Magnesium in PDB 7my0: Sy-Crte Ipp Structure

Protein crystallography data

The structure of Sy-Crte Ipp Structure, PDB code: 7my0 was solved by T.S.Peat, J.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.93 / 1.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.43, 73.643, 132.229, 90, 95.21, 90
R / Rfree (%) 12.8 / 16

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sy-Crte Ipp Structure (pdb code 7my0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Sy-Crte Ipp Structure, PDB code: 7my0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7my0

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Magnesium binding site 1 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.2
occ:1.00
 O A:HOH537 2.0 13.0 1.0
O A:HOH680 2.1 12.3 1.0
OE2 A:GLU281 2.1 9.8 1.0
O A:HOH539 2.1 11.6 1.0
O A:HOH526 2.1 12.2 1.0
O A:HOH692 2.1 11.2 1.0
CD A:GLU281 3.0 11.6 1.0
OE1 A:GLU281 3.3 13.3 1.0
OE1 A:GLN291 4.0 11.7 1.0
OE2 A:GLU288 4.2 16.3 1.0
O A:GLY284 4.2 9.9 1.0
NE2 A:GLN291 4.2 9.5 1.0
CG A:GLU281 4.4 12.4 1.0
O A:HOH713 4.4 30.5 1.0
C A:GLY284 4.5 9.1 1.0
CG A:GLU288 4.5 11.0 1.0
CD A:GLN291 4.5 9.2 1.0
O A:GLU281 4.6 10.2 1.0
CA A:GLU281 4.7 9.4 1.0
N A:PRO285 4.7 9.6 1.0
CA A:PRO285 4.7 10.0 1.0
CD A:GLU288 4.9 14.5 1.0
CB A:GLU281 4.9 11.0 1.0

Magnesium binding site 2 out of 8 in 7my0

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Magnesium binding site 2 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:30.4
occ:1.00
 OD2 A:ASP97 1.6 36.2 1.0
O A:HOH501 1.8 18.6 1.0
O2A A:IPE401 1.9 11.7 0.8
O1B A:IPE401 1.9 19.8 0.8
OD2 A:ASP91 2.1 20.9 1.0
O A:HOH506 2.2 37.2 1.0
CG A:ASP97 2.7 24.7 1.0
O A:HOH502 3.0 32.4 1.0
CG A:ASP91 3.1 14.6 1.0
O A:HOH693 3.2 33.2 1.0
CB A:ASP97 3.2 19.5 1.0
MG A:MG405 3.2 21.4 1.0
PA A:IPE401 3.3 26.4 0.8
PB A:IPE401 3.3 24.5 0.8
OD2 A:ASP99 3.4 34.0 1.0
OD1 A:ASP91 3.7 17.4 1.0
O3A A:IPE401 3.7 33.2 0.8
OD1 A:ASP97 3.8 35.0 1.0
O A:HOH629 3.8 22.8 1.0
O A:ASP91 4.1 13.6 1.0
O A:HOH717 4.2 34.6 1.0
O2B A:IPE401 4.2 37.9 0.8
O3B A:IPE401 4.3 39.4 0.8
CB A:ASP91 4.3 11.4 1.0
O1A A:IPE401 4.4 26.8 0.8
CG A:ASP99 4.5 32.8 1.0
O1 A:IPE401 4.5 25.9 0.8
C A:ASP91 4.6 11.2 1.0
OD1 A:ASP92 4.6 17.9 1.0
CA A:ASP97 4.7 19.1 1.0
C1 A:IPE401 4.7 28.6 0.8
NH2 A:ARG102 4.7 22.6 1.0
OD1 A:ASP99 4.8 32.8 1.0
O A:HOH588 4.9 32.6 1.0

