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Magnesium in PDB 5oes: The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.

Enzymatic activity of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.

All present enzymatic activity of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.:
6.3.2.3;

Protein crystallography data

The structure of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation., PDB code: 5oes was solved by C.J.Lilley, A.Maqbool, D.Wu, H.B.Yusup, L.M.Jones, P.R.J.Birch, M.J.Banfield, P.E.Urwin, S.Eves-Van Den Akker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.48
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 154.390, 154.390, 344.325, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. (pdb code 5oes). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation., PDB code: 5oes:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5oes

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Magnesium binding site 1 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:45.3
occ:1.00
 O A:GLY316 2.3 37.8 1.0
O A:LEU154 2.4 39.6 1.0
O A:HOH666 2.6 27.6 1.0
O A:HOH635 3.2 50.5 1.0
C A:LEU154 3.3 38.9 1.0
C A:GLY316 3.4 38.8 1.0
CA A:ASN155 4.0 37.2 1.0
N A:ASN155 4.0 37.1 1.0
CA A:GLY316 4.1 38.6 1.0
N A:LEU154 4.2 40.6 1.0
O A:HOH646 4.2 38.1 1.0
OE1 A:GLU153 4.3 59.0 1.0
CA A:LEU154 4.4 40.3 1.0
N A:SER317 4.5 41.3 1.0
OD1 A:ASN155 4.5 40.4 1.0
CB A:GLU153 4.6 48.5 1.0
NZ A:LYS318 4.6 51.1 1.0
O A:HOH668 4.7 58.2 1.0
N A:THR156 4.8 36.7 1.0
CD A:GLU153 4.8 54.6 1.0
CG A:ASN155 4.8 38.8 1.0
C A:SER317 4.8 44.4 1.0
CA A:SER317 4.8 43.4 1.0
N A:LYS318 4.9 45.9 1.0
C A:ASN155 5.0 36.3 1.0

Magnesium binding site 2 out of 10 in 5oes

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Magnesium binding site 2 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:64.3
occ:1.00
 O1A A:ADP501 2.6 93.4 1.0
OE2 A:GLU153 2.7 56.1 1.0
OE2 A:GLU434 2.9 53.2 1.0
OD2 A:ASP139 3.1 35.9 1.0
CD A:GLU153 3.3 54.6 1.0
NH2 A:ARG459 3.4 58.5 1.0
CG A:GLU153 3.6 50.3 1.0
CG A:ASP139 3.7 35.0 1.0
O3B A:ADP501 4.0 99.7 1.0
CB A:ASP139 4.0 34.0 1.0
CD A:GLU434 4.0 50.7 1.0
PA A:ADP501 4.1 92.6 1.0
OE1 A:GLU153 4.3 59.0 1.0
O3' A:ADP501 4.4 64.3 1.0
CG2 A:ILE152 4.4 43.4 1.0
CZ A:ARG459 4.5 57.0 1.0
NH2 A:ARG137 4.5 37.0 1.0
OD1 A:ASP139 4.6 35.4 1.0
OE1 A:GLU434 4.7 53.1 1.0
C3' A:ADP501 4.7 63.9 1.0
NH1 A:ARG459 4.8 58.3 1.0
O2A A:ADP501 4.8 88.4 1.0
ND2 A:ASN155 4.9 38.6 1.0
O3A A:ADP501 4.9 0.3 1.0

Magnesium binding site 3 out of 10 in 5oes

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Magnesium binding site 3 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:47.0
occ:1.00
 O B:GLY316 2.3 36.9 1.0
O B:HOH655 2.5 27.8 1.0
O B:LEU154 2.5 38.5 1.0
C B:GLY316 3.4 37.0 1.0
C B:LEU154 3.5 39.5 1.0
O B:HOH628 3.8 42.7 1.0
O B:HOH616 3.9 41.3 1.0
CA B:ASN155 3.9 37.3 1.0
CA B:GLY316 4.0 36.2 1.0
N B:ASN155 4.1 38.3 1.0
OD1 B:ASN155 4.4 43.6 1.0
N B:SER317 4.4 38.8 1.0
N B:LEU154 4.5 42.2 1.0
CA B:LEU154 4.6 41.3 1.0
O B:HOH685 4.6 43.2 1.0
N B:THR156 4.6 35.1 1.0
OE1 B:GLU153 4.7 57.8 1.0
CG B:ASN155 4.7 40.4 1.0
CA B:SER317 4.8 40.7 1.0
C B:ASN155 4.8 35.5 1.0
CB B:GLU153 4.9 49.5 1.0
CB B:ASN155 4.9 38.0 1.0
NZ B:LYS318 4.9 51.9 1.0
C B:SER317 4.9 41.5 1.0

