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Magnesium in PDB 4ryu: Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium

Enzymatic activity of Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium

All present enzymatic activity of Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium:
3.1.3.5; 3.1.3.6;

Protein crystallography data

The structure of Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium, PDB code: 4ryu was solved by Y.K.Mathiharan, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 2.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.390, 95.780, 94.230, 90.00, 100.06, 90.00
R / Rfree (%) 17.8 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium (pdb code 4ryu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium, PDB code: 4ryu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ryu

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Magnesium binding site 1 out of 4 in the Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium


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 C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:21.4
occ:1.00
 OD1 A:ASP8 2.2 17.9 0.8
OD1 A:ASP9 2.3 19.8 0.8
OG A:SER39 2.3 18.8 1.0
OD1 A:ASN92 2.4 17.8 1.0
O A:HOH414 2.5 22.5 1.0
O A:HOH416 2.6 29.7 1.0
CG A:ASP8 3.2 17.8 0.8
CG A:ASP9 3.3 20.6 0.8
CB A:SER39 3.4 19.3 1.0
CG A:ASN92 3.4 19.1 1.0
OD2 A:ASP8 3.6 18.8 0.8
ND2 A:ASN92 3.7 17.0 1.0
O A:HOH434 3.8 26.7 1.0
CA A:SER39 3.9 18.7 1.0
OD2 A:ASP9 3.9 22.1 0.9
O A:HOH440 4.1 20.6 1.0
N A:ASP9 4.1 19.3 1.0
O A:HOH630 4.1 41.4 1.0
O A:HOH598 4.2 40.1 1.0
OD1 A:ASN37 4.3 17.1 0.7
C A:ASP8 4.4 18.8 1.0
CA A:ASP9 4.4 19.4 1.0
N A:SER39 4.4 19.1 1.0
CB A:ASP9 4.5 20.4 1.0
OG1 A:THR106 4.5 22.8 1.0
O A:HOH413 4.6 18.9 1.0
CB A:ASP8 4.6 18.2 1.0
CB A:ASN92 4.8 18.5 1.0
O3 A:PO4301 4.8 27.1 0.9
O A:ASP8 4.8 18.8 1.0
O A:ALA93 4.9 22.5 1.0
CA A:ASP8 4.9 17.6 1.0

Magnesium binding site 2 out of 4 in 4ryu

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Magnesium binding site 2 out of 4 in the Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium


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 C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:21.3
occ:0.90
 OD1 B:ASP8 2.3 25.0 0.8
OD1 B:ASP9 2.4 23.9 0.9
O B:HOH419 2.5 25.0 1.0
OD1 B:ASN92 2.5 21.2 1.0
OG B:SER39 2.5 25.6 1.0
O B:HOH417 2.6 34.3 1.0
CG B:ASP8 3.3 22.3 0.8
CG B:ASN92 3.4 22.3 1.0
CG B:ASP9 3.4 24.6 0.9
CB B:SER39 3.5 25.9 1.0
OD2 B:ASP8 3.6 23.1 0.8
O B:HOH559 3.6 21.6 1.0
ND2 B:ASN92 3.6 21.0 1.0
CA B:SER39 4.0 25.1 1.0
OD2 B:ASP9 4.0 26.9 0.9
O B:HOH410 4.1 48.4 1.0
O B:HOH654 4.2 39.3 1.0
O B:HOH430 4.2 26.4 1.0
N B:ASP9 4.2 21.5 0.9
OD1 B:ASN37 4.4 36.0 1.0
CA B:ASP9 4.4 23.4 0.9
C B:ASP8 4.4 19.9 0.8
N B:SER39 4.5 25.6 1.0
OG1 B:THR106 4.5 25.0 1.0
CB B:ASP9 4.5 23.6 0.9
O B:HOH432 4.6 24.4 1.0
CB B:ASP8 4.6 21.4 0.8
O B:ALA93 4.7 24.6 1.0
O B:ASP8 4.7 18.1 0.8
CB B:ASN92 4.8 21.5 1.0
O4 B:PO4301 4.9 28.0 0.8
O B:HOH412 5.0 43.6 1.0
CA B:ASP8 5.0 20.0 0.8

