Zinc in PDB 7rcz: Crystal Structure of C. Difficile Spovd in Complex with Ampicillin

Protein crystallography data

The structure of Crystal Structure of C. Difficile Spovd in Complex with Ampicillin, PDB code: 7rcz was solved by M.Sacco, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.58 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.64, 95.62, 176.77, 90, 90, 90
R / Rfree (%) 18.7 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of C. Difficile Spovd in Complex with Ampicillin (pdb code 7rcz). 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 C. Difficile Spovd in Complex with Ampicillin, PDB code: 7rcz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7rcz

Go back to Zinc Binding Sites List in 7rcz
Zinc binding site 1 out of 2 in the Crystal Structure of C. Difficile Spovd in Complex with Ampicillin


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 C. Difficile Spovd in Complex with Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn808

b:31.7
occ:1.00
ND1 A:HIS355 2.1 31.8 1.0
SG A:CYS348 2.1 36.0 1.0
SG A:CYS368 2.3 30.1 1.0
SG A:CYS335 2.4 31.2 1.0
CE1 A:HIS355 2.9 32.4 1.0
CG A:HIS355 3.2 34.0 1.0
CB A:CYS335 3.2 34.1 1.0
CB A:CYS348 3.3 35.6 1.0
CB A:CYS368 3.3 30.3 1.0
CB A:HIS355 3.6 35.1 1.0
CA A:CYS368 3.7 29.2 1.0
NE2 A:HIS355 4.1 31.4 1.0
N A:HIS355 4.1 38.3 1.0
CD2 A:HIS355 4.3 33.6 1.0
NE2 A:GLN358 4.4 29.9 1.0
CD A:PRO370 4.4 27.6 1.0
CA A:HIS355 4.5 33.3 1.0
C A:CYS368 4.5 27.4 1.0
CA A:CYS335 4.6 37.7 1.0
CA A:CYS348 4.6 33.1 1.0
OE1 A:GLN358 4.8 33.4 1.0
N A:ASN369 4.8 27.7 1.0
N A:CYS368 5.0 29.6 1.0
CG A:PRO370 5.0 28.5 1.0

Zinc binding site 2 out of 2 in 7rcz

Go back to Zinc Binding Sites List in 7rcz
Zinc binding site 2 out of 2 in the Crystal Structure of C. Difficile Spovd in Complex with Ampicillin


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 C. Difficile Spovd in Complex with Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn608

b:50.1
occ:1.00
ND1 B:HIS355 1.9 34.3 1.0
CE1 B:HIS355 2.3 49.0 1.0
SG B:CYS368 2.3 42.3 1.0
SG B:CYS335 2.4 59.4 1.0
SG B:CYS348 2.5 52.3 1.0
CG B:HIS355 3.2 43.8 1.0
CB B:CYS335 3.4 57.9 1.0
CB B:CYS368 3.4 41.2 1.0
CB B:CYS348 3.5 59.1 1.0
NE2 B:HIS355 3.6 39.3 1.0
CA B:CYS368 3.8 40.8 1.0
CB B:HIS355 4.0 48.8 1.0
CD2 B:HIS355 4.0 39.9 1.0
CD B:PRO370 4.3 53.6 1.0
N B:HIS355 4.3 55.4 1.0
CG B:PRO370 4.6 54.0 1.0
C B:CYS368 4.6 39.7 1.0
CA B:CYS335 4.7 57.0 1.0
NE2 B:GLN358 4.7 53.8 1.0
N B:ASN369 4.8 42.7 1.0
CA B:HIS355 4.8 52.2 1.0
CA B:CYS348 4.8 60.9 1.0

Reference:

M.D.Sacco, S.Wang, S.R.Adapa, X.Zhang, E.M.Lewandowski, M.V.Gongora, D.Keramisanou, Z.D.Atlas, J.A.Townsend, J.R.Gatdula, R.T.Morgan, L.R.Hammond, M.T.Marty, J.Wang, P.J.Eswara, I.Gelis, R.H.Y.Jiang, X.Sun, Y.Chen. A Unique Class of Zn 2+ -Binding Serine-Based Pbps Underlies Cephalosporin Resistance and Sporogenesis in Clostridioides Difficile. Nat Commun V. 13 4370 2022.
ISSN: ESSN 2041-1723
PubMed: 35902581
DOI: 10.1038/S41467-022-32086-6
Page generated: Sat Apr 8 02:47:33 2023

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