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Magnesium in PDB 4if4: Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus

Protein crystallography data

The structure of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus, PDB code: 4if4 was solved by P.G.Leonard, A.M.Stock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.98 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 110.603, 110.603, 284.292, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 22.6

Other elements in 4if4:

The structure of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus (pdb code 4if4). 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 the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus, PDB code: 4if4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4if4

Go back to Magnesium Binding Sites List in 4if4
Magnesium binding site 1 out of 4 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


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 the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg300

b:36.6
occ:1.00
F3 A:BEF301 1.9 39.7 1.0
OD2 A:ASP55 2.0 37.9 1.0
O A:LEU57 2.1 34.7 1.0
O A:HOH447 2.1 35.3 1.0
O A:HOH427 2.1 28.3 1.0
OD1 A:ASP10 2.2 51.8 1.0
CG A:ASP55 3.0 41.8 1.0
BE A:BEF301 3.2 35.2 1.0
CG A:ASP10 3.2 42.6 1.0
C A:LEU57 3.3 32.8 1.0
OD1 A:ASP55 3.3 37.5 1.0
OD2 A:ASP10 3.5 55.3 1.0
OD1 A:ASP9 4.0 43.2 1.0
CA A:LEU57 4.0 34.7 1.0
O A:HOH449 4.1 42.6 1.0
CG A:MET58 4.1 33.5 1.0
CB A:LEU57 4.1 36.1 1.0
N A:LEU57 4.1 33.1 1.0
F1 A:BEF301 4.2 34.4 1.0
F2 A:BEF301 4.2 33.7 1.0
N A:ASP10 4.3 33.6 1.0
CB A:ASP55 4.3 33.6 1.0
N A:MET58 4.3 39.0 1.0
O A:HOH419 4.4 38.5 1.0
CB A:ASP10 4.4 42.3 1.0
NE2 A:HIS11 4.5 42.2 1.0
CG A:ASP9 4.5 46.8 1.0
CE1 A:HIS11 4.5 44.5 1.0
CA A:MET58 4.6 44.4 1.0
OD2 A:ASP9 4.6 35.7 1.0
CG A:LEU57 4.7 63.4 1.0
NZ A:LYS105 4.7 37.0 1.0
CD2 A:HIS11 4.8 39.5 1.0
CA A:ASP10 4.8 37.5 1.0
ND1 A:HIS11 4.9 36.6 1.0
CB A:MET58 5.0 46.0 1.0
CG A:HIS11 5.0 41.1 1.0

Magnesium binding site 2 out of 4 in 4if4

Go back to Magnesium Binding Sites List in 4if4
Magnesium binding site 2 out of 4 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


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 the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:37.4
occ:1.00
F3 B:BEF301 1.9 39.1 1.0
OD1 B:ASP55 2.0 40.6 1.0
O B:HOH425 2.1 38.1 1.0
O B:LEU57 2.1 33.4 1.0
O B:HOH420 2.1 28.3 1.0
OD1 B:ASP10 2.1 51.4 1.0
CG B:ASP55 3.0 41.9 1.0
BE B:BEF301 3.1 32.6 1.0
CG B:ASP10 3.2 40.8 1.0
C B:LEU57 3.3 37.3 1.0
OD2 B:ASP55 3.3 35.4 1.0
OD2 B:ASP10 3.6 51.4 1.0
CA B:LEU57 4.0 35.8 1.0
OD1 B:ASP9 4.1 40.5 1.0
CB B:LEU57 4.1 38.7 1.0
O B:HOH436 4.1 44.3 1.0
F2 B:BEF301 4.1 30.7 1.0
N B:LEU57 4.2 36.8 1.0
F1 B:BEF301 4.2 35.9 1.0
CG B:MET58 4.2 34.1 1.0
O B:HOH415 4.3 43.0 1.0
N B:ASP10 4.3 37.3 1.0
N B:MET58 4.4 39.7 1.0
CB B:ASP55 4.4 31.4 1.0
NE2 B:HIS11 4.4 44.1 1.0
CB B:ASP10 4.4 39.6 1.0
CE1 B:HIS11 4.5 47.8 1.0
CG B:ASP9 4.5 45.6 1.0
OD2 B:ASP9 4.6 35.1 1.0
NZ B:LYS105 4.6 35.8 1.0
CA B:MET58 4.6 40.4 1.0
CG B:LEU57 4.7 61.0 1.0
CD2 B:HIS11 4.7 39.9 1.0
ND1 B:HIS11 4.8 31.0 1.0
CA B:ASP10 4.9 40.5 1.0
CG B:HIS11 4.9 35.7 1.0

Magnesium binding site 3 out of 4 in 4if4

Go back to Magnesium Binding Sites List in 4if4
Magnesium binding site 3 out of 4 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


