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Magnesium in PDB 7my6: Se-Crte C-Term His-Tag with Ipp Added

Enzymatic activity of Se-Crte C-Term His-Tag with Ipp Added

All present enzymatic activity of Se-Crte C-Term His-Tag with Ipp Added:
2.5.1.10;

Protein crystallography data

The structure of Se-Crte C-Term His-Tag with Ipp Added, PDB code: 7my6 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) 45.48 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.423, 144.627, 48.066, 90, 95.25, 90
R / Rfree (%) 18 / 20.9

Other elements in 7my6:

The structure of Se-Crte C-Term His-Tag with Ipp Added also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Se-Crte C-Term His-Tag with Ipp Added (pdb code 7my6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Se-Crte C-Term His-Tag with Ipp Added, PDB code: 7my6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7my6

Go back to Magnesium Binding Sites List in 7my6
Magnesium binding site 1 out of 6 in the Se-Crte C-Term His-Tag with Ipp Added


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Se-Crte C-Term His-Tag with Ipp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:24.9
occ:1.00
 OD1 A:ASP229 2.0 19.8 1.0
O A:HOH541 2.0 27.3 1.0
O A:HOH598 2.1 22.0 1.0
O A:HOH520 2.2 20.3 1.0
O A:HOH609 2.2 23.3 1.0
O A:HOH519 2.3 25.9 1.0
CG A:ASP229 2.9 18.8 1.0
OD2 A:ASP229 3.3 19.1 1.0
O A:HOH528 3.8 26.5 1.0
O A:GLN225 4.1 16.6 1.0
CB A:ASP229 4.3 19.2 1.0
NE2 A:HIS184 4.3 20.7 0.5
OE1 A:GLN225 4.3 17.2 1.0
NE2 A:HIS184 4.4 20.3 0.5
CE1 A:HIS184 4.5 19.6 0.5
OD2 A:ASP228 4.5 33.3 1.0
CE1 A:HIS184 4.5 20.8 0.5
CA A:ASP229 4.6 19.5 1.0
N A:ASP229 4.6 19.8 1.0
OD2 A:ASP232 4.8 37.3 1.0

Magnesium binding site 2 out of 6 in 7my6

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Magnesium binding site 2 out of 6 in the Se-Crte C-Term His-Tag with Ipp Added


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Se-Crte C-Term His-Tag with Ipp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:48.3
occ:1.00
 O A:HOH521 1.6 50.5 1.0
O A:HOH508 1.8 21.5 1.0
O3B A:IPE401 1.9 54.4 0.8
OD2 A:ASP96 2.1 38.5 1.0
OD2 A:ASP90 2.4 20.4 1.0
O2A A:IPE401 2.6 51.7 0.8
CG A:ASP96 3.1 30.9 1.0
PB A:IPE401 3.2 59.4 0.8
O A:HOH583 3.3 30.9 1.0
OD2 A:ASP98 3.3 31.1 1.0
O3A A:IPE401 3.5 62.2 0.8
PA A:IPE401 3.5 67.4 0.8
CB A:ASP96 3.5 26.4 1.0
CG A:ASP90 3.6 20.3 1.0
O1B A:IPE401 3.8 63.7 0.8
O1 A:IPE401 3.8 62.1 0.8
MG A:MG407 3.9 39.7 1.0
NH2 A:ARG101 4.0 25.4 1.0
OD1 A:ASP90 4.1 23.3 1.0
OD1 A:ASP96 4.3 35.1 1.0
OD1 A:ASP91 4.3 18.3 1.0
O2B A:IPE401 4.4 49.4 0.8
O A:HOH584 4.5 29.9 1.0
CG A:ASP98 4.6 26.0 1.0
O A:ASP90 4.6 15.3 1.0
CB A:ASP90 4.8 20.1 1.0
O A:HOH572 4.9 22.9 1.0
O1A A:IPE401 4.9 65.7 0.8
C A:ASP90 4.9 18.4 1.0

Magnesium binding site 3 out of 6 in 7my6

Go back to Magnesium Binding Sites List in 7my6
Magnesium binding site 3 out of 6 in the Se-Crte C-Term His-Tag with Ipp Added