Magnesium binding site 4 out of 10 in 5oes

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Magnesium binding site 4 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:64.5
occ:1.00
 O C:HOH616 2.1 66.3 1.0
O C:HOH634 2.6 34.7 1.0
O C:GLY316 3.0 41.9 1.0
O C:LEU154 3.2 46.8 1.0
O C:HOH643 3.6 48.4 1.0
OD1 C:ASN155 3.8 49.7 1.0
O C:HOH613 3.9 39.1 1.0
C C:GLY316 4.0 43.1 1.0
CA C:ASN155 4.0 45.2 1.0
C C:LEU154 4.0 47.4 1.0
OE1 C:GLU153 4.4 64.0 1.0
N C:ASN155 4.4 45.7 1.0
CG C:ASN155 4.4 47.8 1.0
CA C:GLY316 4.6 43.2 1.0
O C:HOH612 4.7 48.6 1.0
NZ C:LYS318 4.7 55.5 1.0
CB C:ASN155 4.7 46.2 1.0
CD C:GLU153 4.8 60.4 1.0
N C:THR156 4.8 43.5 1.0
N C:SER317 4.9 45.0 1.0
C C:ASN155 5.0 43.9 1.0

Magnesium binding site 5 out of 10 in 5oes

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Magnesium binding site 5 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:60.5
occ:1.00
 OE2 C:GLU153 2.8 63.5 1.0
OE2 C:GLU434 2.8 55.7 1.0
OD2 C:ASP139 3.0 39.6 1.0
NH2 C:ARG459 3.3 62.4 1.0
CD C:GLU153 3.4 60.4 1.0
CG C:GLU153 3.5 55.9 1.0
CG C:ASP139 3.6 38.2 1.0
O2B C:ADP501 3.6 0.5 1.0
O3A C:ADP501 3.8 0.7 1.0
CB C:ASP139 3.8 37.4 1.0
CD C:GLU434 3.9 51.9 1.0
OE1 C:GLU153 4.3 64.0 1.0
CZ C:ARG459 4.4 60.6 1.0
PB C:ADP501 4.4 0.9 1.0
CG2 C:ILE152 4.5 46.6 1.0
OD1 C:ASP139 4.5 38.0 1.0
O3' C:ADP501 4.5 69.0 1.0
NH2 C:ARG137 4.5 38.3 1.0
OE1 C:GLU434 4.6 53.4 1.0
NH1 C:ARG459 4.8 61.9 1.0
ND2 C:ASN155 4.8 48.8 1.0
O2A C:ADP501 4.9 99.7 1.0
CB C:GLU153 5.0 54.3 1.0
CG C:GLU434 5.0 48.6 1.0
PA C:ADP501 5.0 0.8 1.0

Magnesium binding site 6 out of 10 in 5oes

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Magnesium binding site 6 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:68.5
occ:1.00
 OE2 D:GLU153 2.7 64.8 1.0
OE2 D:GLU434 3.0 57.0 1.0
OD2 D:ASP139 3.3 41.0 1.0
CD D:GLU153 3.3 61.1 1.0
O1A D:ADP501 3.3 0.5 1.0
NH2 D:ARG459 3.5 61.9 1.0
CG D:GLU153 3.6 57.1 1.0
CG D:ASP139 3.9 40.7 1.0
CD1 D:ILE152 4.0 53.0 1.0
CD D:GLU434 4.1 55.1 1.0
CB D:ASP139 4.2 40.1 1.0
OE1 D:GLU153 4.2 63.6 1.0
O5' D:ADP501 4.3 97.2 1.0
PA D:ADP501 4.5 0.3 1.0
CZ D:ARG459 4.6 60.9 1.0
OE1 D:GLU434 4.7 57.4 1.0
NH1 D:ARG137 4.7 38.5 1.0
CG1 D:ILE152 4.7 51.8 1.0
O3' D:ADP501 4.9 82.2 1.0
OD1 D:ASP139 4.9 40.5 1.0
NH1 D:ARG459 4.9 61.5 1.0
ND2 D:ASN155 5.0 44.8 1.0

Magnesium binding site 7 out of 10 in 5oes

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Magnesium binding site 7 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:55.3
occ:1.00
 O D:LEU154 2.6 44.4 1.0
O D:HOH629 2.6 28.5 1.0
O D:GLY316 2.8 40.4 1.0
C D:LEU154 3.5 44.9 1.0
C D:GLY316 3.8 41.1 1.0
O D:HOH634 3.8 43.0 1.0
CA D:ASN155 3.8 42.8 1.0
N D:ASN155 4.0 43.6 1.0
O D:HOH609 4.1 47.9 1.0
OD1 D:ASN155 4.1 45.7 1.0
OE1 D:GLN321 4.3 39.8 0.5
CA D:GLY316 4.4 40.6 1.0
OE1 D:GLU153 4.4 63.6 1.0
CG D:ASN155 4.5 44.1 1.0
N D:LEU154 4.5 47.4 1.0
N D:THR156 4.6 42.6 1.0
CA D:LEU154 4.7 47.2 1.0
CB D:ASN155 4.7 42.6 1.0
CD D:GLU153 4.7 61.1 1.0
CB D:GLU153 4.8 55.2 1.0
C D:ASN155 4.8 42.3 1.0
N D:SER317 4.8 42.5 1.0
NE2 D:GLN321 5.0 40.1 0.5

