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Copper in PDB 6qyb: Streptomyces Lividans Ccsp Mutant - H111A

Protein crystallography data

The structure of Streptomyces Lividans Ccsp Mutant - H111A, PDB code: 6qyb was solved by M.L.Straw, M.A.Hough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.25 / 1.18
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.276, 62.202, 65.169, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 19.4

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 39;

Binding sites:

The binding sites of Copper atom in the Streptomyces Lividans Ccsp Mutant - H111A (pdb code 6qyb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 39 binding sites of Copper where determined in the Streptomyces Lividans Ccsp Mutant - H111A, PDB code: 6qyb:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 39 in 6qyb

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Copper binding site 1 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu200

b:14.1
occ:1.00
SG A:CYS100 2.1 16.3 1.0
SG A:CYS38 2.2 13.8 1.0
OD1 A:ASP61 2.5 15.4 1.0
CU A:CU1201 2.8 14.7 1.0
CU A:CU1218 3.0 15.6 1.0
CU A:CU1207 3.0 15.5 1.0
CU A:CU1206 3.1 14.4 1.0
SG A:CYS121 3.2 15.1 1.0
CB A:CYS100 3.2 13.8 1.0
CB A:CYS38 3.3 11.9 1.0
CB A:CYS64 3.5 12.8 1.0
CG A:ASP61 3.6 15.3 1.0
CA A:ASP61 3.6 13.9 1.0
SG A:CYS117 3.9 14.2 1.0
CU A:CU1202 3.9 13.6 1.0
SG A:CYS64 4.0 13.5 1.0
CB A:ASP61 4.0 14.5 1.0
CA A:CYS38 4.1 12.2 1.0
N A:ASP61 4.3 15.2 1.0
CA A:CYS100 4.4 13.7 1.0
SG A:CYS104 4.5 14.8 1.0
O A:THR60 4.5 12.7 1.0
O A:ASP61 4.5 12.1 1.0
C A:ASP61 4.6 12.5 1.0
C A:CYS100 4.6 13.5 1.0
O A:CYS100 4.6 14.7 1.0
OD2 A:ASP61 4.6 15.8 1.0
C A:THR60 4.6 14.8 1.0
CB A:CYS121 5.0 14.7 1.0
N A:CYS38 5.0 12.4 1.0
CA A:CYS64 5.0 12.2 1.0

Copper binding site 2 out of 39 in 6qyb

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Copper binding site 2 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:14.7
occ:1.00
SG A:CYS121 2.2 15.1 1.0
SG A:CYS64 2.2 13.5 1.0
CU A:CU1202 2.7 13.6 1.0
CU A:CU1200 2.8 14.1 1.0
SG A:CYS38 2.9 13.8 1.0
CU A:CU1215 2.9 14.7 1.0
CB A:CYS64 3.2 12.8 1.0
SG A:CYS34 3.3 14.0 1.0
CB A:CYS121 3.5 14.7 1.0
CU A:CU1216 3.5 14.1 1.0
CB A:CYS100 3.5 13.8 1.0
CU A:CU1206 3.6 14.4 1.0
SG A:CYS100 3.9 16.3 1.0
CA A:CYS121 3.9 14.1 1.0
CA A:CYS97 4.2 13.0 1.0
SG A:CYS97 4.2 15.1 1.0
CB A:CYS38 4.4 11.9 1.0
CA A:CYS64 4.5 12.2 1.0
CB A:CYS97 4.6 14.0 1.0
N A:CYS121 4.7 14.2 1.0
O A:CYS97 4.7 15.6 1.0
CA A:CYS100 4.8 13.7 1.0
O A:CYS34 4.9 12.5 1.0
O A:VAL96 4.9 12.9 1.0
CU A:CU1218 4.9 15.6 1.0
C A:CYS100 5.0 13.5 1.0
N A:CYS97 5.0 12.4 1.0
C A:CYS97 5.0 13.0 1.0
CB A:CYS34 5.0 13.3 1.0
C A:CYS64 5.0 10.8 1.0

