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Magnesium in PDB 2iou: Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E).

Protein crystallography data

The structure of Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E)., PDB code: 2iou was solved by J.L.Miller, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 3.16
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 413.464, 413.464, 98.859, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E). (pdb code 2iou). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E)., PDB code: 2iou:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2iou

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Magnesium binding site 1 out of 4 in the Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3

b:51.6
occ:1.00
OE1 A:GLU312 2.1 60.1 1.0
OE1 B:GLU312 2.3 62.9 1.0
OE1 C:GLU312 2.5 58.5 1.0
CD A:GLU312 3.3 59.3 1.0
CD B:GLU312 3.4 61.5 1.0
CD C:GLU312 3.5 56.9 1.0
OE2 C:GLU312 3.8 56.5 1.0
OE2 B:GLU312 3.9 61.2 1.0
OE2 A:GLU312 4.0 60.0 1.0
ND2 C:ASN254 4.1 52.6 1.0
ND2 A:ASN254 4.3 58.6 1.0
CG A:GLU312 4.4 56.8 1.0
O B:ASN311 4.4 57.9 1.0
O C:ASN311 4.5 53.5 1.0
O A:ASN311 4.5 55.1 1.0
ND2 B:ASN254 4.6 61.0 1.0
CG B:GLU312 4.7 59.9 1.0
CG C:GLU312 4.9 55.6 1.0
CA B:GLU312 4.9 58.0 1.0

Magnesium binding site 2 out of 4 in 2iou

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Magnesium binding site 2 out of 4 in the Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:50.5
occ:1.00
OE2 B:GLU312 2.0 61.2 1.0
O C:PHE313 2.1 55.2 1.0
O B:PHE313 2.2 58.5 1.0
O A:PHE313 2.2 55.8 1.0
OE2 C:GLU312 2.6 56.5 1.0
OE2 A:GLU312 2.8 60.0 1.0
CD B:GLU312 3.2 61.5 1.0
C C:PHE313 3.2 55.2 1.0
C A:PHE313 3.3 55.9 1.0
C B:PHE313 3.3 58.4 1.0
CD C:GLU312 3.5 56.9 1.0
N C:PHE313 3.7 54.8 1.0
N B:PHE313 3.8 58.1 1.0
CA C:PHE313 3.8 54.9 1.0
N A:PHE313 3.8 56.0 1.0
CD A:GLU312 3.9 59.3 1.0
OE1 B:GLU312 3.9 62.9 1.0
CA A:PHE313 4.0 55.9 1.0
CA B:PHE313 4.0 58.1 1.0
OE1 C:GLU312 4.2 58.5 1.0
CG B:GLU312 4.2 59.9 1.0
OE1 A:GLU312 4.2 60.1 1.0
CB C:PHE313 4.2 54.7 1.0
CG C:GLU312 4.3 55.6 1.0
CB A:PHE313 4.3 55.6 1.0
N C:GLY314 4.4 55.5 1.0
CB B:PHE313 4.4 57.9 1.0
N B:GLY314 4.4 58.7 1.0
N A:GLY314 4.5 55.8 1.0
C C:GLU312 4.8 54.6 1.0
CA C:GLY314 4.8 55.8 1.0
CA B:GLY314 4.8 58.9 1.0
CA A:GLY314 4.8 55.7 1.0
C B:GLU312 4.9 58.0 1.0
C A:GLU312 5.0 56.0 1.0

Magnesium binding site 3 out of 4 in 2iou

Go back to Magnesium Binding Sites List in 2iou
Magnesium binding site 3 out of 4 in the Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2

b:50.0
occ:1.00
OE2 D:GLU312 2.2 66.2 1.0
O D:PHE313 2.3 61.8 1.0
O E:PHE313 2.3 64.7 1.0
O F:PHE313 2.3 68.5 1.0
OE2 E:GLU312 2.4 66.9 1.0
OE2 F:GLU312 2.5 70.9 1.0
CD D:GLU312 3.3 65.9 1.0
C D:PHE313 3.4 61.7 1.0
C E:PHE313 3.4 64.8 1.0
CD E:GLU312 3.4 67.0 1.0
C F:PHE313 3.4 68.6 1.0
CD F:GLU312 3.5 70.4 1.0
OE1 F:GLU312 3.7 70.6 1.0
N D:PHE313 3.8 61.6 1.0
N E:PHE313 3.8 65.1 1.0
N F:PHE313 3.9 68.3 1.0
CA E:PHE313 4.0 64.8 1.0
CA D:PHE313 4.0 61.5 1.0
CA F:PHE313 4.1 68.5 1.0
OE1 E:GLU312 4.1 67.8 1.0
OE1 D:GLU312 4.1 66.9 1.0
CG D:GLU312 4.3 64.1 1.0
CB E:PHE313 4.4 64.7 1.0
CG E:GLU312 4.4 66.2 1.0
CB D:PHE313 4.4 61.1 1.0
CB F:PHE313 4.5 68.8 1.0
N D:GLY314 4.5 61.8 1.0
N E:GLY314 4.5 64.7 1.0
N F:GLY314 4.5 68.7 1.0
CA D:GLY314 4.8 61.8 1.0
CG F:GLU312 4.9 68.7 1.0
CA E:GLY314 4.9 64.7 1.0
CA F:GLY314 4.9 68.7 1.0
C D:GLU312 4.9 61.5 1.0
MG D:MG4 4.9 57.1 1.0
C F:GLU312 4.9 68.1 1.0
C E:GLU312 4.9 65.3 1.0

Magnesium binding site 4 out of 4 in 2iou

Go back to Magnesium Binding Sites List in 2iou
Magnesium binding site 4 out of 4 in the Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella Brochiseptica Virulence Factor Pertactin Extracellular Domain (Prn-E). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4

b:57.1
occ:1.00
OE1 F:GLU312 2.0 70.6 1.0
OE1 D:GLU312 2.4 66.9 1.0
OE1 E:GLU312 2.5 67.8 1.0
CD F:GLU312 3.3 70.4 1.0
CD D:GLU312 3.4 65.9 1.0
CD E:GLU312 3.5 67.0 1.0
OE2 E:GLU312 3.8 66.9 1.0
OE2 D:GLU312 3.8 66.2 1.0
ND2 D:ASN254 4.0 62.1 1.0
O D:ASN311 4.1 60.9 1.0
OE2 F:GLU312 4.1 70.9 1.0
CG F:GLU312 4.1 68.7 1.0
ND2 F:ASN254 4.4 64.1 1.0
ND2 E:ASN254 4.5 65.5 1.0
O F:ASN311 4.6 67.3 1.0
CA D:GLU312 4.7 61.7 1.0
CG D:GLU312 4.7 64.1 1.0
O E:ASN311 4.8 65.4 1.0
CB D:GLU312 4.8 61.9 1.0
CG E:GLU312 4.9 66.2 1.0
MG D:MG2 4.9 50.0 1.0

Reference:

J.L.Miller, J.Le Coq, A.Hodes, R.Barbalat, J.F.Miller, P.Ghosh. Selective Ligand Recognition By A Diversity-Generating Retroelement Variable Protein Plos Biol. V. 6 E131 2008.
ISSN: ISSN 1544-9173
PubMed: 18532877
DOI: 10.1371/JOURNAL.PBIO.0060131
Page generated: Mon Dec 14 07:27:38 2020

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