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Magnesium in PDB 3rgm: Crystal Structure of Spin-Labeled Btub T156R1

Protein crystallography data

The structure of Crystal Structure of Spin-Labeled Btub T156R1, PDB code: 3rgm was solved by P.S.Horanyi, D.M.Freed, M.C.Wiener, D.S.Cafiso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.34 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.629, 81.629, 227.729, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Spin-Labeled Btub T156R1 (pdb code 3rgm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Spin-Labeled Btub T156R1, PDB code: 3rgm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3rgm

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Magnesium binding site 1 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg595

b:55.9
occ:1.00
 OH A:TYR256 3.0 44.0 1.0
N A:ILE261 3.9 40.5 1.0
N A:GLU259 3.9 49.7 1.0
N A:LEU260 4.0 45.4 1.0
CZ A:TYR256 4.0 43.9 1.0
CE2 A:TYR256 4.0 42.6 1.0
CB A:ILE261 4.2 39.4 1.0
CD1 A:ILE261 4.2 35.5 1.0
CG1 A:ILE261 4.2 39.0 1.0
CA A:GLY258 4.2 49.3 1.0
C A:GLY258 4.5 48.5 1.0
CA A:ILE261 4.6 38.9 1.0
CA A:LEU260 4.7 42.3 1.0
CB A:LEU260 4.7 42.8 1.0
CA A:GLU259 4.8 49.8 1.0
C A:LEU260 4.8 40.1 1.0
C A:GLU259 4.9 47.2 1.0
CB A:GLU259 4.9 51.7 1.0

Magnesium binding site 2 out of 9 in 3rgm

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Magnesium binding site 2 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg596

b:47.4
occ:1.00
 OH A:TYR522 3.4 36.0 1.0
CG2 A:THR525 3.6 46.3 1.0
N A:THR525 4.0 42.3 1.0
CE2 A:TYR522 4.2 27.4 1.0
CZ A:TYR522 4.3 31.7 1.0
NE2 A:GLN501 4.4 34.0 1.0
CB A:THR525 4.4 46.0 1.0
CA A:GLY524 4.5 37.1 1.0
C A:GLY524 4.8 39.8 1.0
CB A:GLN501 4.8 32.3 1.0
CA A:THR525 4.8 44.1 1.0
CG A:GLN501 4.8 34.5 1.0
CD A:GLN501 5.0 36.9 1.0

Magnesium binding site 3 out of 9 in 3rgm

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Magnesium binding site 3 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg597

b:67.2
occ:1.00
 NE2 A:GLN580 4.0 76.0 1.0
OD1 A:ASP570 4.0 52.4 1.0
OD2 A:ASP570 4.5 57.8 1.0
CG A:ASP570 4.7 55.0 1.0
CA A:GLY583 4.9 59.4 1.0

Magnesium binding site 4 out of 9 in 3rgm

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Magnesium binding site 4 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg598

b:55.3
occ:1.00
 O A:GLU419 3.9 29.0 1.0
CB A:ALA387 4.2 30.5 1.0
C A:GLU419 4.3 27.6 1.0
CA A:GLY420 4.5 26.6 1.0
N A:GLY420 4.6 26.9 1.0
CA A:ALA387 4.7 30.0 1.0
O A:SER388 4.9 27.7 1.0
N A:GLU419 4.9 29.2 1.0
N A:SER388 5.0 28.8 1.0

Magnesium binding site 5 out of 9 in 3rgm

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Magnesium binding site 5 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg599

b:62.7
occ:1.00
 CG A:PHE210 4.3 61.0 1.0
CB A:PHE210 4.3 61.5 1.0
CG A:TRP214 4.4 54.8 1.0
CD2 A:TRP214 4.4 52.7 1.0
CD1 A:PHE210 4.5 60.6 1.0
CB A:TRP214 4.6 55.5 1.0
CD2 A:PHE210 4.6 62.7 1.0
CE3 A:TRP214 4.7 51.9 1.0
CD1 A:TRP214 4.8 55.1 1.0
CE2 A:TRP214 4.9 53.2 1.0

Magnesium binding site 6 out of 9 in 3rgm

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Magnesium binding site 6 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:54.3
occ:1.00
 CE3 A:TRP317 4.2 41.0 1.0
CD2 A:TRP317 4.2 43.0 1.0
CZ3 A:TRP317 4.4 41.8 1.0
CE2 A:TRP317 4.4 41.7 1.0
CH2 A:TRP317 4.6 43.9 1.0
CZ2 A:TRP317 4.6 42.5 1.0
CG A:TRP317 4.8 42.5 1.0
CG2 A:VAL298 4.9 38.4 1.0
NE1 A:TRP317 5.0 43.7 1.0

Magnesium binding site 7 out of 9 in 3rgm

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Magnesium binding site 7 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:88.8
occ:1.00
 NE2 A:HIS174 2.5 83.7 1.0
CD2 A:HIS174 2.8 80.8 1.0
CE1 A:HIS176 2.9 98.5 1.0
NE2 A:HIS176 3.0 97.9 1.0
CE1 A:HIS174 3.4 83.2 1.0
ND1 A:HIS176 3.8 95.7 1.0
CG A:HIS174 3.8 76.4 1.0
CD2 A:HIS176 4.0 94.7 1.0
ND1 A:HIS174 4.1 80.5 1.0
CG A:HIS176 4.4 91.5 1.0
CB A:HIS174 5.0 71.5 1.0

Magnesium binding site 8 out of 9 in 3rgm

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Magnesium binding site 8 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:93.0
occ:1.00
 CE1 A:HIS449 3.0 86.8 1.0
NE2 A:HIS449 3.7 86.0 1.0
ND1 A:HIS449 3.8 83.6 1.0
CD2 A:HIS449 4.7 83.6 1.0
CG A:HIS449 4.7 80.6 1.0

Magnesium binding site 9 out of 9 in 3rgm

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Magnesium binding site 9 out of 9 in the Crystal Structure of Spin-Labeled Btub T156R1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Spin-Labeled Btub T156R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:53.8
occ:1.00
 OG A:SER263 3.7 42.1 1.0
CZ3 A:TRP214 4.0 50.5 1.0
NE1 A:TRP300 4.1 46.9 1.0
CB A:LEU265 4.3 40.8 1.0
CB A:SER263 4.3 39.6 1.0
CH2 A:TRP214 4.3 52.0 1.0
CB A:LEU254 4.5 47.1 1.0
O A:LEU254 4.6 43.1 1.0
CD1 A:TRP300 4.6 44.3 1.0
N A:LEU265 4.7 38.4 1.0
C A:GLN264 4.8 37.4 1.0
N A:GLN264 4.8 37.3 1.0
CD2 A:LEU265 4.9 40.7 1.0
C A:SER263 4.9 38.3 1.0
CA A:GLN264 5.0 37.4 1.0

Reference:

D.M.Freed, A.K.Khan, P.S.Horanyi, D.S.Cafiso. Molecular Origin of Electron Paramagnetic Resonance Line Shapes on β-Barrel Membrane Proteins: the Local Solvation Environment Modulates Spin-Label Configuration Biochemistry V. 50 8792 2011.
ISSN: ISSN 0006-2960
PubMed: 21894979
DOI: 10.1021/BI200971X
Page generated: Thu Aug 15 10:29:07 2024

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