Zinc in PDB 4npd: High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature

The structure of High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature, PDB code: 4npd was solved by L.N.Deis, C.W.Pemble Iv, T.G.Oas, J.S.Richardson, D.C.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.39 / 0.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.250, 38.410, 28.610, 90.00, 117.44, 90.00
R / Rfree (%)	11.2 / 13

The binding sites of Zinc atom in the High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature (pdb code 4npd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature, PDB code: 4npd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:5.6 occ:1.00 N A:SCN103 1.9 7.2 1.0 OXT A:LYS58 1.9 7.2 0.5 OXT A:LYS58 2.0 7.4 0.5 C A:LYS58 2.7 7.8 0.5 O A:LYS58 2.8 8.4 0.5 C A:LYS58 2.8 8.1 0.5 O A:LYS58 2.9 9.3 0.5 C A:SCN103 3.0 6.6 1.0 CA A:LYS58 4.1 9.9 0.5 HB3 A:LYS58 4.2 13.0 0.5 CA A:LYS58 4.3 10.2 0.5 HB3 A:LYS58 4.4 13.0 0.5 O A:HOH334 4.4 22.0 1.0 HA A:LYS58 4.5 9.9 0.5 HA A:LYS58 4.6 9.9 0.5 CB A:LYS58 4.7 13.0 0.5 S A:SCN103 4.8 8.1 1.0 CB A:LYS58 4.9 11.2 0.5 HB2 A:LYS58 4.9 13.0 0.5 HB2 A:LYS58 5.0 13.0 0.5

Zinc binding site 2 out of 2 in the High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Structure of C Domain of Staphylococcal Protein A at Cryogenic Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:30.0 occ:0.40 O A:PRO20 1.9 5.4 0.5 O A:HOH330 2.0 28.2 0.9 O A:PRO20 2.1 7.8 0.5 O A:HOH221 2.1 14.3 1.0 O A:HOH264 2.3 21.5 1.0 O A:HOH332 2.6 28.6 1.0 C A:PRO20 3.0 3.7 0.5 HA A:PRO20 3.2 5.5 0.5 C A:PRO20 3.2 5.9 0.5 HA A:PRO20 3.4 5.5 0.5 CA A:PRO20 3.6 4.4 0.5 O A:HOH331 3.8 31.0 0.8 HA A:ASN21 3.9 4.9 0.5 CA A:PRO20 3.9 5.5 0.5 HB2 A:PRO20 4.0 6.9 0.5 HA A:ASN21 4.0 4.9 0.5 HH22 A:ARG27 4.0 8.0 0.7 HH22 A:ARG27 4.0 8.0 0.3 O A:HOH214 4.1 12.2 1.0 N A:ASN21 4.1 3.9 0.5 CB A:PRO20 4.3 4.7 0.5 N A:ASN21 4.3 5.2 0.5 HH21 A:ARG27 4.3 8.0 0.7 HB2 A:PRO20 4.4 6.9 0.5 HB3 A:PRO20 4.5 6.9 0.5 CA A:ASN21 4.5 4.8 0.5 NH2 A:ARG27 4.5 7.6 0.7 HH21 A:ARG27 4.6 8.0 0.3 O A:LEU22 4.6 7.0 1.0 CA A:ASN21 4.6 4.9 0.5 CB A:PRO20 4.6 6.9 0.5 NH2 A:ARG27 4.6 8.0 0.3 O A:LEU19 4.8 4.6 0.5 O A:LEU19 4.8 4.8 0.5 O A:HOH275 4.8 22.8 0.9 HB3 A:PRO20 4.8 6.9 0.5 H A:LEU22 4.9 4.8 0.7 H A:ASN21 4.9 5.2 0.5 N A:PRO20 5.0 4.4 0.5

L.N.Deis, C.W.Pemble, Y.Qi, A.Hagarman, D.C.Richardson, J.S.Richardson, T.G.Oas. Multiscale Conformational Heterogeneity in Staphylococcal Protein A: Possible Determinant of Functional Plasticity. Structure V. 22 1467 2014.
ISSN: ISSN 0969-2126
PubMed: 25295398
DOI: 10.1016/J.STR.2014.08.014