Magnesium in PDB 6h5e: Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp

Protein crystallography data

The structure of Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp, PDB code: 6h5e was solved by E.R.Noeldeke, V.Niemann, E.Stoerk, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.08 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.720, 109.740, 123.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.5

Other elements in 6h5e:

The structure of Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp (pdb code 6h5e). 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 the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp, PDB code: 6h5e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6h5e

Go back to Magnesium Binding Sites List in 6h5e
Magnesium binding site 1 out of 2 in the Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp


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 Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:62.0
occ:1.00
OE1 B:GLU108 2.2 45.0 1.0
O1B B:ANP502 2.2 39.9 0.8
O1G B:ANP502 2.2 52.4 0.8
O B:HOH613 2.3 48.4 1.0
OG1 B:THR60 2.3 38.6 1.0
CD B:GLU108 3.2 45.0 1.0
PB B:ANP502 3.4 41.2 0.8
PG B:ANP502 3.4 55.4 0.8
N3B B:ANP502 3.5 54.3 0.8
OE2 B:GLU108 3.6 49.3 1.0
CB B:THR60 3.6 41.3 1.0
ND2 B:ASN85 3.9 42.6 1.0
O1A B:ANP502 4.1 63.9 0.8
N B:THR60 4.2 41.4 1.0
O2G B:ANP502 4.3 60.6 0.8
CA B:THR60 4.3 42.0 1.0
CE B:LYS59 4.3 40.1 1.0
O2B B:ANP502 4.4 36.4 0.8
O B:HOH622 4.4 67.9 1.0
O3G B:ANP502 4.5 50.0 0.8
O3A B:ANP502 4.5 37.8 0.8
CG B:GLU108 4.5 38.6 1.0
O B:GLY83 4.6 73.0 1.0
CB B:LYS59 4.6 37.1 1.0
CG2 B:THR60 4.7 31.5 1.0
PA B:ANP502 4.7 53.8 0.8
CA B:GLY83 4.7 56.9 1.0
O B:HOH609 4.8 62.4 1.0
NZ B:LYS59 4.9 37.6 1.0
CG B:ASN85 5.0 46.1 1.0

Magnesium binding site 2 out of 2 in 6h5e

Go back to Magnesium Binding Sites List in 6h5e
Magnesium binding site 2 out of 2 in the Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp


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 Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:59.1
occ:1.00
O1G D:ANP502 1.9 41.8 0.8
O1B D:ANP502 1.9 44.2 0.8
OE1 D:GLU108 2.2 42.5 1.0
OG1 D:THR60 2.3 45.3 1.0
O D:HOH604 2.3 53.5 1.0
CD D:GLU108 3.2 48.8 1.0
PG D:ANP502 3.2 51.7 0.8
PB D:ANP502 3.2 44.9 0.8
N3B D:ANP502 3.5 53.7 0.8
CB D:THR60 3.5 46.6 1.0
OE2 D:GLU108 3.5 47.5 1.0
O1A D:ANP502 3.7 56.3 0.8
O2G D:ANP502 3.9 46.8 0.8
ND2 D:ASN85 4.0 46.5 1.0
N D:THR60 4.0 47.0 1.0
O D:HOH602 4.0 59.9 1.0
O2B D:ANP502 4.2 44.3 0.8
CA D:THR60 4.3 39.7 1.0
O D:HOH713 4.3 60.2 1.0
O3A D:ANP502 4.3 40.1 0.8
CE D:LYS59 4.3 37.6 1.0
O3G D:ANP502 4.4 44.2 0.8
CG D:GLU108 4.5 47.9 1.0
PA D:ANP502 4.5 50.8 0.8
CB D:LYS59 4.6 40.7 1.0
CG2 D:THR60 4.7 40.0 1.0
C D:LYS59 4.9 45.1 1.0
O D:GLY83 4.9 70.5 1.0
NZ D:LYS59 5.0 41.8 1.0

Reference:

E.R.Noldeke, L.M.Muckenfuss, V.Niemann, A.Muller, E.Stork, G.Zocher, T.Schneider, T.Stehle. Structural Basis of Cell Wall Peptidoglycan Amidation By the Gatd/Murt Complex of Staphylococcus Aureus. Sci Rep V. 8 12953 2018.
ISSN: ESSN 2045-2322
PubMed: 30154570
DOI: 10.1038/S41598-018-31098-X
Page generated: Mon Dec 14 22:47:33 2020

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