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Gold in PDB 5y0y: Rvfv Gn-Au

Protein crystallography data

The structure of Rvfv Gn-Au, PDB code: 5y0y was solved by Y.Wu, F.Gao, J.X.Qi, Y.Chai, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.97 / 3.40
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.180, 97.180, 184.128, 90.00, 90.00, 120.00
R / Rfree (%) 27.5 / 31.7

Gold Binding Sites:

The binding sites of Gold atom in the Rvfv Gn-Au (pdb code 5y0y). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 6 binding sites of Gold where determined in the Rvfv Gn-Au, PDB code: 5y0y:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6;

Gold binding site 1 out of 6 in 5y0y

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Gold binding site 1 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Rvfv Gn-Au within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au401

b:0.1
occ:1.00
CG A:HIS82 2.1 0.0 1.0
ND1 A:HIS82 2.3 0.4 1.0
CB A:HIS82 2.3 89.4 1.0
CD2 A:HIS82 2.9 85.7 1.0
CE1 A:HIS82 3.1 74.9 1.0
NE2 A:HIS82 3.4 69.2 1.0
CA A:HIS82 3.8 82.9 1.0
C A:HIS82 4.2 78.5 1.0
O A:HIS82 4.5 81.1 1.0
N A:HIS82 4.7 81.9 1.0
N A:GLY83 4.8 70.9 1.0

Gold binding site 2 out of 6 in 5y0y

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Gold binding site 2 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Rvfv Gn-Au within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au402

b:0.4
occ:1.00
ND1 A:HIS56 2.0 39.2 1.0
CE1 A:HIS56 2.4 34.9 1.0
CG A:HIS56 3.3 35.0 1.0
N A:HIS56 3.5 41.7 1.0
O A:GLY286 3.6 69.0 1.0
N A:HIS55 3.7 36.9 1.0
NE2 A:HIS56 3.7 27.3 1.0
CA A:TYR53 3.8 40.5 1.0
C A:HIS55 3.8 51.1 1.0
C A:TYR53 3.8 39.1 1.0
CB A:TYR53 3.8 36.3 1.0
CA A:SER287 3.9 57.9 1.0
C A:GLY286 3.9 63.7 1.0
N A:ALA54 4.0 39.7 1.0
CA A:HIS55 4.1 47.7 1.0
N A:SER287 4.1 59.8 1.0
CB A:HIS56 4.1 32.3 1.0
CD2 A:HIS56 4.2 30.0 1.0
O A:TYR53 4.2 41.5 1.0
CB A:HIS55 4.3 50.7 1.0
CA A:HIS56 4.3 33.6 1.0
CD2 A:TYR53 4.3 44.5 1.0
O A:HIS55 4.3 51.0 1.0
CB A:SER287 4.5 59.6 1.0
CG A:TYR53 4.6 36.0 1.0
C A:ALA54 4.6 27.7 1.0
CA A:GLY286 4.9 67.7 1.0
CA A:ALA54 4.9 34.0 1.0

Gold binding site 3 out of 6 in 5y0y

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Gold binding site 3 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Rvfv Gn-Au within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au403

b:0.4
occ:1.00
CG A:PRO28 1.7 0.4 1.0
CB A:PRO28 2.5 96.7 1.0
NE2 A:HIS13 3.0 87.7 1.0
CD A:PRO28 3.1 92.8 1.0
CD2 A:HIS13 3.7 80.5 1.0
CA A:PRO28 3.7 77.0 1.0
CE1 A:HIS13 3.7 82.8 1.0
N A:PRO28 3.8 81.8 1.0
O A:LYS11 4.2 63.2 1.0
CB A:LYS11 4.6 50.6 1.0
ND1 A:HIS13 4.6 83.0 1.0
CG A:HIS13 4.6 77.7 1.0
C A:LYS11 4.6 57.7 1.0
C A:LYS27 4.9 84.3 1.0
CA A:LYS11 4.9 54.3 1.0

