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

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

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Gatd/Murt Enzyme Complex From Staphylococcus Aureus with Bound Amppnp, PDB code: 6h5e:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:60.1 occ:1.00 SG B:CYS224 2.1 56.8 1.0 SG B:CYS205 2.3 68.1 1.0 SG B:CYS226 2.3 66.6 1.0 SG B:CYS202 2.6 61.4 1.0 CB B:CYS224 3.0 59.4 1.0 CB B:CYS202 3.1 67.1 1.0 CB B:CYS226 3.1 65.7 1.0 CB B:CYS205 3.2 68.4 1.0 N B:CYS205 3.5 68.7 1.0 CA B:CYS205 3.9 67.5 1.0 N B:CYS226 4.1 67.9 1.0 CA B:CYS226 4.2 63.6 1.0 CB B:ASN204 4.4 67.1 1.0 C B:CYS205 4.5 69.9 1.0 N B:GLY206 4.5 64.8 1.0 CA B:CYS224 4.5 63.2 1.0 CB B:PHE228 4.5 55.0 1.0 NH1 B:ARG207 4.6 70.8 1.0 CA B:CYS202 4.6 62.1 1.0 C B:ASN204 4.6 71.5 1.0 ND2 B:ASN204 4.7 60.4 1.0 N B:ARG207 4.8 71.8 1.0 CA B:ASN204 4.9 71.1 1.0 N B:ASN204 4.9 60.4 1.0 CB B:ARG207 4.9 71.8 1.0 N B:GLN225 4.9 75.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:56.2 occ:1.00 SG D:CYS224 2.2 52.3 1.0 SG D:CYS226 2.3 52.7 1.0 SG D:CYS205 2.4 63.9 1.0 SG D:CYS202 2.5 51.7 1.0 CB D:CYS202 3.1 52.8 1.0 CB D:CYS224 3.1 46.6 1.0 CB D:CYS226 3.1 49.3 1.0 CB D:CYS205 3.5 58.4 1.0 N D:CYS205 3.7 54.4 1.0 CA D:CYS205 4.1 51.7 1.0 N D:CYS226 4.2 66.6 1.0 CA D:CYS226 4.2 64.9 1.0 CB D:PHE228 4.5 47.2 1.0 CB D:ASN204 4.5 56.1 1.0 CA D:CYS224 4.5 51.8 1.0 CA D:CYS202 4.6 50.5 1.0 N D:GLY206 4.7 56.0 1.0 C D:CYS205 4.7 57.8 1.0 C D:ASN204 4.8 57.9 1.0 ND2 D:ASN204 4.8 61.2 1.0 NH1 D:ARG207 4.8 62.4 1.0 N D:ARG207 4.8 49.3 1.0 C D:CYS226 5.0 61.3 1.0 N D:ASN204 5.0 51.4 1.0 CA D:ASN204 5.0 55.9 1.0

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