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Magnesium in PDB 4xgb: Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp

Enzymatic activity of Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp

All present enzymatic activity of Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp:
3.1.3.5; 3.1.3.6; 3.6.1.11;

Protein crystallography data

The structure of Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp, PDB code: 4xgb 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) 59.38 / 2.23
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.420, 96.520, 94.510, 90.00, 99.34, 90.00
R / Rfree (%) 20.8 / 26.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp (pdb code 4xgb). 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp, PDB code: 4xgb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xgb

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Magnesium binding site 1 out of 4 in the Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:14.7
occ:1.00
 O2 A:PO4302 2.2 14.6 0.8
OD1 A:ASN92 2.3 14.8 1.0
OD1 A:ASP8 2.3 11.3 0.8
OD1 A:ASP9 2.3 12.7 1.0
O A:HOH650 2.5 23.6 1.0
OG A:SER39 2.6 16.3 1.0
CG A:ASN92 3.3 14.8 1.0
CG A:ASP9 3.3 12.3 1.0
CG A:ASP8 3.3 11.3 0.8
O A:HOH658 3.3 29.9 1.0
CB A:SER39 3.4 16.2 1.0
P A:PO4302 3.6 14.7 0.8
ND2 A:ASN92 3.7 14.3 1.0
OD2 A:ASP8 3.7 11.2 0.8
CA A:SER39 3.8 16.1 1.0
OD2 A:ASP9 3.9 12.2 1.0
O A:HOH648 4.0 10.9 1.0
O A:HOH607 4.1 21.9 1.0
N A:ASP9 4.2 11.7 1.0
O A:HOH534 4.2 28.2 1.0
O4 A:PO4302 4.2 14.6 0.8
O1 A:PO4302 4.3 14.3 0.8
C A:ASP8 4.4 11.4 0.8
N A:SER39 4.4 16.2 1.0
CA A:ASP9 4.4 12.2 1.0
OG1 A:THR106 4.4 13.2 1.0
CB A:ASP9 4.5 12.2 1.0
OD1 A:ASN37 4.5 15.2 1.0
O3 A:PO4302 4.5 14.9 0.8
CB A:ASP8 4.7 11.1 0.8
O A:ASP8 4.7 11.7 0.8
CB A:ASN92 4.7 14.8 1.0
O A:ALA93 4.7 17.3 1.0
CA A:ASP8 4.9 11.1 0.8
O A:HOH477 4.9 15.1 1.0
N A:ALA93 5.0 16.3 1.0

Magnesium binding site 2 out of 4 in 4xgb

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Magnesium binding site 2 out of 4 in the Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:22.9
occ:1.00
 OD1 B:ASP8 2.0 13.8 0.8
O B:HOH640 2.3 26.0 1.0
OD1 B:ASN92 2.4 16.2 1.0
OD1 B:ASP9 2.4 17.1 1.0
O4 B:PO4302 2.4 17.4 1.0
OG B:SER39 2.5 16.4 1.0
CG B:ASP8 3.3 13.9 0.8
CG B:ASP9 3.3 16.6 1.0
CG B:ASN92 3.4 15.6 1.0
CB B:SER39 3.5 16.7 1.0
ND2 B:ASN92 3.7 15.2 1.0
P B:PO4302 3.7 17.6 1.0
OD2 B:ASP9 3.8 16.6 1.0
O B:HOH498 3.8 22.9 1.0
O B:HOH465 3.9 11.5 1.0
N B:ASP9 4.0 15.3 1.0
CA B:SER39 4.0 16.8 1.0
OD2 B:ASP8 4.1 13.9 0.8
O3 B:PO4302 4.1 17.4 1.0
C B:ASP8 4.1 14.8 0.8
O B:HOH626 4.2 17.2 1.0
CB B:ASP8 4.2 14.1 0.8
CA B:ASP9 4.2 16.1 1.0
O2 B:PO4302 4.3 17.6 1.0
CB B:ASP9 4.3 16.1 1.0
O B:ASP8 4.4 14.5 0.8
OG1 B:THR106 4.5 13.9 1.0
N B:SER39 4.5 17.4 1.0
OD1 B:ASN37 4.6 25.2 1.0
CA B:ASP8 4.7 14.5 0.8
CB B:ASN92 4.8 15.2 1.0
O B:ALA93 4.8 16.4 1.0
O1 B:PO4302 4.9 17.5 1.0

Magnesium binding site 3 out of 4 in 4xgb

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Magnesium binding site 3 out of 4 in the Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:20.6
occ:1.00
 O C:HOH563 2.5 22.2 1.0
OD1 C:ASN92 2.5 31.8 1.0
OD1 C:ASP8 2.6 25.5 1.0
OD1 C:ASP9 2.7 23.1 1.0
O C:HOH565 2.8 25.9 1.0
O C:HOH566 3.0 29.9 1.0
O C:HOH558 3.2 20.6 1.0
ND2 C:ASN92 3.2 30.6 1.0
CG C:ASN92 3.2 30.2 1.0
O C:HOH557 3.3 12.3 1.0
CG C:ASP8 3.6 25.3 1.0
CG C:ASP9 3.7 23.3 1.0
OD2 C:ASP9 4.0 22.8 1.0
O C:HOH556 4.0 25.8 1.0
CB C:ASP8 4.0 24.9 1.0
OG1 C:THR106 4.3 21.2 1.0
O C:HOH437 4.5 30.3 1.0
OD2 C:ASP8 4.7 26.0 1.0
CB C:ASN92 4.7 28.9 1.0
O C:ALA93 4.9 28.9 1.0
C C:ASP8 4.9 24.7 1.0

Magnesium binding site 4 out of 4 in 4xgb

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Magnesium binding site 4 out of 4 in the Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:25.5
occ:1.00
 O1 D:PO4302 2.2 21.5 0.8
OD1 D:ASN92 2.5 20.1 1.0
OD1 D:ASP9 2.5 22.4 1.0
OD1 D:ASP8 2.6 19.1 1.0
OG D:SER39 2.6 27.2 1.0
O D:HOH540 3.1 29.5 1.0
CG D:ASP8 3.3 19.1 1.0
OD2 D:ASP8 3.4 20.2 1.0
CG D:ASN92 3.4 20.8 1.0
CG D:ASP9 3.5 21.9 1.0
P D:PO4302 3.6 21.4 0.8
ND2 D:ASN92 3.6 20.3 1.0
CB D:SER39 3.7 28.5 1.0
OD2 D:ASP9 4.0 22.6 1.0
CA D:SER39 4.1 28.9 1.0
O2 D:PO4302 4.1 21.1 0.8
OD1 D:ASN37 4.2 26.3 1.0
O3 D:PO4302 4.3 21.1 0.8
O D:HOH428 4.5 17.1 1.0
OG1 D:THR106 4.6 20.1 1.0
O4 D:PO4302 4.6 21.6 0.8
C D:ASP8 4.7 18.8 1.0
O D:ASP8 4.7 19.1 1.0
N D:ASP9 4.7 19.6 1.0
CB D:ASP9 4.7 21.1 1.0
N D:SER39 4.8 28.9 1.0
CB D:ASP8 4.8 18.4 1.0
CB D:ASN92 4.8 20.8 1.0
CA D:ASP9 4.8 20.1 1.0
O D:ALA93 4.9 22.3 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 15:29:59 2024

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