Copper in PDB 7l6g: Mbnp From Methylosinus Trichosporium

Protein crystallography data

The structure of Mbnp From Methylosinus Trichosporium, PDB code: 7l6g was solved by A.C.Manesis, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.89 / 2.04
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 91.276, 91.276, 383.567, 90, 90, 120
R / Rfree (%) 20.4 / 25.1

Other elements in 7l6g:

The structure of Mbnp From Methylosinus Trichosporium also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Mbnp From Methylosinus Trichosporium (pdb code 7l6g). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Mbnp From Methylosinus Trichosporium, PDB code: 7l6g:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7l6g

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Copper binding site 1 out of 6 in the Mbnp From Methylosinus Trichosporium


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:44.9
occ:1.00
ND1 A:HIS207 2.1 41.8 1.0
O A:HOH614 2.3 25.2 1.0
SD A:MET269 2.4 41.4 1.0
N1 A:KYN174 2.9 29.1 1.0
CG A:HIS207 3.0 32.4 1.0
CE1 A:HIS207 3.1 38.3 1.0
CG A:MET269 3.3 42.2 1.0
CE A:MET269 3.3 43.0 1.0
CB A:HIS207 3.3 29.2 1.0
CB A:MET269 3.8 37.2 1.0
CD A:ARG181 4.1 34.7 1.0
NE2 A:HIS207 4.2 33.5 1.0
CD2 A:HIS207 4.2 36.2 1.0
CG A:KYN174 4.3 29.2 1.0
NE A:ARG181 4.3 49.1 1.0
O2 A:KYN174 4.5 47.9 1.0
CA A:HIS207 4.8 32.4 1.0
CZ A:ARG181 4.9 55.9 1.0
CA A:MET269 4.9 31.6 1.0

Copper binding site 2 out of 6 in 7l6g

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Copper binding site 2 out of 6 in the Mbnp From Methylosinus Trichosporium


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:49.4
occ:1.00
ND1 B:HIS207 2.1 42.9 1.0
O B:HOH585 2.3 23.8 1.0
SD B:MET269 2.3 43.4 1.0
CE1 B:HIS207 3.0 44.4 1.0
CG B:HIS207 3.1 38.7 1.0
N1 B:KYN174 3.1 46.2 1.0
CE B:MET269 3.3 34.1 1.0
CG B:MET269 3.3 41.6 1.0
CB B:HIS207 3.4 34.0 1.0
CB B:MET269 3.8 40.4 1.0
NH1 B:ARG181 4.0 58.6 1.0
NE2 B:HIS207 4.2 48.1 1.0
CD2 B:HIS207 4.2 46.0 1.0
CD B:ARG181 4.5 47.3 1.0
CG B:KYN174 4.5 41.6 1.0
O2 B:KYN174 4.5 63.4 1.0
CZ B:ARG181 4.9 57.0 1.0
CA B:HIS207 5.0 36.0 1.0
CA B:MET269 5.0 47.9 1.0

Copper binding site 3 out of 6 in 7l6g

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Copper binding site 3 out of 6 in the Mbnp From Methylosinus Trichosporium


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:49.1
occ:1.00
ND1 C:HIS207 2.2 42.3 1.0
O C:HOH593 2.4 34.8 1.0
SD C:MET269 2.4 42.6 1.0
N1 C:KYN174 2.9 30.6 1.0
CE C:MET269 3.2 44.5 1.0
CE1 C:HIS207 3.2 42.7 1.0
CG C:HIS207 3.2 40.4 1.0
CG C:MET269 3.3 34.7 1.0
CB C:HIS207 3.5 33.1 1.0
CB C:MET269 3.9 34.9 1.0
CD C:ARG181 4.2 46.7 1.0
CG C:KYN174 4.3 43.8 1.0
NE2 C:HIS207 4.3 45.1 1.0
O2 C:KYN174 4.3 43.8 1.0
NE C:ARG181 4.3 45.0 1.0
CD2 C:HIS207 4.4 37.5 1.0
CA C:MET269 5.0 36.1 1.0