Magnesium binding site 3 out of 8 in 7my0

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Magnesium binding site 3 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:21.4
occ:1.00
 O A:HOH717 2.1 34.6 1.0
O2A A:IPE401 2.1 11.7 0.8
O A:HOH588 2.2 32.6 1.0
OD1 A:ASP91 2.2 17.4 1.0
OD2 A:ASP97 2.4 36.2 1.0
CG A:ASP91 3.0 14.6 1.0
OD1 A:ASP97 3.0 35.0 1.0
CG A:ASP97 3.0 24.7 1.0
O A:HOH502 3.0 32.4 1.0
OD2 A:ASP91 3.1 20.9 1.0
PA A:IPE401 3.1 26.4 0.8
NZ A:LYS188 3.1 27.7 1.0
MG A:MG404 3.2 30.4 1.0
O1A A:IPE401 3.6 26.8 0.8
O A:HOH728 3.8 44.5 1.0
O A:HOH671 3.9 26.8 1.0
O1 A:IPE401 4.1 25.9 0.8
OE1 A:GLN164 4.1 19.8 1.0
O A:HOH511 4.1 38.8 1.0
OD2 A:ASP167 4.3 23.5 1.0
O1B A:IPE401 4.4 19.8 0.8
CE A:LYS188 4.4 25.9 1.0
CB A:ASP91 4.4 11.4 1.0
NE2 A:GLN164 4.5 15.8 1.0
CB A:ASP97 4.5 19.5 1.0
O3A A:IPE401 4.6 33.2 0.8
C1 A:IPE401 4.7 28.6 0.8
CD A:GLN164 4.7 15.4 1.0
O A:ASP91 4.8 13.6 1.0
C2 A:IPE401 4.8 29.3 0.8
O A:HOH506 5.0 37.2 1.0

Magnesium binding site 4 out of 8 in 7my0

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Magnesium binding site 4 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:20.8
occ:0.80
 O A:HOH621 1.9 25.8 1.0
O A:HOH533 2.0 18.7 1.0
OD1 A:ASP230 2.1 15.6 1.0
O A:HOH774 2.1 23.1 1.0
O A:HOH742 2.2 26.8 1.0
O A:HOH559 2.4 27.2 1.0
CG A:ASP230 3.1 13.2 1.0
OD2 A:ASP230 3.5 15.2 1.0
O A:HOH540 3.9 20.5 1.0
O A:HOH523 4.1 34.6 1.0
O A:HOH548 4.1 18.4 1.0
NE2 A:GLN226 4.2 12.1 1.0
CE1 A:HIS185 4.4 15.2 1.0
NE2 A:HIS185 4.4 15.9 1.0
O A:GLN226 4.4 11.8 1.0
CB A:ASP230 4.5 11.8 1.0
O A:HOH631 4.6 37.8 1.0
CA A:ASP230 4.7 11.2 1.0
N A:ASP230 4.8 11.7 1.0
OD2 A:ASP233 4.9 37.6 1.0
CG2 A:THR255 5.0 16.8 1.0

Magnesium binding site 5 out of 8 in 7my0

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Magnesium binding site 5 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:11.1
occ:1.00
 O B:HOH538 2.0 11.0 1.0
O B:HOH584 2.0 11.7 1.0
O B:HOH679 2.1 13.3 1.0
OE2 B:GLU281 2.1 9.9 1.0
O B:HOH523 2.1 11.9 1.0
CD B:GLU281 3.0 10.9 1.0
OE1 B:GLU281 3.3 13.6 1.0
OE1 B:GLN291 4.0 11.3 1.0
O B:GLY284 4.2 10.2 1.0
NE2 B:GLN291 4.2 9.9 1.0
OE2 B:GLU288 4.3 14.8 1.0
CG B:GLU281 4.4 11.2 1.0
C B:GLY284 4.4 9.2 1.0
O B:HOH716 4.5 29.3 1.0
CD B:GLN291 4.5 8.8 1.0
CG B:GLU288 4.5 12.1 1.0
O B:GLU281 4.6 10.3 1.0
CA B:GLU281 4.6 9.7 1.0
CA B:PRO285 4.7 10.2 1.0
N B:PRO285 4.7 9.7 1.0
CD B:GLU288 4.9 14.1 1.0
CB B:GLU281 5.0 11.0 1.0

