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

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

All present enzymatic activity of Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized and 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized and Soaked with Amp., PDB code: 4xgp 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) 32.87 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.520, 96.230, 93.940, 90.00, 98.41, 90.00
R / Rfree (%) 18.9 / 24

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 and Soaked with Amp. (pdb code 4xgp). 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 and Soaked with Amp., PDB code: 4xgp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xgp

Go back to Magnesium Binding Sites List in 4xgp
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 and 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized and Soaked with Amp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.8
occ:1.00
 OD1 A:ASP9 2.3 38.2 1.0
O A:HOH651 2.3 31.9 1.0
O2 A:PO4302 2.3 35.9 0.8
OD1 A:ASN92 2.3 26.1 1.0
OG A:SER39 2.5 34.1 1.0
OD1 A:ASP8 2.5 35.8 1.0
O A:HOH656 2.9 51.6 1.0
CG A:ASP9 3.2 39.6 1.0
CG A:ASN92 3.2 34.1 1.0
CB A:SER39 3.3 30.8 1.0
OD2 A:ASP9 3.5 48.2 1.0
ND2 A:ASN92 3.5 29.3 1.0
CG A:ASP8 3.6 34.8 1.0
P A:PO4302 3.7 39.0 0.8
O A:HOH664 3.9 52.0 1.0
OD2 A:ASP8 4.0 40.3 1.0
CA A:SER39 4.0 30.9 0.7
O1 A:PO4302 4.1 25.8 1.0
O A:HOH652 4.3 41.8 1.0
N A:ASP9 4.4 27.4 1.0
C A:ASP8 4.5 23.7 1.0
CB A:ASP9 4.5 32.7 1.0
O A:HOH687 4.5 41.2 1.0
O4 A:PO4302 4.5 37.7 0.8
OG1 A:THR106 4.6 21.8 1.0
N A:SER39 4.6 30.6 0.7
O3 A:PO4302 4.6 40.2 0.8
CA A:ASP9 4.6 30.1 1.0
CB A:ASN92 4.7 26.6 1.0
OD1 A:ASN37 4.7 40.0 1.0
O A:ALA93 4.8 33.5 1.0
O A:ASP8 4.8 27.1 1.0
CB A:ASP8 4.8 34.4 1.0
N A:ALA93 5.0 31.6 1.0
CA A:ASP8 5.0 26.6 1.0

Magnesium binding site 2 out of 4 in 4xgp

Go back to Magnesium Binding Sites List in 4xgp
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 and 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized and Soaked with Amp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:32.3
occ:1.00
 OD1 B:ASP8 2.2 31.4 1.0
OD1 B:ASP9 2.4 33.3 1.0
O B:HOH624 2.4 43.3 1.0
OD1 B:ASN92 2.5 31.2 1.0
O B:HOH619 2.6 41.8 1.0
O B:HOH623 2.6 28.6 1.0
CG B:ASP8 3.1 32.2 1.0
O B:HOH622 3.2 29.6 1.0
CG B:ASP9 3.4 36.1 1.0
CB B:ASP8 3.4 29.5 1.0
CG B:ASN92 3.5 34.1 1.0
OD2 B:ASP9 3.6 40.6 1.0
ND2 B:ASN92 3.7 34.2 1.0
O B:HOH672 3.8 22.5 1.0
O B:HOH620 3.9 59.0 1.0
O B:HOH632 4.0 46.7 1.0
O B:HOH618 4.2 49.8 1.0
OD2 B:ASP8 4.2 34.9 1.0
C B:ASP8 4.4 29.1 1.0
N B:ASP9 4.4 28.8 1.0
O B:HOH669 4.5 43.4 1.0
OG1 B:THR106 4.5 24.6 1.0
CA B:ASP8 4.6 30.0 1.0
O B:HOH663 4.7 43.7 1.0
CB B:ASP9 4.7 32.5 1.0
O B:ALA93 4.7 35.5 1.0
O B:ASP8 4.8 28.5 1.0
CB B:ASN92 4.8 32.4 1.0
CA B:ASP9 4.8 33.0 1.0

Magnesium binding site 3 out of 4 in 4xgp

Go back to Magnesium Binding Sites List in 4xgp
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 and 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized and Soaked with Amp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:40.8
occ:1.00
 O C:HOH568 2.4 46.5 1.0
OD1 C:ASP9 2.4 32.0 1.0
OD1 C:ASP8 2.5 33.2 1.0
OD1 C:ASN92 2.5 32.3 1.0
O C:HOH567 2.6 38.6 1.0
O C:HOH563 2.8 35.9 1.0
O C:HOH585 3.3 25.8 1.0
O C:HOH562 3.3 28.8 1.0
CG C:ASP9 3.3 34.7 1.0
CG C:ASP8 3.4 31.6 1.0
CG C:ASN92 3.5 30.3 1.0
OD2 C:ASP9 3.5 32.8 1.0
CB C:ASP8 3.6 29.5 1.0
ND2 C:ASN92 3.7 29.1 1.0
O C:HOH574 3.8 33.5 1.0
O C:HOH564 4.1 54.8 1.0
O C:HOH573 4.3 26.9 1.0
O C:HOH570 4.4 39.4 1.0
C C:ASP8 4.5 40.1 1.0
OD2 C:ASP8 4.6 32.9 1.0
OG1 C:THR106 4.6 32.3 1.0
CA C:ASP8 4.7 35.4 1.0
O C:ASP8 4.7 35.1 1.0
CB C:ASP9 4.7 34.7 1.0
N C:ASP9 4.8 34.4 1.0
O C:ALA93 4.8 40.1 1.0
CB C:ASN92 4.9 28.9 1.0
OD1 C:ASN37 4.9 41.6 1.0

Magnesium binding site 4 out of 4 in 4xgp

Go back to Magnesium Binding Sites List in 4xgp
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 and 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/H234A Mutant of Stationary Phase Survival Protein (Sure) From Salmonella Typhimurium Co-Crystallized and Soaked with Amp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:43.8
occ:1.00
 OD1 D:ASP8 2.2 42.5 1.0
O D:HOH576 2.2 52.4 1.0
OD1 D:ASN92 2.4 43.6 1.0
OD1 D:ASP9 2.5 46.9 1.0
O D:HOH525 2.6 42.9 1.0
O D:HOH527 2.6 48.5 1.0
O D:HOH585 3.0 38.1 1.0
CG D:ASP8 3.2 42.9 1.0
O D:HOH526 3.4 34.4 1.0
CB D:ASP8 3.4 42.7 1.0
CG D:ASP9 3.4 48.6 1.0
CG D:ASN92 3.5 42.7 1.0
OD2 D:ASP9 3.6 48.1 1.0
O D:HOH583 3.7 27.2 1.0
O D:HOH539 3.8 55.0 1.0
ND2 D:ASN92 3.9 38.5 1.0
O D:HOH528 4.3 59.6 1.0
C D:ASP8 4.3 39.6 1.0
OD2 D:ASP8 4.3 42.0 1.0
CA D:ASP8 4.4 39.9 1.0
O D:ASP8 4.5 39.2 1.0
N D:ASP9 4.5 45.1 1.0
O D:HOH540 4.5 53.5 1.0
OG1 D:THR106 4.6 36.0 1.0
O D:HOH581 4.6 53.9 1.0
CB D:ASP9 4.8 46.1 1.0
CB D:ASN92 4.8 43.8 1.0
O D:ALA93 5.0 59.5 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: Mon Dec 14 19:46:35 2020

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