Copper binding site 4 out of 6 in 7l6g

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Copper binding site 4 out of 6 in the Mbnp From Methylosinus Trichosporium


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:52.8
occ:1.00
ND1 D:HIS207 2.1 42.3 1.0
O D:HOH572 2.3 28.2 1.0
SD D:MET269 2.4 54.0 1.0
N1 D:KYN174 2.9 39.3 1.0
CE1 D:HIS207 3.0 40.3 1.0
CG D:HIS207 3.1 41.8 1.0
CE D:MET269 3.3 47.9 1.0
CB D:HIS207 3.4 37.1 1.0
CG D:MET269 3.6 51.0 1.0
CD D:ARG181 4.1 43.7 1.0
NE2 D:HIS207 4.1 39.4 1.0
CD2 D:HIS207 4.2 37.3 1.0
CB D:MET269 4.2 44.4 1.0
CG D:KYN174 4.3 44.2 1.0
NH1 D:ARG181 4.5 52.7 1.0
O2 D:KYN174 4.6 59.1 1.0
NE D:ARG181 4.7 49.1 1.0
CZ D:ARG181 4.9 50.9 1.0
CA D:HIS207 4.9 40.7 1.0
CD1 D:KYN174 5.0 44.1 1.0

Copper binding site 5 out of 6 in 7l6g

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Copper binding site 5 out of 6 in the Mbnp From Methylosinus Trichosporium


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:54.4
occ:1.00
ND1 E:HIS207 2.1 45.6 1.0
SD E:MET269 2.4 43.2 1.0
O E:HOH578 2.5 27.4 1.0
N1 E:KYN174 2.7 35.4 1.0
CE1 E:HIS207 3.1 40.9 1.0
CG E:HIS207 3.1 40.9 1.0
CG E:MET269 3.2 47.2 1.0
CE E:MET269 3.3 37.5 1.0
CB E:HIS207 3.4 39.0 1.0
CB E:MET269 3.9 48.3 1.0
CG E:KYN174 4.1 34.0 1.0
CD E:ARG181 4.2 43.0 1.0
NE2 E:HIS207 4.2 40.8 1.0
CD2 E:HIS207 4.2 41.9 1.0
O2 E:KYN174 4.4 51.3 1.0
NE E:ARG181 4.5 44.9 1.0
CZ E:ARG181 4.9 61.8 1.0
CD1 E:KYN174 4.9 32.5 1.0
O2 E:EDO405 4.9 54.2 1.0
NH1 E:ARG181 4.9 77.0 1.0
CA E:HIS207 4.9 41.2 1.0
CA E:MET269 5.0 55.1 1.0

Copper binding site 6 out of 6 in 7l6g

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Copper binding site 6 out of 6 in the Mbnp From Methylosinus Trichosporium


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu401

b:54.4
occ:1.00
ND1 F:HIS207 2.1 38.2 1.0
O F:HOH572 2.3 25.1 1.0
SD F:MET269 2.4 38.6 1.0
N1 F:KYN174 3.0 27.2 1.0
CE1 F:HIS207 3.0 29.0 1.0
CG F:HIS207 3.1 36.9 1.0
CG F:MET269 3.3 35.3 1.0
CE F:MET269 3.4 36.4 1.0
CB F:HIS207 3.4 36.7 1.0
CB F:MET269 3.9 29.1 1.0
CD F:ARG181 4.1 39.6 1.0
NE2 F:HIS207 4.1 36.1 1.0
CD2 F:HIS207 4.2 39.2 1.0
NE F:ARG181 4.2 56.0 1.0
CG F:KYN174 4.3 41.3 1.0
O2 F:KYN174 4.4 38.2 1.0
C2 F:EDO403 4.9 56.6 1.0
CA F:HIS207 4.9 46.2 1.0
CA F:MET269 5.0 44.5 1.0
CZ F:ARG181 5.0 65.9 1.0

Reference:

A.C.Manesis, R.J.Jodts, B.M.Hoffman, A.C.Rosenzweig. Copper Binding By A Unique Family of Metalloproteins Is Dependent on Kynurenine Formation To Be Published.
Page generated: Sat Jul 10 13:37:08 2021

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