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Copper in PDB 5fc9: Novel Purple Cupredoxin From Nitrosopumilus Maritimus

Protein crystallography data

The structure of Novel Purple Cupredoxin From Nitrosopumilus Maritimus, PDB code: 5fc9 was solved by P.Hosseinzadeh, Y.Lu, H.Robinson, Y.-G.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.87 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.887, 68.887, 184.450, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.8

Copper Binding Sites:

The binding sites of Copper atom in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus (pdb code 5fc9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus, PDB code: 5fc9:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 5fc9

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Copper binding site 1 out of 5 in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Novel Purple Cupredoxin From Nitrosopumilus Maritimus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1401

b:17.2
occ:1.00
 ND1 A:HIS1043 2.0 12.4 1.0
ND1 A:HIS1086 2.1 15.6 1.0
SG A:CYS1083 2.2 14.4 1.0
O A:HOH1508 2.2 19.5 1.0
CE1 A:HIS1043 2.8 15.5 1.0
CE1 A:HIS1086 3.0 14.4 1.0
CB A:CYS1083 3.1 17.0 1.0
CG A:HIS1043 3.1 14.1 1.0
CG A:HIS1086 3.1 16.2 1.0
CB A:HIS1086 3.5 14.3 1.0
CB A:HIS1043 3.6 12.1 1.0
CA A:HIS1043 3.8 11.8 1.0
N A:HIS1086 3.9 15.4 1.0
OD1 A:ASN1011 4.0 15.2 1.0
NE2 A:HIS1043 4.0 14.1 1.0
NE2 A:HIS1086 4.1 17.4 1.0
CD2 A:HIS1043 4.1 12.8 1.0
CD2 A:HIS1086 4.2 17.3 1.0
O A:PRO1042 4.2 15.3 1.0
CB A:PHE1085 4.3 16.4 1.0
CA A:HIS1086 4.3 15.0 1.0
N A:ASN1044 4.5 15.8 1.0
CA A:CYS1083 4.5 16.4 1.0
C A:PHE1085 4.6 16.7 1.0
C A:HIS1043 4.7 16.8 1.0
CD2 A:PHE1085 4.8 19.8 1.0
CA A:PHE1085 4.8 17.5 1.0
O A:HIS1086 4.9 14.8 1.0
N A:HIS1043 4.9 13.2 1.0
N A:PHE1085 4.9 16.5 1.0
OH A:TYR1020 4.9 16.2 1.0
C A:CYS1083 4.9 17.1 1.0
CG A:PHE1085 5.0 21.0 1.0
C A:PRO1042 5.0 14.7 1.0

Copper binding site 2 out of 5 in 5fc9

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Copper binding site 2 out of 5 in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Novel Purple Cupredoxin From Nitrosopumilus Maritimus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2401

b:14.6
occ:1.00
 ND1 B:HIS2043 2.0 13.5 1.0
ND1 B:HIS2086 2.1 12.3 1.0
O B:HOH2514 2.2 16.5 1.0
SG B:CYS2083 2.3 12.5 1.0
CE1 B:HIS2043 2.9 12.2 1.0
CE1 B:HIS2086 3.0 14.7 1.0
CB B:CYS2083 3.1 13.4 1.0
CG B:HIS2086 3.1 11.8 1.0
CG B:HIS2043 3.1 12.4 1.0
CB B:HIS2086 3.5 12.4 1.0
CB B:HIS2043 3.6 13.0 1.0
CA B:HIS2043 3.9 13.4 1.0
OD1 B:ASN2011 3.9 16.4 1.0
N B:HIS2086 3.9 14.2 1.0
NE2 B:HIS2043 4.1 12.9 1.0
NE2 B:HIS2086 4.1 12.5 1.0
CD2 B:HIS2043 4.2 13.2 1.0
CD2 B:HIS2086 4.2 13.8 1.0
CB B:PHE2085 4.3 13.9 1.0
O B:PRO2042 4.3 14.3 1.0
CA B:HIS2086 4.3 12.3 1.0
CA B:CYS2083 4.5 13.1 1.0
N B:ASN2044 4.5 13.1 1.0
C B:PHE2085 4.6 14.3 1.0
OH B:TYR2020 4.8 14.6 1.0
C B:HIS2043 4.8 14.7 1.0
O B:HIS2086 4.8 12.8 1.0
CA B:PHE2085 4.8 12.4 1.0
N B:PHE2085 4.9 13.4 1.0
N B:HIS2043 4.9 14.7 1.0
C B:CYS2083 5.0 12.2 1.0

