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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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 6h5e

Go back to Zinc Binding Sites List in 6h5e
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 6h5e

Go back to Zinc Binding Sites List in 6h5e
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

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: Wed Dec 16 11:55:29 2020

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