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Copper in PDB 3t9w: Small Laccase From Amycolatopsis Sp. Atcc 39116

Enzymatic activity of Small Laccase From Amycolatopsis Sp. Atcc 39116

All present enzymatic activity of Small Laccase From Amycolatopsis Sp. Atcc 39116:
1.10.3.2;

Protein crystallography data

The structure of Small Laccase From Amycolatopsis Sp. Atcc 39116, PDB code: 3t9w was solved by T.Lukk, S.Majumdar, J.A.Gerlt, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.66 / 1.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 110.180, 110.180, 178.820, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20.2

Other elements in 3t9w:

The structure of Small Laccase From Amycolatopsis Sp. Atcc 39116 also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Small Laccase From Amycolatopsis Sp. Atcc 39116 (pdb code 3t9w). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Small Laccase From Amycolatopsis Sp. Atcc 39116, PDB code: 3t9w:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 3t9w

Go back to Copper Binding Sites List in 3t9w
Copper binding site 1 out of 4 in the Small Laccase From Amycolatopsis Sp. Atcc 39116


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Small Laccase From Amycolatopsis Sp. Atcc 39116 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu308

b:27.9
occ:0.60
NE2 A:HIS222 2.2 16.2 1.0
O A:HOH375 2.4 21.1 1.0
O2 A:PEO312 2.6 34.8 1.0
CE1 A:HIS222 3.1 17.5 1.0
CD2 A:HIS224 3.2 20.8 1.0
CD2 A:HIS222 3.2 15.0 1.0
NE2 A:HIS224 3.3 18.7 1.0
CU A:CU310 3.5 22.9 1.0
CU A:CU309 3.9 20.9 1.0
CG A:HIS224 3.9 16.0 1.0
O1 A:PEO312 4.0 16.6 0.9
CE1 A:HIS224 4.1 19.6 1.0
ND1 A:HIS222 4.2 17.6 1.0
CG A:HIS222 4.3 14.6 1.0
ND1 A:HIS224 4.4 19.8 1.0
CA A:HIS224 4.6 15.2 1.0
CB A:HIS224 4.8 14.5 1.0
O A:HOH414 4.8 19.7 1.0
NE2 A:HIS275 4.8 15.4 1.0

Copper binding site 2 out of 4 in 3t9w

Go back to Copper Binding Sites List in 3t9w
Copper binding site 2 out of 4 in the Small Laccase From Amycolatopsis Sp. Atcc 39116


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Small Laccase From Amycolatopsis Sp. Atcc 39116 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu309

b:20.9
occ:0.98
NE2 A:HIS277 2.0 9.6 1.0
O2 A:PEO312 2.1 34.8 1.0
O1 A:PEO312 2.8 16.6 0.9
CE1 A:HIS277 2.9 13.7 1.0
CD2 A:HIS277 3.0 13.1 1.0
CU A:CU308 3.9 27.9 0.6
ND1 A:HIS277 4.1 12.2 1.0
CG A:HIS277 4.1 12.2 1.0
NE2 A:HIS222 4.3 16.2 1.0
O A:HOH633 4.4 42.0 1.0
CD2 A:HIS222 4.5 15.0 1.0
CU A:CU310 4.5 22.9 1.0
CE1 A:HIS222 5.0 17.5 1.0

Copper binding site 3 out of 4 in 3t9w

Go back to Copper Binding Sites List in 3t9w
Copper binding site 3 out of 4 in the Small Laccase From Amycolatopsis Sp. Atcc 39116


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Small Laccase From Amycolatopsis Sp. Atcc 39116 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu310

b:22.9
occ:0.97
NE2 A:HIS224 2.1 18.7 1.0
NE2 A:HIS275 2.1 15.4 1.0
O1 A:PEO312 2.2 16.6 0.9
O2 A:PEO312 2.5 34.8 1.0
CE1 A:HIS224 3.0 19.6 1.0
CE1 A:HIS275 3.0 19.5 1.0
CD2 A:HIS275 3.1 16.7 1.0
CD2 A:HIS224 3.2 20.8 1.0
CU A:CU308 3.5 27.9 0.6
CD2 A:HIS222 3.9 15.0 1.0
ND1 A:HIS275 4.1 16.4 1.0
ND1 A:HIS224 4.1 19.8 1.0
NE2 A:HIS222 4.2 16.2 1.0
CG A:HIS275 4.2 14.9 1.0
CG A:HIS224 4.3 16.0 1.0
SD A:MET273 4.4 38.8 1.0
CU A:CU309 4.5 20.9 1.0
NE2 A:HIS277 4.8 9.6 1.0
CD2 A:HIS277 4.9 13.1 1.0

Copper binding site 4 out of 4 in 3t9w

Go back to Copper Binding Sites List in 3t9w
Copper binding site 4 out of 4 in the Small Laccase From Amycolatopsis Sp. Atcc 39116


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Small Laccase From Amycolatopsis Sp. Atcc 39116 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu311

b:15.9
occ:1.00
ND1 A:HIS281 2.0 13.7 1.0
ND1 A:HIS219 2.0 15.4 1.0
SG A:CYS276 2.1 13.6 1.0
CG A:HIS281 3.0 16.7 1.0
CE1 A:HIS219 3.0 16.4 1.0
CE1 A:HIS281 3.0 18.3 1.0
CG A:HIS219 3.0 13.1 1.0
CB A:CYS276 3.2 13.3 1.0
CB A:HIS281 3.3 15.5 1.0
SD A:MET286 3.3 17.9 1.0
CB A:HIS219 3.4 12.8 1.0
O A:PHE218 3.6 13.1 1.0
CA A:HIS219 3.6 11.3 1.0
CB A:VAL278 4.1 13.3 1.0
CE A:MET286 4.1 19.9 1.0
CG2 A:VAL278 4.1 12.8 1.0
NE2 A:HIS281 4.1 20.8 1.0
NE2 A:HIS219 4.1 13.6 1.0
CD2 A:HIS281 4.1 18.0 1.0
CD2 A:HIS219 4.2 14.8 1.0
C A:PHE218 4.4 12.5 1.0
N A:HIS219 4.5 12.7 1.0
CA A:CYS276 4.6 12.4 1.0
N A:THR220 4.6 11.9 1.0
C A:HIS219 4.7 11.5 1.0
CG A:MET286 4.8 18.6 1.0
CG1 A:VAL278 4.8 16.0 1.0
CA A:HIS281 4.8 13.9 1.0
CD2 A:PHE183 4.9 14.1 1.0

Reference:

S.Majumdar, T.Lukk, J.O.Solbiati, S.Bauer, S.K.Nair, J.E.Cronan, J.A.Gerlt. Roles of Small Laccases From Streptomyces in Lignin Degradation. Biochemistry V. 53 4047 2014.
ISSN: ISSN 0006-2960
PubMed: 24870309
DOI: 10.1021/BI500285T
Page generated: Sun Dec 13 11:12:23 2020

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