA C:GLY37 4.1 23.2 1.0
CA C:GLY87 4.1 21.6 1.0
O1A C:ATP200 4.1 20.1 1.0
N C:GLN39 4.1 22.3 1.0
C C:GLY37 4.3 23.2 1.0
O5' C:ATP200 4.3 20.7 1.0
C3 C:AKG201 4.4 23.0 1.0
CB C:GLN39 4.4 20.6 1.0
CG C:GLN39 4.4 20.6 1.0
CB C:ILE86 4.5 22.3 1.0
N C:GLY37 4.5 22.1 1.0
O2G C:ATP200 4.5 23.1 1.0
O2B C:ATP200 4.6 18.4 1.0
C C:ILE86 4.6 22.1 1.0
CG C:ARG38 4.6 28.1 1.0
CA C:ILE86 4.9 22.7 1.0
CA C:GLN39 4.9 22.9 1.0
C4 C:AKG201 5.0 26.2 1.0

Magnesium binding site 4 out of 6 in 2xzw

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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 Low 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 Low 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:22.8
occ:1.00
 O3G F:ATP200 1.9 22.2 1.0
O2 F:AKG201 2.0 22.4 1.0
O2A F:ATP200 2.0 21.7 1.0
O1B F:ATP200 2.1 22.9 1.0
OE1 F:GLN39 2.1 23.6 1.0
O5 F:AKG201 2.1 23.3 1.0
C1 F:AKG201 2.8 23.7 1.0
C2 F:AKG201 2.8 23.0 1.0
PB F:ATP200 3.0 22.0 1.0
PA F:ATP200 3.2 21.2 1.0
PG F:ATP200 3.2 22.8 1.0
CD F:GLN39 3.3 25.1 1.0
O3B F:ATP200 3.5 23.1 1.0
O3A F:ATP200 3.5 26.0 1.0
N F:GLY87 3.7 22.4 1.0
NE2 F:GLN39 3.9 22.4 1.0
O1G F:ATP200 3.9 23.3 1.0
O F:HOH2037 3.9 22.3 1.0
O1 F:AKG201 4.0 23.0 1.0
O1A F:ATP200 4.0 19.8 1.0
N F:ARG38 4.1 24.4 1.0
CA F:GLY87 4.1 21.7 1.0
N F:GLN39 4.1 23.6 1.0
CA F:GLY37 4.2 23.5 1.0
C3 F:AKG201 4.3 24.1 1.0
O5' F:ATP200 4.3 21.3 1.0
C F:GLY37 4.4 24.6 1.0
O2G F:ATP200 4.4 23.9 1.0
O2B F:ATP200 4.5 23.9 1.0
CB F:ILE86 4.5 22.4 1.0
C F:ILE86 4.5 22.8 1.0
CG F:GLN39 4.5 23.9 1.0
CB F:GLN39 4.6 23.5 1.0
N F:GLY37 4.6 24.6 1.0
CA F:ILE86 4.8 23.7 1.0
C4 F:AKG201 4.9 25.8 1.0
CA F:ARG38 4.9 26.5 1.0
CB F:ARG38 4.9 27.2 1.0
CA F:GLN39 4.9 25.3 1.0

Magnesium binding site 5 out of 6 in 2xzw

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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 Low 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 Low 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:24.2
occ:1.00
 O2A H:ATP200 2.0 23.9 1.0
O1B H:ATP200 2.1 23.8 1.0
OE1 H:GLN39 2.1 26.7 1.0
O3G H:ATP200 2.1 26.2 1.0
O2 H:AKG201 2.1 26.3 1.0
O5 H:AKG201 2.2 25.8 1.0
C1 H:AKG201 2.9 29.0 1.0
C2 H:AKG201 3.0 29.1 1.0
PB H:ATP200 3.1 24.4 1.0
PG H:ATP200 3.2 26.3 1.0
CD H:GLN39 3.2 22.4 1.0
PA H:ATP200 3.2 25.3 1.0
O3B H:ATP200 3.5 22.7 1.0
O3A H:ATP200 3.5 24.4 1.0
NE2 H:GLN39 3.8 23.5 1.0
N H:GLY87 3.8 22.3 1.0
O1G H:ATP200 3.8 28.4 1.0
N H:ARG38 4.0 23.8 1.0
O1A H:ATP200 4.1 23.0 1.0
O1 H:AKG201 4.1 29.8 1.0
O H:HOH2026 4.1 23.7 1.0
CA H:GLY87 4.1 22.8 1.0
N H:GLN39 4.2 23.4 1.0
CA H:GLY37 4.3 21.9 1.0
O5' H:ATP200 4.4 24.4 1.0
O2G H:ATP200 4.4 23.3 1.0
C H:GLY37 4.4 23.7 1.0
C3 H:AKG201 4.5 29.1 1.0
CG H:GLN39 4.5 25.4 1.0
O2B H:ATP200 4.6 24.9 1.0
CB H:ILE86 4.6 25.3 1.0
C H:ILE86 4.6 22.8 1.0
N H:GLY37 4.6 20.9 1.0
CB H:GLN39 4.7 23.8 1.0
CA H:ARG38 4.9 25.5 1.0
CB H:ARG38 4.9 26.4 1.0
CA H:ILE86 5.0 24.0 1.0

Magnesium binding site 6 out of 6 in 2xzw

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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 Low 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 Low 2-Og Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:24.7
occ:1.00
 O3G I:ATP200 1.9 20.6 1.0
OE1 I:GLN39 2.0 19.4 1.0
O2A I:ATP200 2.1 23.9 1.0
O2 I:AKG201 2.1 24.2 1.0
O1B I:ATP200 2.2 23.0 1.0
O5 I:AKG201 2.3 27.4 1.0
C1 I:AKG201 3.0 26.5 1.0
C2 I:AKG201 3.0 28.0 1.0
PB I:ATP200 3.0 22.2 1.0
PG I:ATP200 3.2 23.5 1.0
CD I:GLN39 3.2 21.7 1.0
PA I:ATP200 3.2 26.0 1.0
O3B I:ATP200 3.5 23.3 1.0
O3A I:ATP200 3.5 26.0 1.0
N I:GLY87 3.7 21.9 1.0
O1G I:ATP200 3.8 25.1 1.0
NE2 I:GLN39 3.9 18.4 1.0
N I:ARG38 4.0 22.7 1.0
CA I:GLY87 4.1 18.8 1.0
O1A I:ATP200 4.1 21.4 1.0
O I:HOH2038 4.1 18.3 1.0
CA I:GLY37 4.2 20.6 1.0
O1 I:AKG201 4.2 29.0 1.0
N I:GLN39 4.2 23.1 1.0
C I:GLY37 4.4 23.1 1.0
O2G I:ATP200 4.4 23.0 1.0
O2B I:ATP200 4.4 23.6 1.0
O5' I:ATP200 4.4 25.1 1.0
CG I:GLN39 4.5 22.4 1.0
CB I:GLN39 4.5 22.9 1.0
C3 I:AKG201 4.5 32.4 1.0
C I:ILE86 4.5 22.5 1.0
CB I:ILE86 4.6 23.7 1.0
CG I:ARG38 4.6 27.1 1.0
N I:GLY37 4.7 20.4 1.0
CA I:ILE86 4.9 22.6 1.0
CA I:ARG38 5.0 24.6 1.0
CA I:GLN39 5.0 24.4 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 07:22:13 2024

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