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 the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg300

b:48.4
occ:1.00
F3 C:BEF301 1.8 42.6 1.0
OD2 C:ASP55 2.0 41.9 1.0
O C:HOH412 2.1 35.9 1.0
O C:HOH418 2.1 36.8 1.0
OD1 C:ASP10 2.1 49.9 1.0
O C:LEU57 2.1 47.0 1.0
CG C:ASP55 3.0 39.9 1.0
BE C:BEF301 3.0 44.4 1.0
CG C:ASP10 3.1 47.1 1.0
OD1 C:ASP55 3.2 35.0 1.0
C C:LEU57 3.3 46.5 1.0
OD2 C:ASP10 3.6 48.0 1.0
F2 C:BEF301 4.0 40.2 1.0
F1 C:BEF301 4.0 40.8 1.0
O C:HOH422 4.0 39.3 1.0
CA C:LEU57 4.1 39.5 1.0
OD1 C:ASP9 4.2 47.9 1.0
CB C:LEU57 4.2 33.1 1.0
O C:HOH426 4.2 37.2 1.0
CG C:MET58 4.3 39.5 1.0
N C:LEU57 4.3 38.5 1.0
N C:MET58 4.4 47.1 1.0
CB C:ASP55 4.4 30.9 1.0
NE2 C:HIS11 4.4 41.4 1.0
N C:ASP10 4.4 43.6 1.0
CB C:ASP10 4.4 45.1 1.0
CG C:LEU57 4.5 60.7 1.0
CE1 C:HIS11 4.6 42.4 1.0
CA C:MET58 4.6 43.0 1.0
CD2 C:HIS11 4.6 37.5 1.0
CG C:ASP9 4.7 53.6 1.0
OD2 C:ASP9 4.7 44.5 1.0
NZ C:LYS105 4.7 38.2 1.0
CD2 C:LEU57 4.8 41.5 1.0
ND1 C:HIS11 4.9 32.7 1.0
CA C:ASP10 4.9 50.5 1.0
CG C:HIS11 4.9 39.0 1.0

Magnesium binding site 4 out of 4 in 4if4

Go back to Magnesium Binding Sites List in 4if4
Magnesium binding site 4 out of 4 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


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 the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg300

b:51.6
occ:1.00
F3 D:BEF301 1.8 43.8 1.0
O D:HOH415 2.0 38.0 1.0
OD1 D:ASP10 2.1 57.3 1.0
O D:HOH426 2.1 41.1 1.0
O D:LEU57 2.1 46.9 1.0
OD2 D:ASP55 2.1 39.8 1.0
CG D:ASP10 3.1 51.3 1.0
CG D:ASP55 3.1 42.0 1.0
BE D:BEF301 3.1 44.7 1.0
C D:LEU57 3.3 44.1 1.0
OD1 D:ASP55 3.4 37.2 1.0
OD2 D:ASP10 3.4 43.5 1.0
O D:HOH423 4.1 40.7 1.0
CA D:LEU57 4.1 40.2 1.0
F2 D:BEF301 4.1 37.0 1.0
F1 D:BEF301 4.1 46.0 1.0
CB D:LEU57 4.2 32.4 1.0
O D:HOH424 4.2 36.4 1.0
OD1 D:ASP9 4.3 41.3 1.0
CG D:MET58 4.3 43.7 1.0
N D:LEU57 4.3 40.0 1.0
N D:MET58 4.3 46.1 1.0
NE2 D:HIS11 4.4 44.3 1.0
CB D:ASP10 4.4 47.8 1.0
CG D:LEU57 4.4 57.5 1.0
N D:ASP10 4.5 41.8 1.0
CB D:ASP55 4.5 38.9 1.0
CE1 D:HIS11 4.5 47.7 1.0
CA D:MET58 4.6 48.2 1.0
CD2 D:HIS11 4.6 40.1 1.0
CD2 D:LEU57 4.7 38.4 1.0
CG D:ASP9 4.8 48.4 1.0
NZ D:LYS105 4.8 33.1 1.0
OD2 D:ASP9 4.8 41.9 1.0
ND1 D:HIS11 4.9 29.8 1.0
CA D:ASP10 4.9 47.9 1.0
CG D:HIS11 4.9 36.9 1.0

Reference:

P.G.Leonard, D.Golemi-Kotra, A.M.Stock. Phosphorylation-Dependent Conformational Changes and Domain Rearrangements in Staphylococcus Aureus Vrar Activation. Proc.Natl.Acad.Sci.Usa V. 110 8525 2013.
ISSN: ISSN 0027-8424
PubMed: 23650349
DOI: 10.1073/PNAS.1302819110
Page generated: Mon Dec 14 18:52:55 2020

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