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Magnesium in PDB 4r2l: Crystal Structure of Ynaf (Universal Stress Protein F) From Salmonella Typhimurium

Protein crystallography data

The structure of Crystal Structure of Ynaf (Universal Stress Protein F) From Salmonella Typhimurium, PDB code: 4r2l was solved by M.Bangera, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.19 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.760, 132.760, 32.710, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.5

Other elements in 4r2l:

The structure of Crystal Structure of Ynaf (Universal Stress Protein F) From Salmonella Typhimurium also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ynaf (Universal Stress Protein F) From Salmonella Typhimurium (pdb code 4r2l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ynaf (Universal Stress Protein F) From Salmonella Typhimurium, PDB code: 4r2l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4r2l

Go back to Magnesium Binding Sites List in 4r2l
Magnesium binding site 1 out of 2 in the Crystal Structure of Ynaf (Universal Stress Protein F) 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 Ynaf (Universal Stress Protein F) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:24.8
occ:1.00
O A:HOH304 1.9 25.8 1.0
O A:HOH301 2.0 25.6 1.0
O A:HOH306 2.1 31.0 1.0
O1B A:ATP202 2.1 28.8 1.0
O3G A:ATP202 2.1 30.5 1.0
O2A A:ATP202 2.2 27.3 1.0
PB A:ATP202 3.2 25.1 1.0
PG A:ATP202 3.3 33.0 1.0
PA A:ATP202 3.3 24.5 1.0
O3B A:ATP202 3.4 27.1 1.0
O3A A:ATP202 3.6 24.1 1.0
O A:HOH324 3.7 39.1 1.0
ND2 A:ASN128 3.8 26.6 1.0
O1G A:ATP202 3.9 34.5 1.0
O5' A:ATP202 4.0 23.9 1.0
NE A:ARG117 4.1 48.5 1.0
N7 A:ATP202 4.1 27.5 1.0
NH2 A:ARG117 4.2 50.1 1.0
OD2 A:ASP10 4.2 31.5 1.0
C8 A:ATP202 4.2 25.8 1.0
O A:HOH347 4.3 45.7 1.0
O2G A:ATP202 4.4 32.9 1.0
O A:HOH362 4.5 41.7 1.0
O1A A:ATP202 4.5 23.0 1.0
O2B A:ATP202 4.5 24.7 1.0
O A:HOH321 4.5 34.2 1.0
CZ A:ARG117 4.6 50.8 1.0

Magnesium binding site 2 out of 2 in 4r2l

Go back to Magnesium Binding Sites List in 4r2l
Magnesium binding site 2 out of 2 in the Crystal Structure of Ynaf (Universal Stress Protein F) 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 Ynaf (Universal Stress Protein F) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:19.1
occ:1.00
O1B B:ATP202 2.0 19.5 1.0
O2A B:ATP202 2.0 16.1 1.0
O B:HOH306 2.1 19.9 1.0
O B:HOH301 2.1 15.2 1.0
O2G B:ATP202 2.1 22.3 1.0
O B:HOH303 2.3 20.9 1.0
PB B:ATP202 3.1 19.3 1.0
PA B:ATP202 3.2 16.7 1.0
PG B:ATP202 3.4 30.8 1.0
O3A B:ATP202 3.5 16.3 1.0
O3B B:ATP202 3.6 19.4 1.0
O5' B:ATP202 3.9 17.8 1.0
ND2 B:ASN128 4.0 19.7 1.0
O B:HOH355 4.1 33.5 1.0
N7 B:ATP202 4.2 18.0 1.0
OD2 B:ASP10 4.2 23.0 1.0
C8 B:ATP202 4.2 15.6 1.0
O1G B:ATP202 4.2 34.0 1.0
NE B:ARG117 4.2 34.5 1.0
CZ B:ARG117 4.3 42.9 1.0
NH2 B:ARG117 4.3 45.7 1.0
O1A B:ATP202 4.5 16.8 1.0
O2B B:ATP202 4.5 19.6 1.0
O B:HOH340 4.7 28.1 1.0
O3G B:ATP202 4.7 35.6 1.0
O B:HOH315 4.8 28.0 1.0
CD B:ARG117 4.8 33.3 1.0
NH1 B:ARG117 4.9 50.5 1.0

Reference:

M.Bangera, R.Panigrahi, S.R.Sagurthi, H.S.Savithri, M.R.N.Murthy. Structural and Functional Analysis of Two Universal Stress Proteins Ydaa and Ynaf From Salmonella Typhimurium: Possible Roles in Microbial Stress Tolerance J.Struct.Biol. 2015.
ISSN: ESSN 1095-8657
PubMed: 25600413
DOI: 10.1016/J.JSB.2015.01.003
Page generated: Tue Aug 20 02:47:06 2024

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