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Copper in PDB 4qkt: Azurin Mutant M121EM44K with Copper

Protein crystallography data

The structure of Azurin Mutant M121EM44K with Copper, PDB code: 4qkt was solved by J.Liu, H.Robinson, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.38 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 55.285, 48.695, 95.068, 90.00, 94.65, 90.00
R / Rfree (%) 18.1 / 21.6

Copper Binding Sites:

The binding sites of Copper atom in the Azurin Mutant M121EM44K with Copper (pdb code 4qkt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Azurin Mutant M121EM44K with Copper, PDB code: 4qkt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4qkt

Go back to Copper Binding Sites List in 4qkt
Copper binding site 1 out of 6 in the Azurin Mutant M121EM44K with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azurin Mutant M121EM44K with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:22.5
occ:1.00
 ND1 A:HIS46 2.0 19.4 1.0
ND1 A:HIS117 2.1 17.4 1.0
SG A:CYS112 2.2 17.8 1.0
OE1 A:GLU121 2.4 39.8 1.0
CE1 A:HIS46 2.9 24.6 1.0
CD A:GLU121 3.1 34.0 1.0
CG A:HIS117 3.1 19.9 1.0
CE1 A:HIS117 3.1 21.7 1.0
OE2 A:GLU121 3.1 31.9 1.0
CG A:HIS46 3.1 21.4 1.0
CB A:CYS112 3.2 19.0 1.0
O A:GLY45 3.2 21.5 1.0
CB A:HIS117 3.4 17.9 1.0
CA A:HIS46 3.5 21.0 1.0
CB A:HIS46 3.5 20.1 1.0
O A:HOH381 3.6 37.8 1.0
NE2 A:HIS46 4.1 21.4 1.0
CB A:PHE114 4.1 20.6 1.0
C A:GLY45 4.2 20.4 1.0
CD2 A:HIS46 4.2 29.4 1.0
NE2 A:HIS117 4.2 18.7 1.0
CD2 A:HIS117 4.2 21.3 1.0
N A:HIS46 4.3 18.1 1.0
N A:ASN47 4.4 16.1 1.0
CG A:GLU121 4.5 34.3 1.0
C A:HIS46 4.5 18.4 1.0
CA A:CYS112 4.7 15.0 1.0
CB A:GLU121 4.8 22.6 1.0
CA A:HIS117 4.9 18.8 1.0
N A:PHE114 5.0 16.7 1.0

Copper binding site 2 out of 6 in 4qkt

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Copper binding site 2 out of 6 in the Azurin Mutant M121EM44K with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azurin Mutant M121EM44K with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:28.9
occ:0.69
 CU A:CU203 2.0 24.1 0.4
N A:ALA1 2.0 25.7 1.0
N A:TRS204 2.2 25.7 1.0
O A:ALA1 2.2 23.5 1.0
O1 A:TRS204 2.4 25.3 1.0
O A:HOH360 2.5 28.2 1.0
C A:ALA1 2.9 24.8 1.0
CA A:ALA1 2.9 27.1 1.0
C1 A:TRS204 3.0 19.3 1.0
C A:TRS204 3.1 25.2 1.0
CB A:ALA1 3.6 25.8 1.0
C2 A:TRS204 3.8 27.4 1.0
N A:GLU2 4.2 26.2 1.0
C3 A:TRS204 4.3 21.1 1.0
O2 A:TRS204 4.4 32.0 1.0
O A:HOH364 4.5 35.6 1.0
OG A:SER25 4.5 25.8 1.0
SG A:CYS3 4.5 26.4 1.0
O A:HOH310 4.9 30.4 1.0
CA A:GLU2 4.9 23.6 1.0

Copper binding site 3 out of 6 in 4qkt

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Copper binding site 3 out of 6 in the Azurin Mutant M121EM44K with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azurin Mutant M121EM44K with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu203

b:24.1
occ:0.44
 N A:TRS204 1.8 25.7 1.0
CU A:CU202 2.0 28.9 0.7
O A:HOH360 2.5 28.2 1.0
O A:HOH364 2.6 35.6 1.0
C A:TRS204 2.8 25.2 1.0
C1 A:TRS204 3.0 19.3 1.0
O1 A:TRS204 3.3 25.3 1.0
C3 A:TRS204 3.4 21.1 1.0
O A:ALA1 3.7 23.5 1.0
N A:ALA1 3.8 25.7 1.0
C2 A:TRS204 4.1 27.4 1.0
O A:HOH347 4.4 34.3 1.0
SG A:CYS3 4.4 26.4 1.0
O2 A:TRS204 4.4 32.0 1.0
O A:HOH343 4.5 30.5 1.0
OG A:SER25 4.5 25.8 1.0
O3 A:TRS204 4.6 26.3 1.0
C A:ALA1 4.6 24.8 1.0
O A:SER25 4.8 28.1 1.0
CA A:ALA1 4.8 27.1 1.0

