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Copper in PDB 8hct: Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin

Enzymatic activity of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin

All present enzymatic activity of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin, PDB code: 8hct 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) 106.78 / 2.26
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 151.011, 151.011, 151.011, 90, 90, 90
R / Rfree (%) 16.4 / 22.6

Other elements in 8hct:

The structure of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin (pdb code 8hct). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin, PDB code: 8hct:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 8hct

Go back to Copper Binding Sites List in 8hct
Copper binding site 1 out of 5 in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu203

b:31.9
occ:0.29
 O A:HOH369 2.6 33.7 1.0
OD2 A:ASP122 2.7 32.0 1.0
N A:HIS9 2.9 28.0 1.0
SG A:CYS12 3.2 32.2 1.0
CB A:ASP122 3.4 26.5 1.0
CG A:ASP122 3.4 29.6 1.0
O A:ASN7 3.5 23.9 1.0
CB A:HIS9 3.5 33.3 1.0
CA A:TYR8 3.6 25.2 1.0
C A:TYR8 3.7 26.3 1.0
CB A:CYS12 3.7 29.6 1.0
CA A:HIS9 3.8 30.2 1.0
CB A:HIS120 4.0 32.9 1.0
CD1 A:TYR8 4.1 20.6 1.0
C A:ASN7 4.2 24.5 1.0
N A:TYR8 4.3 23.3 1.0
O A:HIS9 4.5 31.9 1.0
CA A:ASP122 4.6 27.1 1.0
O A:HIS120 4.6 28.5 1.0
OD1 A:ASP122 4.7 28.3 1.0
C A:HIS9 4.7 33.7 1.0
CB A:TYR8 4.7 22.8 1.0
CG A:TYR8 4.8 21.5 1.0
CG A:HIS120 4.8 33.8 1.0
O A:TYR8 4.8 25.5 1.0
CE1 A:TYR8 4.9 21.7 1.0
CG A:HIS9 4.9 34.9 1.0
N A:ASP122 4.9 27.8 1.0
SD A:MET125 4.9 30.0 1.0

Copper binding site 2 out of 5 in 8hct

Go back to Copper Binding Sites List in 8hct
Copper binding site 2 out of 5 in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu204

b:147.0
occ:0.33
 CU A:CU205 3.6 400.3 0.3
O A:HOH374 3.7 57.0 1.0
OE2 A:GLU130 4.6 40.8 1.0

Copper binding site 3 out of 5 in 8hct

Go back to Copper Binding Sites List in 8hct
Copper binding site 3 out of 5 in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu205

b:400.3
occ:0.33
 O A:HOH374 2.4 57.0 1.0
CU A:CU206 2.6 124.0 0.3
OE1 A:GLU130 2.9 44.7 1.0
OE2 A:GLU130 3.6 40.8 1.0
CU A:CU204 3.6 147.0 0.3
CD A:GLU130 3.7 37.4 1.0

Copper binding site 4 out of 5 in 8hct

Go back to Copper Binding Sites List in 8hct
Copper binding site 4 out of 5 in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu206

b:124.0
occ:0.33
 CU A:CU205 2.6 400.3 0.3
OE1 A:GLU130 2.9 44.7 1.0
OD1 A:ASP127 3.4 26.5 1.0
O A:HOH383 3.6 54.4 1.0
O A:HOH374 4.0 57.0 1.0
CD A:GLU130 4.2 37.4 1.0
CG A:ASP127 4.5 26.9 1.0
OE2 A:GLU130 4.8 40.8 1.0
CB A:ASP127 4.8 26.5 1.0
CU A:CU207 4.9 339.1 0.3
CA A:ASP127 4.9 26.8 1.0
CB A:GLU130 5.0 31.3 1.0

Copper binding site 5 out of 5 in 8hct

Go back to Copper Binding Sites List in 8hct
Copper binding site 5 out of 5 in the Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of CU2+ Binding to Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu207

b:339.1
occ:0.33
 O A:HOH383 3.2 54.4 1.0
ND2 A:ASN131 3.8 41.3 1.0
OD1 A:ASP127 4.4 26.5 1.0
CG A:ASN131 4.7 38.1 1.0
CU A:CU206 4.9 124.0 0.3

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: Wed Jul 31 09:44:33 2024

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