Copper binding site 3 out of 39 in 6qyb

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Copper binding site 3 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:13.6
occ:1.00
SG A:CYS38 2.1 13.8 1.0
SG A:CYS34 2.2 14.0 1.0
O A:CYS34 2.2 12.5 1.0
CU A:CU1201 2.7 14.7 1.0
C A:CYS34 2.9 11.5 1.0
CB A:CYS34 3.2 13.3 1.0
CA A:CYS34 3.3 12.7 1.0
CU A:CU1215 3.3 14.7 1.0
CB A:CYS38 3.3 11.9 1.0
SG A:CYS121 3.8 15.1 1.0
CU A:CU1216 3.8 14.1 1.0
CU A:CU1206 3.8 14.4 1.0
N A:CYS38 3.8 12.4 1.0
CU A:CU1200 3.9 14.1 1.0
SG A:CYS64 3.9 13.5 1.0
N A:ALA35 4.0 11.4 1.0
CA A:CYS38 4.1 12.2 1.0
CB A:CYS64 4.5 12.8 1.0
CB A:ALA37 4.5 13.4 1.0
CA A:ALA35 4.6 12.3 1.0
SG A:CYS68 4.7 15.4 1.0
SG A:CYS117 4.7 14.2 1.0
N A:CYS34 4.7 11.6 1.0
CA A:CYS121 4.8 14.1 1.0
C A:ALA37 4.8 13.6 1.0
N A:CYS121 4.8 14.2 1.0
CB A:CYS121 4.9 14.7 1.0
C A:ALA35 5.0 12.7 1.0

Copper binding site 4 out of 39 in 6qyb

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Copper binding site 4 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu203

b:18.5
occ:0.50
ND1 A:HIS113 2.1 23.0 1.0
SG A:CYS41 2.3 16.2 1.0
CU A:CU1204 2.4 18.8 0.5
CG A:HIS113 2.8 23.5 1.0
CB A:HIS113 2.8 26.0 1.0
CU A:CU1205 3.0 18.1 1.0
C A:HIS113 3.0 19.4 1.0
O A:HIS113 3.2 19.9 1.0
CB A:CYS41 3.2 15.8 1.0
CA A:CYS41 3.3 14.8 1.0
CE1 A:HIS113 3.3 21.8 1.0
N A:CYS114 3.3 18.7 1.0
CA A:HIS113 3.4 23.7 1.0
CB A:ALA44 3.8 16.0 1.0
O A:CYS41 3.9 16.9 1.0
CA A:CYS114 3.9 21.5 1.0
CD2 A:HIS113 4.0 22.6 1.0
C A:CYS41 4.1 15.6 1.0
CU A:CU1219 4.1 17.4 1.0
NE2 A:HIS113 4.2 22.2 1.0
SG A:CYS114 4.3 19.1 1.0
N A:CYS41 4.4 14.7 1.0
SG A:CYS45 4.5 20.3 1.0
O A:HOH306 4.5 30.4 1.0
O A:HOH338 4.5 30.2 1.0
CB A:CYS114 4.6 21.1 1.0
N A:HIS113 4.6 24.4 1.0
CB A:CYS117 4.8 13.8 1.0
O A:ALA40 4.8 15.3 1.0
CA A:ALA44 5.0 16.5 1.0

Copper binding site 5 out of 39 in 6qyb

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Copper binding site 5 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu204

b:18.8
occ:0.50
ND1 A:HIS113 2.2 23.0 1.0
SG A:CYS114 2.3 19.1 1.0
CU A:CU1203 2.4 18.5 0.5
CU A:CU1205 2.5 18.1 1.0
CE1 A:HIS113 2.7 21.8 1.0
CB A:CYS114 2.8 21.1 1.0
SG A:CYS41 2.9 16.2 1.0
N A:CYS114 2.9 18.7 1.0
CA A:CYS114 3.0 21.5 1.0
SG A:CYS45 3.1 20.3 1.0
CU A:CU1219 3.3 17.4 1.0
CG A:HIS113 3.4 23.5 1.0
CU A:CU1217 3.5 23.0 0.5
C A:HIS113 3.6 19.4 1.0
NE2 A:HIS113 3.9 22.2 1.0
CB A:HIS113 4.1 26.0 1.0
O A:HIS113 4.1 19.9 1.0
CD2 A:HIS113 4.3 22.6 1.0
CA A:HIS113 4.3 23.7 1.0
CE A:MET110 4.4 37.2 1.0
O A:CYS41 4.5 16.9 1.0
C A:CYS114 4.5 20.5 1.0
CB A:CYS41 4.5 15.8 1.0
CB A:CYS45 4.7 17.5 1.0
CB A:ALA111 4.8 28.9 1.0
CA A:CYS41 4.9 14.8 1.0
O A:ALA111 4.9 24.3 1.0
N A:HIS113 4.9 24.4 1.0

