Silver in PDB 8gy1: Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin

Enzymatic activity of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin

All present enzymatic activity of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin, PDB code: 8gy1 was solved by T.H.Ming, X.R.Su, C.H.Huo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.80 / 1.90
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 148.212, 148.212, 148.212, 90, 90, 90
R / Rfree (%) 15.1 / 19

Silver Binding Sites:

The binding sites of Silver atom in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin (pdb code 8gy1). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 5 binding sites of Silver where determined in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin, PDB code: 8gy1:
Jump to Silver binding site number: 1; 2; 3; 4; 5;

Silver binding site 1 out of 5 in 8gy1

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Silver binding site 1 out of 5 in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag203

b:28.2
occ:0.14
 O A:HOH399 2.7 35.9 1.0
OD2 A:ASP122 2.7 33.6 1.0
N A:HIS9 2.8 31.0 1.0
SG A:CYS12 3.1 36.5 1.0
CB A:ASP122 3.3 27.8 1.0
O A:ASN7 3.4 30.1 1.0
CG A:ASP122 3.4 30.6 1.0
CB A:HIS9 3.4 34.1 1.0
CA A:TYR8 3.5 30.9 1.0
CB A:CYS12 3.5 33.1 1.0
C A:TYR8 3.6 28.9 1.0
CA A:HIS9 3.7 34.0 1.0
CB A:HIS120 3.9 32.3 1.0
CD1 A:TYR8 4.1 29.4 1.0
C A:ASN7 4.1 28.5 1.0
N A:TYR8 4.2 28.5 1.0
O A:HIS9 4.4 31.1 1.0
O A:HIS120 4.5 31.0 1.0
CA A:ASP122 4.5 27.8 1.0
O A:HOH469 4.6 55.0 1.0
C A:HIS9 4.6 32.5 1.0
OD1 A:ASP122 4.6 28.9 1.0
CB A:TYR8 4.7 30.4 1.0
CG A:TYR8 4.7 26.8 1.0
CG A:HIS120 4.7 31.7 1.0
CE1 A:TYR8 4.8 29.0 1.0
SD A:MET125 4.8 30.1 1.0
O A:TYR8 4.8 31.5 1.0
CG A:HIS9 4.9 38.0 1.0
N A:ASP122 4.9 29.9 1.0
C A:HIS120 4.9 32.9 1.0
CA A:CYS12 5.0 33.7 1.0
NH2 A:ARG72 5.0 29.0 1.0

Silver binding site 2 out of 5 in 8gy1

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Silver binding site 2 out of 5 in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag204

b:30.4
occ:0.13
 O A:HOH467 2.7 35.6 1.0
O A:MET31 2.8 26.7 1.0
SD A:MET31 3.2 37.0 1.0
N A:SER35 3.3 25.9 1.0
CB A:SER35 3.4 29.6 1.0
CB A:ALA34 3.6 29.8 1.0
CA A:SER35 3.7 26.8 1.0
C A:MET31 3.8 29.3 1.0
OG A:SER35 3.8 28.4 1.0
CD2 A:LEU52 3.8 37.5 1.0
CG A:MET31 3.8 30.3 1.0
C A:ALA34 4.0 25.6 1.0
CA A:MET31 4.1 29.2 1.0
CA A:ALA34 4.3 26.3 1.0
CB A:MET31 4.5 27.5 1.0
O A:ALA34 4.7 28.0 1.0
CE1 A:HIS48 4.7 33.2 1.0
CG A:LEU52 4.8 37.7 1.0
N A:ALA34 4.8 25.4 1.0
CE A:MET31 4.9 37.3 1.0
N A:SER32 4.9 26.9 1.0
O A:HOH368 5.0 31.0 1.0

Silver binding site 3 out of 5 in 8gy1

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Silver binding site 3 out of 5 in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag205

b:169.8
occ:1.00
 O A:HOH414 2.8 64.6 1.0
O A:HOH374 2.9 65.4 1.0
OE2 A:GLU103 3.3 41.5 1.0
OE2 A:GLU58 3.7 47.9 1.0
OE1 A:GLU57 4.0 60.9 1.0
O A:HOH301 4.0 52.8 1.0
CD A:GLU103 4.0 37.9 1.0
OE1 A:GLU103 4.2 41.0 1.0
CG A:GLU58 4.3 34.4 1.0
CE1 A:HIS61 4.4 63.6 1.0
CB A:ALA140 4.4 30.9 1.0
CD A:GLU58 4.4 41.2 1.0
O A:HOH406 4.4 41.2 1.0
CE2 A:TYR30 4.6 33.1 1.0
O A:SER54 4.6 28.9 1.0
CB A:GLU57 4.7 33.8 1.0
ND1 A:HIS61 4.7 63.1 1.0
O A:HOH400 4.8 57.2 1.0
CB A:SER54 4.8 28.5 1.0
OH A:TYR30 4.8 39.1 1.0
CA A:SER54 4.9 29.3 1.0
OG A:SER54 5.0 34.0 1.0
OE1 A:GLN137 5.0 50.2 1.0

Silver binding site 4 out of 5 in 8gy1

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Silver binding site 4 out of 5 in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag206

b:151.1
occ:0.28
 AG A:AG207 2.5 124.9 0.1
OE1 A:GLU130 2.9 48.1 1.0
OD1 A:ASP127 3.1 35.6 1.0
O A:HOH409 3.3 49.2 1.0
O A:HOH331 4.1 51.5 1.0
CD A:GLU130 4.1 40.2 1.0
CG A:ASP127 4.2 34.4 1.0
CB A:ASP127 4.7 29.1 1.0
CA A:ASP127 4.7 30.1 1.0
CB A:GLU130 4.8 28.5 1.0
OE2 A:GLU130 4.8 37.0 1.0

Silver binding site 5 out of 5 in 8gy1

Go back to Silver Binding Sites List in 8gy1
Silver binding site 5 out of 5 in the Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Crystal Structure of Ag+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag207

b:124.9
occ:0.08
 O A:HOH331 2.3 51.5 1.0
AG A:AG206 2.5 151.1 0.3
OE1 A:GLU130 2.7 48.1 1.0
O A:HOH470 3.0 116.4 0.3
CD A:GLU130 3.5 40.2 1.0
OE2 A:GLU130 3.5 37.0 1.0
O A:HOH308 4.0 50.6 1.0
OD1 A:ASP127 4.8 35.6 1.0
CG A:GLU130 4.9 30.7 1.0

Reference:

C.Huo, T.Ming, Y.Wu, H.Huan, X.Qiu, C.Lu, Y.Li, Z.Zhang, J.Han, X.Su. Structural and Biochemical Characterization of Silver/Copper Binding By Dendrorhynchus Zhejiangensis Ferritin. Polymers (Basel) V. 15 2023.
ISSN: ISSN 2073-4360
PubMed: 36904538
DOI: 10.3390/POLYM15051297
Page generated: Tue Apr 11 12:17:33 2023

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