Copper binding site 4 out of 6 in 4qkt

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Copper binding site 4 out of 6 in the Azurin Mutant M121EM44K with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azurin Mutant M121EM44K with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:20.8
occ:1.00
 ND1 B:HIS46 2.0 18.3 1.0
ND1 B:HIS117 2.1 17.6 1.0
SG B:CYS112 2.2 16.0 1.0
OE2 B:GLU121 2.3 28.7 1.0
CE1 B:HIS46 2.9 24.8 1.0
CE1 B:HIS117 3.0 18.9 1.0
CG B:HIS117 3.1 14.6 1.0
CG B:HIS46 3.1 20.5 1.0
CD B:GLU121 3.1 27.4 1.0
CB B:CYS112 3.2 17.4 1.0
OE1 B:GLU121 3.3 32.0 1.0
O B:GLY45 3.3 18.0 1.0
CB B:HIS117 3.4 17.6 1.0
CA B:HIS46 3.5 15.6 1.0
CB B:HIS46 3.5 16.5 1.0
O B:HOH401 3.7 33.0 1.0
NE2 B:HIS46 4.1 21.9 1.0
CB B:PHE114 4.1 15.5 1.0
NE2 B:HIS117 4.2 16.8 1.0
C B:GLY45 4.2 15.8 1.0
CD2 B:HIS46 4.2 21.8 1.0
CD2 B:HIS117 4.2 20.8 1.0
N B:HIS46 4.3 16.3 1.0
N B:ASN47 4.5 13.7 1.0
CG B:GLU121 4.5 30.4 1.0
C B:HIS46 4.5 13.4 1.0
CA B:CYS112 4.6 16.3 1.0
CB B:GLU121 4.8 19.4 1.0
CA B:HIS117 4.9 17.1 1.0
N B:PHE114 4.9 15.3 1.0
CG B:PHE114 5.0 17.7 1.0

Copper binding site 5 out of 6 in 4qkt

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Copper binding site 5 out of 6 in the Azurin Mutant M121EM44K with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azurin Mutant M121EM44K with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:22.7
occ:0.50
 CU B:CU203 1.9 19.8 0.5
N B:ALA1 1.9 24.1 1.0
N B:TRS204 2.2 21.4 1.0
O B:ALA1 2.2 22.1 1.0
O B:HOH309 2.4 24.8 1.0
O3 B:TRS204 2.4 21.4 1.0
CA B:ALA1 2.8 23.0 1.0
C B:ALA1 2.9 20.5 1.0
C3 B:TRS204 3.0 22.8 1.0
C B:TRS204 3.1 21.8 1.0
CB B:ALA1 3.7 26.1 1.0
C1 B:TRS204 3.8 23.0 1.0
O B:HOH380 4.0 38.1 1.0
N B:GLU2 4.2 23.8 1.0
C2 B:TRS204 4.3 20.1 1.0
O B:HOH320 4.3 26.6 1.0
SG B:CYS3 4.3 21.3 1.0
OG B:SER25 4.3 23.5 1.0
O B:HOH311 4.3 23.9 1.0
O1 B:TRS204 4.4 22.7 1.0
CA B:GLU2 5.0 20.3 1.0

Copper binding site 6 out of 6 in 4qkt

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Copper binding site 6 out of 6 in the Azurin Mutant M121EM44K with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azurin Mutant M121EM44K with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu203

b:19.8
occ:0.51
 N B:TRS204 1.8 21.4 1.0
CU B:CU202 1.9 22.7 0.5
O B:HOH320 2.6 26.6 1.0
O B:HOH309 2.6 24.8 1.0
C B:TRS204 2.7 21.8 1.0
C3 B:TRS204 3.0 22.8 1.0
O3 B:TRS204 3.2 21.4 1.0
C2 B:TRS204 3.3 20.1 1.0
N B:ALA1 3.7 24.1 1.0
O B:ALA1 3.7 22.1 1.0
C1 B:TRS204 4.0 23.0 1.0
O B:SER25 4.3 21.4 1.0
OG B:SER25 4.3 23.5 1.0
SG B:CYS3 4.4 21.3 1.0
O1 B:TRS204 4.4 22.7 1.0
O2 B:TRS204 4.6 23.7 1.0
C B:ALA1 4.6 20.5 1.0
CA B:ALA1 4.7 23.0 1.0
O B:HOH321 4.9 33.2 1.0
C B:SER25 4.9 19.7 1.0

Reference:

J.Liu, K.K.Meier, S.Tian, J.L.Zhang, H.Guo, C.E.Schulz, H.Robinson, M.J.Nilges, E.Munck, Y.Lu. Redesigning the Blue Copper Azurin Into A Redox-Active Mononuclear Nonheme Iron Protein: Preparation and Study of Fe(II)-M121E Azurin. J.Am.Chem.Soc. V. 136 12337 2014.
ISSN: ISSN 0002-7863
PubMed: 25082811
DOI: 10.1021/JA505410U
Page generated: Wed Jul 31 03:25:03 2024

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