Copper binding site 6 out of 39 in 6qyb

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Copper binding site 6 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu205

b:18.1
occ:1.00
O A:CYS41 2.2 16.9 1.0
SG A:CYS45 2.2 20.3 1.0
SG A:CYS41 2.2 16.2 1.0
CU A:CU1204 2.5 18.8 0.5
CU A:CU1217 2.7 23.0 0.5
C A:CYS41 2.9 15.6 1.0
CU A:CU1203 3.0 18.5 0.5
CU A:CU1219 3.1 17.4 1.0
CB A:CYS45 3.2 17.5 1.0
CB A:CYS41 3.3 15.8 1.0
CA A:CYS41 3.3 14.8 1.0
CU A:CU1208 3.4 18.2 1.0
SG A:CYS114 3.5 19.1 1.0
OD2 A:ASP61 3.7 15.8 1.0
N A:CYS45 3.7 17.9 1.0
ND1 A:HIS113 3.7 23.0 1.0
CE1 A:HIS113 4.0 21.8 1.0
CA A:CYS45 4.0 17.8 1.0
N A:ALA42 4.0 16.0 1.0
SG A:CYS57 4.4 19.1 1.0
CA A:ALA42 4.6 16.4 1.0
CB A:ALA44 4.6 16.0 1.0
C A:ALA44 4.7 18.1 1.0
N A:CYS41 4.8 14.7 1.0
CG A:ASP61 4.8 15.3 1.0
CB A:CYS114 4.9 21.1 1.0
C A:ALA42 5.0 16.4 1.0
CG A:HIS113 5.0 23.5 1.0

Copper binding site 7 out of 39 in 6qyb

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Copper binding site 7 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu206

b:14.4
occ:1.00
SG A:CYS121 2.2 15.1 1.0
SG A:CYS117 2.2 14.2 1.0
O A:CYS117 2.4 15.5 1.0
CU A:CU1207 2.8 15.5 1.0
C A:CYS117 2.9 15.0 1.0
CU A:CU1200 3.1 14.1 1.0
SG A:CYS38 3.2 13.8 1.0
CB A:CYS117 3.3 13.8 1.0
CB A:CYS121 3.4 14.7 1.0
CA A:CYS117 3.5 15.4 1.0
CU A:CU1201 3.6 14.7 1.0
N A:CYS121 3.8 14.2 1.0
N A:ALA118 3.8 15.6 1.0
CU A:CU1202 3.8 13.6 1.0
CU A:CU1218 3.8 15.6 1.0
CA A:CYS121 4.1 14.1 1.0
OD1 A:ASP61 4.2 15.4 1.0
CA A:ALA118 4.3 16.2 1.0
SG A:CYS104 4.3 14.8 1.0
SG A:CYS100 4.5 16.3 1.0
SG A:CYS34 4.7 14.0 1.0
CB A:ALA120 4.7 15.8 1.0
CB A:CYS104 4.8 16.7 1.0
CB A:CYS38 4.8 11.9 1.0
C A:ALA120 4.8 14.4 1.0
O A:CYS100 4.8 14.7 1.0
C A:ALA118 4.9 16.4 1.0
N A:CYS117 4.9 15.4 1.0
CA A:CYS38 5.0 12.2 1.0
CB A:CYS100 5.0 13.8 1.0

Copper binding site 8 out of 39 in 6qyb

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Copper binding site 8 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu207

b:15.5
occ:1.00
OD1 A:ASP61 2.2 15.4 1.0
SG A:CYS117 2.2 14.2 1.0
SG A:CYS104 2.2 14.8 1.0
CU A:CU1218 2.6 15.6 1.0
CU A:CU1206 2.8 14.4 1.0
CU A:CU1219 2.9 17.4 1.0
CU A:CU1200 3.0 14.1 1.0
CB A:CYS117 3.1 13.8 1.0
CG A:ASP61 3.2 15.3 1.0
OD2 A:ASP61 3.5 15.8 1.0
CB A:CYS104 3.6 16.7 1.0
SG A:CYS41 3.7 16.2 1.0
CB A:CYS41 3.7 15.8 1.0
CU A:CU1208 3.8 18.2 1.0
SG A:CYS100 3.8 16.3 1.0
SG A:CYS38 4.0 13.8 1.0
CA A:CYS117 4.3 15.4 1.0
SG A:CYS121 4.3 15.1 1.0
C A:CYS117 4.3 15.0 1.0
CB A:ASP61 4.5 14.5 1.0
O A:CYS100 4.5 14.7 1.0
O A:CYS117 4.5 15.5 1.0
CA A:CYS38 4.6 12.2 1.0
N A:ALA118 4.7 15.6 1.0
CB A:CYS38 4.8 11.9 1.0
CA A:CYS104 4.8 17.5 1.0

