Magnesium in PDB 6ewz: Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State

Enzymatic activity of Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State

All present enzymatic activity of Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State:
2.7.6.5;

Protein crystallography data

The structure of Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State, PDB code: 6ewz was solved by M.C.Manav, D.E.Brodersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.07 / 2.24
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 125.120, 125.120, 219.070, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.4

Other elements in 6ewz:

The structure of Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State (pdb code 6ewz). 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 Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State, PDB code: 6ewz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ewz

Go back to Magnesium Binding Sites List in 6ewz
Magnesium binding site 1 out of 2 in the Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State


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 Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:55.5
occ:1.00
 HO3' A:GTP301 1.9 71.0 1.0
OD2 A:ASP107 2.0 58.1 1.0
O A:HOH424 2.1 49.2 1.0
O3G A:APC302 2.1 59.5 1.0
O2B A:APC302 2.2 56.9 1.0
O A:HOH406 2.3 54.8 1.0
O3' A:GTP301 2.4 59.1 1.0
PG A:APC302 3.0 70.0 1.0
CG A:ASP107 3.1 63.9 1.0
PB A:APC302 3.2 59.8 1.0
O3B A:APC302 3.2 60.8 1.0
HO2' A:GTP301 3.5 87.8 1.0
NZ A:LYS88 3.5 63.1 1.0
NZ A:LYS80 3.6 68.4 1.0
H4' A:GTP301 3.7 80.7 1.0
O2G A:APC302 3.7 79.1 1.0
C3' A:GTP301 3.8 66.8 1.0
O1B A:APC302 3.8 53.2 1.0
H5' A:GTP301 3.8 84.0 1.0
CB A:ASP107 3.9 57.6 1.0
OD1 A:ASP107 4.0 60.3 1.0
C4' A:GTP301 4.1 67.2 1.0
O2' A:GTP301 4.2 73.2 1.0
NH2 A:ARG78 4.2 55.5 1.0
O2G A:GTP301 4.3 82.3 1.0
O1G A:APC302 4.3 74.0 1.0
OE2 A:GLU174 4.3 56.0 1.0
H3' A:GTP301 4.3 80.2 1.0
C5' A:GTP301 4.5 70.0 1.0
OE1 A:GLU174 4.5 58.3 1.0
C2' A:GTP301 4.6 73.6 1.0
C3A A:APC302 4.6 55.2 1.0
H3A1 A:APC302 4.6 66.2 1.0
H8 A:APC302 4.7 68.8 1.0
CE A:LYS88 4.7 59.4 1.0
N7 A:APC302 4.8 59.4 1.0
CE A:LYS80 4.9 63.7 1.0
CD A:GLU174 4.9 60.3 1.0
O1A A:APC302 5.0 62.8 1.0
H2' A:GTP301 5.0 88.3 1.0

Magnesium binding site 2 out of 2 in 6ewz

Go back to Magnesium Binding Sites List in 6ewz
Magnesium binding site 2 out of 2 in the Crystal Structure of Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State


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 Relp (SAS2) From Staphylococcus Aureus Bound to Ampcpp and Gtp in the Pre-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:90.4
occ:1.00
 O3G B:APC302 2.1 0.9 1.0
O B:HOH412 2.1 75.3 1.0
OD2 B:ASP107 2.1 0.6 1.0
O B:HOH401 2.2 76.3 1.0
O3' B:GTP301 2.4 0.5 1.0
O1B B:APC302 2.5 100.0 1.0
HO3' B:GTP301 2.8 0.6 1.0
PG B:APC302 3.1 0.5 1.0
CG B:ASP107 3.1 87.7 1.0
O3B B:APC302 3.3 0.1 1.0
H5' B:GTP301 3.3 0.7 1.0
PB B:APC302 3.4 98.4 1.0
H4' B:GTP301 3.4 0.6 1.0
C3' B:GTP301 3.6 0.1 1.0
NZ B:LYS88 3.6 84.0 1.0
NZ B:LYS80 3.6 96.7 1.0
CB B:ASP107 3.8 86.3 1.0
HO2' B:GTP301 3.8 0.8 1.0
C4' B:GTP301 3.8 1.0 1.0
O1G B:APC302 3.9 0.7 1.0
O2B B:APC302 4.0 89.2 1.0
OD1 B:ASP107 4.0 86.7 1.0
C5' B:GTP301 4.0 0.8 1.0
OE2 B:GLU174 4.1 81.9 1.0
O2G B:APC302 4.2 0.6 1.0
H3' B:GTP301 4.2 0.8 1.0
O2' B:GTP301 4.2 99.8 1.0
NH2 B:ARG78 4.3 84.5 1.0
OE1 B:GLU174 4.4 81.4 1.0
C2' B:GTP301 4.5 0.7 1.0
H5'' B:GTP301 4.6 0.7 1.0
O1B B:GTP301 4.6 0.8 1.0
CD B:GLU174 4.7 78.7 1.0
H8 B:APC302 4.8 0.4 1.0
O1A B:APC302 4.8 0.6 1.0
O3G B:GTP301 4.9 0.7 1.0
N7 B:APC302 4.9 0.9 1.0
CE B:LYS80 4.9 95.2 1.0
C3A B:APC302 4.9 0.2 1.0
CE B:LYS88 5.0 86.0 1.0

Reference:

M.C.Manav, J.Beljantseva, M.S.Bojer, T.Tenson, H.Ingmer, V.Hauryliuk, D.E.Brodersen. Structural Basis For (P)Ppgpp Synthesis By Thestaphylococcus Aureussmall Alarmone Synthetase Relp. J. Biol. Chem. V. 293 3254 2018.
ISSN: ESSN 1083-351X
PubMed: 29326162
DOI: 10.1074/JBC.RA117.001374
Page generated: Mon Dec 14 22:39:49 2020

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