Gold binding site 4 out of 6 in 5y0y

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Gold binding site 4 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Rvfv Gn-Au within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au404

b:0.7
occ:1.00
CE A:MET19 2.3 91.1 1.0
SD A:MET19 2.5 55.7 1.0
NE2 A:GLN102 3.1 0.1 1.0
CD A:LYS117 3.2 94.0 1.0
CE A:LYS117 3.4 90.8 1.0
CG A:LYS117 3.5 80.8 1.0
CD A:GLN102 3.8 91.7 1.0
CG A:GLN102 4.0 81.4 1.0
CB A:LYS117 4.1 69.2 1.0
NZ A:LYS117 4.2 72.5 1.0
CG A:MET19 4.2 87.8 1.0
CB A:SER103 4.4 60.6 1.0
O A:GLN102 4.4 61.4 1.0
O A:CYS118 4.4 71.4 1.0
CA A:LYS117 4.7 59.5 1.0
OE1 A:GLN102 4.7 82.0 1.0
N A:CYS118 4.9 63.4 1.0
C A:GLN102 4.9 59.5 1.0

Gold binding site 5 out of 6 in 5y0y

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Gold binding site 5 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Rvfv Gn-Au within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au405

b:0.8
occ:0.50
CD2 A:HIS187 3.3 17.8 1.0
N A:HIS187 4.0 42.9 1.0
NE2 A:HIS187 4.1 14.2 1.0
CG A:HIS187 4.2 42.5 1.0
CA A:ALA186 4.4 30.7 1.0
CB A:HIS187 4.6 42.1 1.0
CB A:ALA186 4.7 35.4 1.0
C A:ALA186 4.8 34.2 1.0
CA A:HIS187 4.8 36.3 1.0
O A:HIS187 4.9 47.6 1.0

Gold binding site 6 out of 6 in 5y0y

Go back to Gold Binding Sites List in 5y0y
Gold binding site 6 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Rvfv Gn-Au within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au406

b:97.9
occ:1.00
ND1 A:HIS13 2.2 83.0 1.0
CE1 A:HIS13 2.6 82.8 1.0
CG A:HIS13 2.6 77.7 1.0
NE2 A:HIS13 3.1 87.7 1.0
CD2 A:HIS13 3.2 80.5 1.0
CG A:HIS64 3.3 44.8 1.0
ND1 A:HIS64 3.3 41.0 1.0
CB A:HIS13 3.4 80.0 1.0
CE1 A:TYR15 3.5 58.0 1.0
CD2 A:HIS64 3.5 41.2 1.0
CE1 A:HIS64 3.5 38.4 1.0
NE2 A:HIS64 3.6 48.6 1.0
OH A:TYR15 3.9 56.4 1.0
CB A:HIS64 3.9 39.1 1.0
CZ A:TYR15 4.2 57.4 1.0
NZ A:LYS11 4.2 49.5 1.0
CD A:LYS11 4.3 58.5 1.0
O A:HIS64 4.5 32.9 1.0
CD1 A:TYR15 4.5 55.0 1.0
CE A:LYS11 4.7 51.4 1.0
CE A:LYS27 4.8 67.5 1.0
CA A:HIS13 4.8 59.6 1.0

Reference:

Y.Wu, Y.H.Zhu, F.Gao, Y.J.Jiao, B.O.Oladejo, Y.Chai, Y.H.Bi, S.Lu, M.Q.Dong, C.Zhang, G.M.Huang, G.Wong, N.Li, Y.F.Zhang, Y.Li, W.H.Feng, Y.Shi, M.F.Liang, R.G.Zhang, J.X.Qi, G.F.Gao. Structures of Phlebovirus Glycoprotein Gn and Identification of A Neutralizing Antibody Epitope Proc. Natl. Acad. Sci. V. 114 E7564 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28827346
DOI: 10.1073/PNAS.1705176114
Page generated: Sat Dec 12 01:54:25 2020

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