Copper binding site 9 out of 39 in 6qyb

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Copper binding site 9 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu208

b:18.2
occ:1.00
OD2 A:ASP61 1.9 15.8 1.0
SG A:CYS57 2.2 19.1 1.0
CU A:CU1217 2.6 23.0 0.5
CG A:ASP61 2.8 15.3 1.0
CU A:CU1219 2.8 17.4 1.0
O A:CYS57 2.9 15.2 1.0
C A:CYS57 3.2 17.3 1.0
SG A:CYS104 3.2 14.8 1.0
CB A:CYS57 3.3 18.8 1.0
OD1 A:ASP61 3.3 15.4 1.0
CU A:CU1205 3.4 18.1 1.0
CA A:CYS57 3.6 17.8 1.0
CU A:CU1207 3.8 15.5 1.0
SG A:CYS41 3.9 16.2 1.0
N A:ILE58 3.9 15.9 1.0
CB A:ASP61 3.9 14.5 1.0
SG A:CYS45 4.2 20.3 1.0
SG A:CYS114 4.2 19.1 1.0
CU A:CU1218 4.2 15.6 1.0
CA A:ILE58 4.4 15.9 1.0
O A:CYS41 4.5 16.9 1.0
CB A:CYS41 4.5 15.8 1.0
C A:CYS41 4.6 15.6 1.0
N A:ASP61 4.8 15.2 1.0
CB A:CYS104 4.8 16.7 1.0
CB A:CYS45 4.9 17.5 1.0
CA A:ASP61 4.9 13.9 1.0
N A:ALA42 4.9 16.0 1.0

Copper binding site 10 out of 39 in 6qyb

Go back to Copper Binding Sites List in 6qyb
Copper binding site 10 out of 39 in the Streptomyces Lividans Ccsp Mutant - H111A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Streptomyces Lividans Ccsp Mutant - H111A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu209

b:14.3
occ:1.00
SG A:CYS68 2.1 15.4 1.0
SG A:CYS124 2.2 14.5 1.0
CU A:CU1214 2.6 13.4 1.0
CU A:CU1213 3.0 13.7 1.0
CU A:CU1215 3.1 14.7 1.0
CB A:CYS124 3.2 15.4 1.0
SG A:CYS97 3.2 15.1 1.0
CU A:CU1212 3.3 14.5 1.0
CB A:CYS68 3.4 11.2 1.0
SG A:CYS93 3.5 12.6 1.0
CA A:CYS31 3.6 11.7 1.0
CB A:CYS34 3.7 13.3 1.0
CU A:CU1216 3.7 14.1 1.0
SG A:CYS31 3.8 13.4 1.0
SG A:CYS34 4.1 14.0 1.0
CB A:CYS31 4.2 11.7 1.0
CA A:CYS68 4.2 10.7 1.0
N A:CYS31 4.3 10.8 1.0
O A:GLU30 4.3 14.4 1.0
O A:CYS31 4.4 11.9 1.0
CA A:CYS124 4.5 15.3 1.0
C A:CYS31 4.5 11.6 1.0
C A:GLU30 4.6 12.9 1.0
C A:CYS124 4.8 15.1 1.0
SG A:CYS128 4.9 14.8 1.0
O A:CYS124 4.9 15.0 1.0
CB A:CYS97 5.0 14.0 1.0
CA A:CYS34 5.0 12.7 1.0

Reference:

M.L.Straw, M.A.Hough, M.T.Wilson, J.A.R.Worrall. A Histidine Residue and A Tetranuclear Cuprous-Thiolate Cluster Dominate the Copper Loading Landscape of A Copper Storage Protein From Streptomyces Lividans. Chemistry V. 25 10678 2019.
ISSN: ISSN 0947-6539
PubMed: 31111982
DOI: 10.1002/CHEM.201901411
Page generated: Sun Dec 13 11:25:12 2020

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