Magnesium binding site 6 out of 8 in 7my0

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Magnesium binding site 6 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:18.6
occ:0.70
 OD2 B:ASP97 1.9 29.3 1.0
O1A B:IPE401 1.9 16.4 0.7
O2B B:IPE401 1.9 21.9 0.7
OD2 B:ASP91 2.0 21.6 1.0
O B:HOH544 2.0 33.7 1.0
O B:HOH505 2.2 34.3 1.0
CG B:ASP91 3.0 16.7 1.0
CG B:ASP97 3.0 30.7 1.0
MG B:MG404 3.1 16.3 0.7
PA B:IPE401 3.2 22.5 0.7
PB B:IPE401 3.2 24.9 0.7
OD1 B:ASP91 3.4 20.8 1.0
CB B:ASP97 3.4 21.6 1.0
O3A B:IPE401 3.4 31.6 0.7
O B:HOH571 3.9 38.6 1.0
O B:HOH671 4.1 33.2 1.0
OD1 B:ASP97 4.1 32.4 1.0
O3B B:IPE401 4.1 34.0 0.7
OD2 B:ASP99 4.2 31.4 1.0
O1 B:IPE401 4.2 23.0 0.7
CB B:ASP91 4.2 13.4 1.0
C1 B:IPE401 4.3 26.4 0.7
O B:ASP91 4.3 14.7 1.0
O2A B:IPE401 4.3 25.6 0.7
O1B B:IPE401 4.4 30.5 0.7
NH2 B:ARG102 4.4 22.9 1.0
OD1 B:ASP92 4.5 16.4 1.0
C B:ASP91 4.7 12.4 1.0
O B:HOH537 4.7 37.6 1.0
O B:HOH510 4.8 27.4 1.0
CA B:ASP97 4.9 19.6 1.0

Magnesium binding site 7 out of 8 in 7my0

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Magnesium binding site 7 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:16.3
occ:0.70
 O B:HOH537 2.0 37.6 1.0
O1A B:IPE401 2.1 16.4 0.7
O B:HOH671 2.1 33.2 1.0
OD1 B:ASP91 2.1 20.8 1.0
OD2 B:ASP97 2.2 29.3 1.0
O B:HOH510 2.2 27.4 1.0
CG B:ASP91 3.0 16.7 1.0
CG B:ASP97 3.0 30.7 1.0
MG B:MG403 3.1 18.6 0.7
OD1 B:ASP97 3.1 32.4 1.0
OD2 B:ASP91 3.2 21.6 1.0
PA B:IPE401 3.2 22.5 0.7
O2A B:IPE401 3.8 25.6 0.7
O1 B:IPE401 3.9 23.0 0.7
OD2 B:ASP167 4.0 26.1 1.0
OE1 B:GLN164 4.1 24.0 1.0
O B:HOH544 4.1 33.7 1.0
NE2 B:GLN164 4.3 23.7 1.0
CB B:ASP91 4.4 13.4 1.0
CB B:ASP97 4.4 21.6 1.0
C1 B:IPE401 4.5 26.4 0.7
O3A B:IPE401 4.6 31.6 0.7
O2B B:IPE401 4.6 21.9 0.7
CD B:GLN164 4.6 20.0 1.0
C2 B:IPE401 4.7 29.4 0.7
O B:ASP91 4.8 14.7 1.0
O B:HOH505 5.0 34.3 1.0

Magnesium binding site 8 out of 8 in 7my0

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Magnesium binding site 8 out of 8 in the Sy-Crte Ipp Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Sy-Crte Ipp Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:43.6
occ:0.80
 O B:HOH670 2.0 22.1 1.0
OE1 B:GLN226 2.0 15.6 0.5
OD1 B:ASP230 2.1 16.1 1.0
O B:HOH684 2.2 43.7 1.0
O B:HOH598 2.8 33.1 1.0
O B:HOH592 2.9 19.4 1.0
O B:HOH735 3.0 45.3 1.0
CG B:ASP230 3.1 13.3 1.0
CD B:GLN226 3.2 15.6 0.5
OD2 B:ASP230 3.5 15.4 1.0
O B:HOH599 3.7 17.6 1.0
NE2 B:GLN226 4.1 14.4 0.5
CG B:GLN226 4.2 15.9 0.5
NE2 B:GLN226 4.2 11.4 0.5
O B:HOH574 4.3 28.2 1.0
O B:GLN226 4.4 11.9 0.5
O B:GLN226 4.4 12.3 0.5
CB B:ASP230 4.5 12.8 1.0
NE2 B:HIS185 4.6 15.9 1.0
CE1 B:HIS185 4.6 18.1 1.0
CE B:LYS253 4.7 45.4 1.0
N B:ASP230 4.8 11.8 1.0
CA B:ASP230 4.8 12.2 1.0

Reference:

A.Satta, L.Esquirol, B.E.Ebert, J.Newman, T.S.Peat, M.Plan, G.Schenk, C.E.Vickers. Molecular Characterization of Cyanobacterial Short-Chain Prenyltransferases and Discovery of A Novel Ggpp Phosphatase. Febs J. V. 289 6672 2022.
ISSN: ISSN 1742-464X
PubMed: 35704353
DOI: 10.1111/FEBS.16556
Page generated: Thu Apr 6 17:34:58 2023

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