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Magnesium in PDB 4xj7: Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp

Enzymatic activity of Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp

All present enzymatic activity of Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp:
3.1.3.5; 3.1.3.6; 3.6.1.11;

Protein crystallography data

The structure of Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp, PDB code: 4xj7 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) 24.89 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.620, 95.780, 94.750, 90.00, 100.07, 90.00
R / Rfree (%) 17.5 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp (pdb code 4xj7). 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 E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp, PDB code: 4xj7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xj7

Go back to Magnesium Binding Sites List in 4xj7
Magnesium binding site 1 out of 4 in the Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp


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 E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:16.8
occ:1.00
 O2 A:PO4302 2.3 16.8 0.9
OD1 A:ASP8 2.3 17.0 1.0
OG A:SER39 2.3 14.5 1.0
OD1 A:ASN92 2.3 11.6 0.8
OD1 A:ASP9 2.4 17.6 1.0
O A:HOH492 2.7 21.9 1.0
CG A:ASN92 3.3 12.2 0.8
CG A:ASP9 3.4 17.4 1.0
CB A:SER39 3.4 13.7 1.0
CG A:ASP8 3.5 16.0 1.0
P A:PO4302 3.5 16.0 0.8
O A:HOH491 3.5 33.4 1.0
ND2 A:ASN92 3.7 13.5 1.0
CA A:SER39 3.8 13.4 1.0
O1 A:PO4302 3.9 14.2 0.9
O A:HOH764 3.9 38.2 1.0
O A:HOH511 3.9 15.4 1.0
OD2 A:ASP9 4.0 20.5 1.0
OD2 A:ASP8 4.0 19.7 1.0
O4 A:PO4302 4.0 15.8 0.9
N A:ASP9 4.1 14.1 1.0
C A:ASP8 4.3 13.2 1.0
OG1 A:THR106 4.3 13.1 1.0
CA A:ASP9 4.4 15.0 1.0
OD1 A:ASN37 4.4 15.9 1.0
N A:SER39 4.4 12.8 1.0
CB A:ASP9 4.5 15.1 1.0
O A:ASP8 4.6 15.0 1.0
CB A:ASN92 4.7 13.7 1.0
CB A:ASP8 4.7 15.9 1.0
O3 A:PO4302 4.7 18.8 0.9
CA A:ASP8 4.9 13.4 1.0

Magnesium binding site 2 out of 4 in 4xj7

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


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 E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:17.1
occ:0.90
 OD1 B:ASN92 2.3 16.3 1.0
O4 B:PO4302 2.3 17.2 0.9
OD1 B:ASP8 2.4 16.7 1.0
OG B:SER39 2.5 15.7 1.0
OD1 B:ASP9 2.5 20.2 1.0
O B:HOH471 2.6 25.5 1.0
CG B:ASN92 3.3 15.5 1.0
CB B:SER39 3.4 15.5 1.0
CG B:ASP9 3.5 20.8 1.0
CG B:ASP8 3.5 15.9 1.0
P B:PO4302 3.5 16.4 0.9
ND2 B:ASN92 3.6 15.8 1.0
O B:HOH472 3.8 30.5 1.0
CA B:SER39 3.9 15.2 1.0
O3 B:PO4302 3.9 15.9 0.9
OD2 B:ASP9 4.0 22.3 1.0
O B:HOH689 4.0 33.8 1.0
O2 B:PO4302 4.0 15.2 0.9
O B:HOH483 4.0 16.8 1.0
OD2 B:ASP8 4.1 17.3 1.0
N B:ASP9 4.2 16.0 1.0
C B:ASP8 4.3 15.8 1.0
OG1 B:THR106 4.3 14.2 1.0
ND2 B:ASN37 4.4 19.8 1.0
N B:SER39 4.5 15.6 1.0
CA B:ASP9 4.5 17.4 1.0
O B:ASP8 4.5 17.1 1.0
O B:HOH692 4.6 46.2 1.0
CB B:ASP9 4.6 19.0 1.0
CB B:ASN92 4.7 15.3 1.0
CB B:ASP8 4.8 15.5 1.0
O1 B:PO4302 4.8 16.2 0.9
CA B:ASP8 4.9 14.7 1.0
O B:ALA93 4.9 19.3 1.0
N B:ALA93 5.0 17.4 1.0

Magnesium binding site 3 out of 4 in 4xj7

Go back to Magnesium Binding Sites List in 4xj7
Magnesium binding site 3 out of 4 in the Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp


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 E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:17.1
occ:0.60
 OD2 C:ASP8 2.3 23.9 0.5
OD1 C:ASP9 2.3 30.5 0.5
OD1 C:ASN92 2.3 22.4 1.0
O3 C:PO4302 2.3 29.9 1.0
OD1 C:ASP9 2.4 22.3 0.5
OG C:SER39 2.4 22.8 0.8
O C:HOH556 2.6 34.8 1.0
OD1 C:ASP8 2.6 18.9 0.5
CG C:ASN92 3.3 22.4 1.0
CG C:ASP9 3.3 30.2 0.5
CG C:ASP8 3.3 22.4 0.5
CB C:SER39 3.4 27.6 0.9
CG C:ASP9 3.4 22.8 0.5
P C:PO4302 3.5 23.0 0.7
ND2 C:ASN92 3.5 23.4 1.0
OD2 C:ASP9 3.7 31.8 0.5
CG C:ASP8 3.7 18.8 0.5
CB C:ASP8 3.8 21.2 0.5
O C:ASP8 3.8 19.2 0.5
O4 C:PO4302 3.8 24.6 1.0
O C:HOH512 3.9 38.3 1.0
OD2 C:ASP9 3.9 23.3 0.5
O C:HOH640 3.9 40.4 1.0
CA C:SER39 4.0 24.4 0.8
C C:ASP8 4.0 21.9 0.5
O1 C:PO4302 4.1 26.6 1.0
OD2 C:ASP8 4.2 18.4 0.5
O C:HOH483 4.2 27.7 1.0
O C:ASP8 4.3 19.9 0.5
C C:ASP8 4.3 21.0 0.5
N C:ASP9 4.4 23.3 0.5
OG1 C:THR106 4.4 21.6 1.0
N C:ASP9 4.4 21.6 0.5
OD1 C:ASP8 4.5 22.4 0.5
CB C:ASP9 4.5 27.6 0.5
N C:SER39 4.5 23.6 0.7
CA C:ASP8 4.5 20.9 0.5
OD1 C:ASN37 4.5 43.0 1.0
CB C:ASP9 4.6 22.9 0.5
CA C:ASP9 4.6 24.5 0.5
CB C:ASN92 4.7 21.9 1.0
CA C:ASP9 4.7 27.0 0.5
O2 C:PO4302 4.8 28.6 1.0
O C:ALA93 4.9 27.4 1.0
CB C:ASP8 4.9 19.7 0.5

Magnesium binding site 4 out of 4 in 4xj7

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


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 E112A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Soaked with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:21.2
occ:1.00
 O1 D:PO4302 2.3 20.5 0.8
OD1 D:ASP8 2.3 22.7 1.0
OG D:SER39 2.3 16.9 0.9
OD1 D:ASN92 2.4 17.5 0.8
OD1 D:ASP9 2.4 25.2 1.0
O D:HOH438 2.9 25.3 1.0
CG D:ASN92 3.3 18.3 1.0
CG D:ASP9 3.4 24.7 1.0
CB D:SER39 3.4 17.7 0.9
CG D:ASP8 3.5 21.7 1.0
P D:PO4302 3.5 20.2 0.8
ND2 D:ASN92 3.6 19.8 1.0
O D:HOH439 3.6 31.6 1.0
CA D:SER39 3.9 18.2 0.9
OD2 D:ASP9 3.9 26.2 1.0
O2 D:PO4302 4.0 17.3 0.8
OD2 D:ASP8 4.0 26.0 1.0
O D:HOH468 4.0 23.9 1.0
O4 D:PO4302 4.1 19.7 0.8
N D:ASP9 4.1 18.8 1.0
C D:ASP8 4.2 19.2 1.0
CA D:ASP9 4.3 21.5 1.0
OG1 D:THR106 4.3 19.6 1.0
OD1 D:ASN37 4.4 20.1 1.0
CB D:ASP9 4.4 22.2 1.0
O D:ASP8 4.5 18.5 1.0
N D:SER39 4.5 17.5 0.9
O D:HOH561 4.6 45.2 1.0
CB D:ASP8 4.7 20.0 1.0
CB D:ASN92 4.7 18.3 1.0
O3 D:PO4302 4.7 22.1 0.8
CA D:ASP8 4.8 18.4 1.0

Reference:

Y.K.Mathiharan, H.S.Savithri, M.R.N.Murthy. Insights Into Stabilizing Interactions in the Distorted Domain-Swapped Dimer of Salmonella Typhimurium Survival Protein Acta Crystallogr.,Sect.D V. 71 1812 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715011992
Page generated: Tue Aug 20 15:32:24 2024

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