Magnesium binding site 3 out of 4 in 4ryu

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Magnesium binding site 3 out of 4 in the Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium


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 C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:28.8
occ:1.00
 O C:HOH507 2.3 31.9 1.0
OD2 C:ASP8 2.3 35.5 0.8
OD1 C:ASN92 2.4 30.8 1.0
OD1 C:ASP9 2.4 41.4 1.0
O C:HOH565 2.5 45.0 1.0
OG C:SER39 2.6 32.7 0.9
CG C:ASN92 3.3 30.8 1.0
CG C:ASP8 3.3 32.9 0.8
CG C:ASP9 3.4 40.1 1.0
ND2 C:ASN92 3.4 28.9 1.0
O C:HOH516 3.6 29.0 1.0
CB C:SER39 3.6 34.6 0.9
CB C:ASP8 3.6 33.0 0.8
OD2 C:ASP9 3.9 43.5 1.0
O C:HOH469 4.1 34.5 1.0
CA C:SER39 4.2 34.7 0.9
O C:HOH564 4.2 46.9 1.0
N C:ASP9 4.3 33.9 1.0
C C:ASP8 4.4 33.0 0.8
OD1 C:ASP8 4.5 33.7 0.6
CB C:ASP9 4.6 38.4 1.0
CA C:ASP9 4.6 37.0 1.0
O C:HOH460 4.6 41.5 1.0
OG1 C:THR106 4.6 32.3 1.0
CA C:ASP8 4.7 32.0 0.8
N C:SER39 4.7 34.6 0.9
CB C:ASN92 4.7 31.3 1.0
O C:ASP8 4.7 30.9 0.8
O C:ALA93 4.8 33.8 1.0
O4 C:PO4301 4.9 37.4 0.7
OD1 C:ASN37 5.0 51.5 1.0

Magnesium binding site 4 out of 4 in 4ryu

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Magnesium binding site 4 out of 4 in the Crystal Structure of C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium


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 C2 Form of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:26.6
occ:1.00
 OD1 D:ASP8 2.3 22.0 0.8
O D:HOH418 2.4 28.1 1.0
OD1 D:ASN92 2.4 20.2 0.9
OG D:SER39 2.5 22.3 1.0
OD1 D:ASP9 2.5 23.4 0.8
O D:HOH417 2.6 26.5 1.0
CG D:ASP8 3.3 21.5 0.8
CG D:ASN92 3.3 20.8 0.9
CG D:ASP9 3.5 23.1 0.8
CB D:SER39 3.5 22.3 1.0
ND2 D:ASN92 3.6 18.9 0.9
OD2 D:ASP8 3.6 22.9 0.8
O D:HOH595 3.6 36.1 1.0
OD2 D:ASP9 4.0 23.8 0.8
O D:HOH447 4.0 26.7 1.0
CA D:SER39 4.1 22.2 1.0
O D:HOH535 4.1 51.7 1.0
N D:ASP9 4.2 20.1 0.8
O D:HOH549 4.4 47.2 1.0
OG1 D:THR106 4.4 30.5 1.0
C D:ASP8 4.4 19.7 0.8
O D:HOH421 4.5 22.8 1.0
OD1 D:ASN37 4.5 27.0 1.0
CA D:ASP9 4.5 20.7 0.8
CB D:ASP9 4.6 21.8 0.8
CB D:ASP8 4.6 20.7 0.8
N D:SER39 4.6 22.4 1.0
O D:ALA93 4.7 24.8 1.0
CB D:ASN92 4.7 20.7 0.9
O D:ASP8 4.8 18.8 0.8
O2 D:PO4301 4.8 29.4 0.9
CA D:ASP8 5.0 20.3 0.8

Reference:

Y.K.Mathiharan, H.S.Savithri, M.R.Murthy. Insights Into Stabilizing Interactions in the Distorted Domain-Swapped Dimer of Salmonella Typhimurium Survival Protein. Acta Crystallogr. D Biol. V. 71 1812 2015CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 26327371
DOI: 10.1107/S1399004715011992
Page generated: Mon Aug 11 23:41:29 2025

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