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Gold in PDB 4zgh: Structure of Sugar Binding Protein Pneumolysin

Protein crystallography data

The structure of Structure of Sugar Binding Protein Pneumolysin, PDB code: 4zgh was solved by M.W.Parker, S.C.Feil, C.Morton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.51 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.857, 133.619, 220.442, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 30.7

Gold Binding Sites:

The binding sites of Gold atom in the Structure of Sugar Binding Protein Pneumolysin (pdb code 4zgh). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 2 binding sites of Gold where determined in the Structure of Sugar Binding Protein Pneumolysin, PDB code: 4zgh:
Jump to Gold binding site number: 1; 2;

Gold binding site 1 out of 2 in 4zgh

Go back to Gold Binding Sites List in 4zgh
Gold binding site 1 out of 2 in the Structure of Sugar Binding Protein Pneumolysin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Structure of Sugar Binding Protein Pneumolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au508

b:58.2
occ:0.78
AU A:AUC508 0.0 58.2 0.8
C2 A:AUC508 2.1 48.6 0.8
H21 A:PEG507 2.6 0.8 1.0
H31 A:PEG507 2.6 74.6 1.0
N2 A:AUC508 3.2 38.8 0.8
AU A:AUC509 3.3 63.5 0.7
SG A:CYS428 3.3 0.0 1.0
HB2 A:CYS428 3.3 0.4 1.0
HB3 A:TRP435 3.4 59.0 1.0
C2 A:PEG507 3.5 92.3 1.0
C3 A:PEG507 3.5 62.2 1.0
H12 A:PEG507 3.6 60.1 1.0
CB A:CYS428 3.9 85.3 1.0
O2 A:PEG507 3.9 77.4 1.0
H32 A:PEG507 4.0 74.6 1.0
C1 A:PEG507 4.1 50.0 1.0
H22 A:PEG507 4.1 0.8 1.0
CZ2 A:TRP436 4.2 36.5 1.0
HO4 A:PEG507 4.2 77.9 1.0
O A:TRP435 4.3 64.0 1.0
CB A:TRP435 4.3 49.2 1.0
HZ2 A:TRP436 4.3 43.8 1.0
CE2 A:TRP436 4.4 37.1 1.0
O4 A:PEG507 4.4 64.9 1.0
CH2 A:TRP436 4.4 34.5 1.0
C4 A:PEG507 4.5 77.1 1.0
HA A:TRP435 4.5 70.8 1.0
HA A:CYS428 4.5 99.0 1.0
HB3 A:CYS428 4.6 0.4 1.0
H A:GLY430 4.6 82.5 1.0
CG A:TRP435 4.6 59.4 1.0
H41 A:PEG507 4.6 92.5 1.0
HH2 A:TRP436 4.7 41.4 1.0
O A:HOH617 4.7 38.8 1.0
CA A:CYS428 4.7 82.5 1.0
C A:TRP435 4.7 58.9 1.0
CA A:TRP435 4.8 59.0 1.0
O1 A:PEG507 4.8 52.4 1.0
CD2 A:TRP436 4.8 54.8 1.0
CZ3 A:TRP436 4.8 33.6 1.0
NE1 A:TRP436 4.8 49.8 1.0
H11 A:PEG507 4.8 60.1 1.0
C2 A:AUC509 4.9 38.8 0.7
HB2 A:TRP435 5.0 59.0 1.0
H A:THR429 5.0 37.7 1.0
HE1 A:TRP436 5.0 59.8 1.0

Gold binding site 2 out of 2 in 4zgh

Go back to Gold Binding Sites List in 4zgh
Gold binding site 2 out of 2 in the Structure of Sugar Binding Protein Pneumolysin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Structure of Sugar Binding Protein Pneumolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au509

b:63.5
occ:0.73
AU A:AUC509 0.0 63.5 0.7
C2 A:AUC509 2.1 38.8 0.7
SG A:CYS428 2.7 0.0 1.0
C2 A:AUC508 2.8 48.6 0.8
H41 A:PEG507 2.8 92.5 1.0
N2 A:AUC508 3.0 38.8 0.8
H31 A:PEG507 3.0 74.6 1.0
H12 A:PEG507 3.2 60.1 1.0
AU A:AUC508 3.3 58.2 0.8
C4 A:PEG507 3.4 77.1 1.0
C3 A:PEG507 3.4 62.2 1.0
O2 A:PEG507 3.4 77.4 1.0
H21 A:PEG507 3.6 0.8 1.0
O4 A:PEG507 3.6 64.9 1.0
C2 A:PEG507 3.8 92.3 1.0
C1 A:PEG507 3.8 50.0 1.0
H11 A:PEG507 3.9 60.1 1.0
CB A:CYS428 4.0 85.3 1.0
HB A:VAL372 4.0 39.1 1.0
HB2 A:CYS428 4.1 0.4 1.0
HO4 A:PEG507 4.1 77.9 1.0
HB3 A:CYS428 4.1 0.4 1.0
HG11 A:VAL372 4.3 40.0 1.0
H42 A:PEG507 4.3 92.5 1.0
H32 A:PEG507 4.4 74.6 1.0
HG21 A:VAL372 4.7 39.7 1.0
H22 A:PEG507 4.8 0.8 1.0
HG12 A:VAL372 4.8 40.0 1.0
CB A:VAL372 4.8 32.6 1.0
CG1 A:VAL372 4.8 33.3 1.0

Reference:

S.L.Lawrence, S.C.Feil, C.J.Morton, A.J.Farrand, T.D.Mulhern, M.A.Gorman, K.R.Wade, R.K.Tweten, M.W.Parker. Crystal Structure of Streptococcus Pneumoniae Pneumolysin Provides Key Insights Into Early Steps of Pore Formation. Sci Rep V. 5 14352 2015.
ISSN: ESSN 2045-2322
PubMed: 26403197
DOI: 10.1038/SREP14352
Page generated: Sat Dec 12 01:54:12 2020

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