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Se-Crte C-Term His-Tag with Ipp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:39.7
occ:1.00
 O A:HOH584 1.8 29.9 1.0
O A:HOH513 2.0 21.6 1.0
O A:HOH515 2.1 27.5 1.0
O2A A:IPE401 2.3 51.7 0.8
OD1 A:ASP90 2.3 23.3 1.0
OD2 A:ASP96 2.5 38.5 1.0
OD1 A:ASP96 2.9 35.1 1.0
CG A:ASP96 3.0 30.9 1.0
CG A:ASP90 3.2 20.3 1.0
PA A:IPE401 3.3 67.4 0.8
OD2 A:ASP90 3.4 20.4 1.0
O1 A:IPE401 3.6 62.1 0.8
O1A A:IPE401 3.9 65.7 0.8
MG A:MG406 3.9 48.3 1.0
OE1 A:GLN163 3.9 28.6 1.0
OD2 A:ASP166 4.3 24.1 1.0
NE2 A:GLN163 4.3 28.8 1.0
CB A:ASP96 4.5 26.4 1.0
O A:HOH521 4.6 50.5 1.0
CD A:GLN163 4.6 25.7 1.0
CB A:ASP90 4.6 20.1 1.0
O3A A:IPE401 4.7 62.2 0.8
C1 A:IPE401 4.9 51.0 0.8
O3B A:IPE401 5.0 54.4 0.8
O A:ASP90 5.0 15.3 1.0
NZ A:LYS187 5.0 31.1 1.0

Magnesium binding site 4 out of 6 in 7my6

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Magnesium binding site 4 out of 6 in the Se-Crte C-Term His-Tag with Ipp Added


Mono view


Stereo pair view

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

b:22.3
occ:1.00
 O B:HOH569 1.9 23.4 1.0
OD1 B:ASP229 2.1 19.5 1.0
O B:HOH526 2.2 32.5 1.0
O B:HOH530 2.2 23.3 1.0
O B:HOH613 2.2 25.3 1.0
O B:HOH543 2.2 19.7 1.0
CG B:ASP229 3.1 19.3 1.0
OD2 B:ASP229 3.4 19.6 1.0
O B:HOH544 3.5 29.2 1.0
O B:HOH540 3.9 27.1 1.0
O B:GLN225 4.3 15.1 1.0
CB B:ASP229 4.4 19.6 1.0
NE2 B:HIS184 4.5 17.1 0.5
OE1 B:GLN225 4.5 18.1 1.0
OD2 B:ASP228 4.5 31.1 1.0
NE2 B:HIS184 4.5 16.8 0.5
O B:HOH612 4.6 36.2 1.0
CE1 B:HIS184 4.6 16.7 0.5
CE1 B:HIS184 4.6 16.8 0.5
CA B:ASP229 4.7 20.0 1.0
OD2 B:ASP232 4.7 40.4 1.0
N B:ASP229 4.7 19.6 1.0

Magnesium binding site 5 out of 6 in 7my6

Go back to Magnesium Binding Sites List in 7my6
Magnesium binding site 5 out of 6 in the Se-Crte C-Term His-Tag with Ipp Added


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Se-Crte C-Term His-Tag with Ipp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:32.7
occ:1.00
 O B:HOH593 1.9 37.1 1.0
O B:HOH515 2.1 25.3 1.0
O B:HOH507 2.1 31.1 1.0
OD1 B:ASP90 2.2 23.7 1.0
OD2 B:ASP96 2.6 41.4 1.0
CG B:ASP90 3.1 19.3 1.0
OD1 B:ASP96 3.1 40.5 1.0
CG B:ASP96 3.2 31.8 1.0
OD2 B:ASP90 3.2 20.6 1.0
MG B:MG408 3.5 49.2 1.0
OE1 B:GLN163 3.8 26.4 1.0
OD2 B:ASP166 4.2 25.5 1.0
O B:HOH600 4.3 43.9 1.0
NE2 B:GLN163 4.3 26.2 1.0
CD B:GLN163 4.5 25.1 1.0
CB B:ASP90 4.5 17.8 1.0
CB B:ASP96 4.6 26.5 1.0
NZ B:LYS187 4.6 30.3 1.0
O B:HOH607 4.8 31.3 1.0
O B:HOH501 5.0 23.5 1.0

Magnesium binding site 6 out of 6 in 7my6

Go back to Magnesium Binding Sites List in 7my6
Magnesium binding site 6 out of 6 in the Se-Crte C-Term His-Tag with Ipp Added


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Se-Crte C-Term His-Tag with Ipp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:49.2
occ:1.00
 O B:HOH600 1.8 43.9 1.0
O B:HOH501 2.0 23.5 1.0
OD2 B:ASP96 2.0 41.4 1.0
O B:HOH515 2.2 25.3 1.0
OD2 B:ASP90 2.3 20.6 1.0
CG B:ASP96 3.2 31.8 1.0
CG B:ASP90 3.4 19.3 1.0
MG B:MG407 3.5 32.7 1.0
CB B:ASP96 3.7 26.5 1.0
OD2 B:ASP98 3.8 28.9 1.0
OD1 B:ASP90 3.8 23.7 1.0
NH2 B:ARG101 3.9 23.9 1.0
OD1 B:ASP96 4.2 40.5 1.0
O B:HOH604 4.3 29.1 1.0
O B:HOH593 4.3 37.1 1.0
OD1 B:ASP91 4.5 16.9 1.0
CB B:ASP90 4.6 17.8 1.0
O B:ASP90 4.7 15.4 1.0
C B:ASP90 5.0 16.0 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 Oct 3 01:10:05 2024

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