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Copper in PDB 4gyb: Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709

Protein crystallography data

The structure of Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709, PDB code: 4gyb was solved by A.Gabdulkhakov, S.Tischenko, L.Yurevich, A.Lisov, A.Leontievsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.38 / 2.40
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 177.540, 177.540, 177.540, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 17.7

Other elements in 4gyb:

The structure of Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 (pdb code 4gyb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709, PDB code: 4gyb:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 4gyb

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Copper binding site 1 out of 4 in the Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:33.3
occ:1.00
ND1 A:HIS293 2.0 28.8 1.0
ND1 A:HIS231 2.0 34.1 1.0
SG A:CYS288 2.2 35.2 1.0
CE1 A:HIS293 2.9 32.4 1.0
CG A:HIS293 3.0 31.9 1.0
CE1 A:HIS231 3.0 32.1 1.0
CG A:HIS231 3.0 32.6 1.0
CB A:CYS288 3.2 29.4 1.0
CB A:HIS293 3.3 28.1 1.0
CB A:HIS231 3.4 29.1 1.0
SD A:MET298 3.6 37.1 1.0
CA A:HIS231 3.7 29.0 1.0
CE A:MET298 3.9 33.7 1.0
NE2 A:HIS293 4.1 34.6 1.0
CG2 A:VAL290 4.1 32.6 1.0
CD2 A:HIS293 4.1 30.2 1.0
O A:TYR230 4.1 27.8 1.0
CB A:VAL290 4.1 33.0 1.0
NE2 A:HIS231 4.1 32.2 1.0
CD2 A:HIS231 4.2 33.6 1.0
N A:THR232 4.5 26.4 1.0
CA A:CYS288 4.6 30.9 1.0
C A:HIS231 4.7 30.0 1.0
N A:HIS231 4.7 32.3 1.0
C A:TYR230 4.8 30.1 1.0
CA A:HIS293 4.9 31.5 1.0
CD2 A:PHE195 4.9 29.0 1.0
CG1 A:VAL290 5.0 30.9 1.0

Copper binding site 2 out of 4 in 4gyb

Go back to Copper Binding Sites List in 4gyb
Copper binding site 2 out of 4 in the Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:34.0
occ:1.00
NE2 A:HIS289 2.1 29.6 1.0
O A:HOH512 2.7 41.5 1.0
CD2 A:HIS289 3.0 28.6 1.0
CE1 A:HIS289 3.1 32.4 1.0
CU A:CU404 3.9 41.1 0.4
CG A:HIS289 4.1 30.2 1.0
ND1 A:HIS289 4.2 33.8 1.0
NE2 A:HIS234 4.2 38.8 1.0
CD2 A:HIS234 4.4 34.2 1.0
O A:HOH513 4.7 39.0 1.0
CE1 A:HIS234 4.8 31.5 1.0

Copper binding site 3 out of 4 in 4gyb

Go back to Copper Binding Sites List in 4gyb
Copper binding site 3 out of 4 in the Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:42.5
occ:1.00
NE2 A:HIS236 2.0 33.1 1.0
NE2 A:HIS287 2.2 35.0 1.0
O A:HOH512 2.5 41.5 1.0
CE1 A:HIS236 2.9 33.0 1.0
CD2 A:HIS287 3.2 34.4 1.0
CE1 A:HIS287 3.2 34.1 1.0
CD2 A:HIS236 3.2 36.1 1.0
O A:HOH513 3.6 39.0 1.0
ND1 A:HIS236 4.0 36.6 1.0
CU A:CU404 4.1 41.1 0.4
CD2 A:HIS234 4.1 34.2 1.0
CE A:MET285 4.2 43.1 1.0
CG A:HIS236 4.2 34.1 1.0
ND1 A:HIS287 4.3 37.0 1.0
CG A:HIS287 4.3 34.7 1.0
NE2 A:HIS234 4.4 38.8 1.0
SD A:MET285 4.7 51.9 0.8
NE2 A:HIS289 5.0 29.6 1.0

Copper binding site 4 out of 4 in 4gyb

Go back to Copper Binding Sites List in 4gyb
Copper binding site 4 out of 4 in the Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:41.1
occ:0.38
NE2 A:HIS234 2.0 38.8 1.0
O A:HOH511 2.8 37.0 1.0
CE1 A:HIS234 2.8 31.5 1.0
O A:HOH512 3.0 41.5 1.0
CD2 A:HIS234 3.0 34.2 1.0
CD2 A:HIS236 3.3 36.1 1.0
NE2 A:HIS236 3.4 33.1 1.0
CU A:CU402 3.9 34.0 1.0
CG A:HIS236 3.9 34.1 1.0
ND1 A:HIS234 4.0 35.4 1.0
CE1 A:HIS236 4.0 33.0 1.0
CU A:CU403 4.1 42.5 1.0
CG A:HIS234 4.1 33.8 1.0
ND1 A:HIS236 4.3 36.6 1.0
CA A:HIS236 4.6 32.7 1.0
CB A:HIS236 4.8 31.1 1.0
N A:HIS236 4.9 33.8 1.0
O A:HOH588 5.0 35.4 1.0
O A:MET235 5.0 33.9 1.0

Reference:

A.Gabdulkhakov, S.Tischenko, L.Yurevich, A.Lisov, A.Leontievsky. Two-Domain Laccase From Streptomyces Lividans at 2.4 A Resolution AC1709 To Be Published.
Page generated: Sun Dec 13 11:14:35 2020

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