Magnesium binding site 8 out of 10 in 5oes

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Magnesium binding site 8 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:67.7
occ:1.00
 O E:LEU154 2.5 42.3 1.0
O E:GLY316 2.7 41.8 1.0
O E:HOH651 2.8 31.0 1.0
OE1 E:GLU376 3.1 96.7 1.0
O E:HOH629 3.3 50.4 1.0
C E:LEU154 3.4 42.4 1.0
OE1 E:GLU153 3.8 59.7 1.0
C E:GLY316 3.8 42.0 1.0
CD E:GLU376 3.9 96.7 1.0
OE2 E:GLU376 4.0 0.0 1.0
CA E:ASN155 4.0 40.4 1.0
N E:ASN155 4.0 41.2 1.0
N E:LEU154 4.1 44.8 1.0
OD1 E:ASN155 4.3 43.7 1.0
CB E:GLU153 4.4 50.6 1.0
CA E:LEU154 4.4 43.7 1.0
NZ E:LYS318 4.4 52.3 1.0
O E:HOH642 4.4 35.6 1.0
CA E:GLY316 4.4 41.2 1.0
CD E:GLU153 4.4 55.8 1.0
CG E:ASN155 4.6 42.0 1.0
N E:SER317 4.8 43.8 1.0
CG E:GLU153 4.9 52.7 1.0
CB E:ASN155 4.9 40.4 1.0
N E:THR156 4.9 38.5 1.0

Magnesium binding site 9 out of 10 in 5oes

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Magnesium binding site 9 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg504

b:67.2
occ:1.00
 OE2 E:GLU434 2.8 59.2 1.0
OE2 E:GLU153 2.8 59.2 1.0
OD2 E:ASP139 3.0 44.2 1.0
NH1 E:ARG459 3.3 61.2 1.0
CD E:GLU153 3.4 55.8 1.0
CG E:GLU153 3.6 52.7 1.0
CG E:ASP139 3.6 44.5 1.0
CD1 E:ILE152 3.8 48.6 1.0
CB E:ASP139 3.8 43.7 1.0
O3A E:ADP501 3.9 99.6 1.0
CD E:GLU434 3.9 57.4 1.0
O5' E:ADP501 4.0 89.1 1.0
O2A E:ADP501 4.0 92.0 1.0
O2B E:ADP501 4.2 98.6 1.0
PA E:ADP501 4.3 95.2 1.0
CZ E:ARG459 4.5 60.5 1.0
CG1 E:ILE152 4.5 47.5 1.0
OD1 E:ASP139 4.5 44.5 1.0
OE1 E:GLU434 4.5 59.7 1.0
OE1 E:GLU153 4.5 59.7 1.0
NH2 E:ARG137 4.5 40.5 1.0
O3' E:ADP501 4.7 71.7 1.0
PB E:ADP501 4.8 0.3 1.0
NH2 E:ARG459 4.8 60.4 1.0
ND2 E:ASN155 4.9 44.1 1.0
C3' E:ADP501 4.9 71.8 1.0
CG E:GLU434 4.9 54.4 1.0
C5' E:ADP501 5.0 79.4 1.0

Magnesium binding site 10 out of 10 in 5oes

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Magnesium binding site 10 out of 10 in the The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of A Glutathione Synthetase (STGSS1) From Solanum Tuberosum in Adp and Y-Ec Bound Closed Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:61.6
occ:1.00
 O F:GLY316 2.4 43.7 1.0
O F:LEU154 2.6 42.4 1.0
O F:HOH642 3.0 34.0 1.0
C F:LEU154 3.5 43.0 1.0
C F:GLY316 3.6 44.2 1.0
NE2 F:GLN321 3.7 41.8 0.5
OE1 F:GLU153 4.1 55.2 1.0
N F:ASN155 4.2 42.4 1.0
CA F:ASN155 4.2 42.8 1.0
N F:LEU154 4.2 44.0 1.0
CA F:GLY316 4.3 44.0 1.0
O F:HOH639 4.4 59.4 1.0
CB F:GLU153 4.4 51.1 1.0
ND2 F:ASN155 4.4 47.7 1.0
CA F:LEU154 4.5 43.8 1.0
NZ F:LYS318 4.5 54.5 1.0
CD F:GLU153 4.6 54.7 1.0
N F:SER317 4.6 45.5 1.0
CD F:GLN321 4.6 42.5 0.5
OE1 F:GLN321 4.7 42.1 0.5
C F:SER317 4.8 46.5 1.0
N F:LYS318 4.8 47.1 1.0
CG F:ASN155 4.8 46.7 1.0
CA F:SER317 4.8 46.6 1.0

Reference:

C.J.Lilley, A.Maqbool, D.Wu, H.B.Yusup, L.M.Jones, P.R.J.Birch, M.J.Banfield, P.E.Urwin, S.Eves-Van Den Akker. Effector Gene Birth in Plant Parasitic Nematodes: Neofunctionalization of A Housekeeping Glutathione Synthetase Gene. Plos Genet. V. 14 07310 2018.
ISSN: ESSN 1553-7404
PubMed: 29641602
DOI: 10.1371/JOURNAL.PGEN.1007310
Page generated: Mon Sep 30 00:57:00 2024

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