Copper binding site 3 out of 5 in 5fc9

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Copper binding site 3 out of 5 in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Novel Purple Cupredoxin From Nitrosopumilus Maritimus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2402

b:24.0
occ:1.00
 ND1 B:HIS2071 2.0 19.3 1.0
O B:HOH2560 2.4 31.1 1.0
O B:HOH2559 2.8 30.9 1.0
CE1 B:HIS2071 2.9 17.7 1.0
CG B:HIS2071 3.1 18.3 1.0
O B:HOH2606 3.4 36.2 1.0
CB B:HIS2071 3.5 16.9 1.0
CA B:HIS2071 3.6 16.7 1.0
NE2 B:HIS2071 4.0 17.6 1.0
CD2 B:HIS2071 4.2 18.1 1.0
N B:VAL2072 4.2 14.1 1.0
O B:GLU2070 4.2 17.8 1.0
C B:HIS2071 4.4 16.8 1.0
CB B:PHE2058 4.5 18.6 1.0
O B:HOH2576 4.6 25.9 1.0
N B:HIS2071 4.7 17.0 1.0
O B:LEU2057 4.8 20.8 1.0
C B:GLU2070 4.9 18.6 1.0

Copper binding site 4 out of 5 in 5fc9

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Copper binding site 4 out of 5 in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Novel Purple Cupredoxin From Nitrosopumilus Maritimus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3401

b:19.5
occ:0.97
 ND1 C:HIS3043 2.0 17.4 1.0
ND1 C:HIS3086 2.1 19.9 1.0
SG C:CYS3083 2.3 17.6 1.0
O C:HOH3507 2.3 22.0 1.0
CE1 C:HIS3043 2.9 18.6 1.0
CE1 C:HIS3086 3.0 18.4 1.0
CG C:HIS3043 3.1 18.3 1.0
CB C:CYS3083 3.1 18.6 1.0
CG C:HIS3086 3.1 20.6 1.0
CB C:HIS3086 3.5 17.8 1.0
CB C:HIS3043 3.6 16.8 1.0
CA C:HIS3043 3.8 20.2 1.0
N C:HIS3086 3.9 18.3 1.0
OD1 C:ASN3011 3.9 18.5 1.0
NE2 C:HIS3043 4.0 18.0 1.0
NE2 C:HIS3086 4.1 18.8 1.0
CD2 C:HIS3043 4.2 17.7 1.0
CB C:PHE3085 4.2 19.6 1.0
CD2 C:HIS3086 4.2 18.8 1.0
O C:PRO3042 4.2 21.7 1.0
CA C:HIS3086 4.3 17.7 1.0
N C:ASN3044 4.5 19.4 1.0
CA C:CYS3083 4.6 17.2 1.0
C C:PHE3085 4.6 19.0 1.0
C C:HIS3043 4.7 20.8 1.0
O C:HIS3086 4.8 18.0 1.0
CA C:PHE3085 4.8 20.3 1.0
OH C:TYR3020 4.8 18.9 1.0
N C:HIS3043 4.9 21.2 1.0
CD2 C:PHE3085 4.9 26.1 1.0
N C:PHE3085 4.9 18.1 1.0
C C:CYS3083 5.0 16.9 1.0
C C:HIS3086 5.0 18.9 1.0
C C:PRO3042 5.0 19.8 1.0

Copper binding site 5 out of 5 in 5fc9

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Copper binding site 5 out of 5 in the Novel Purple Cupredoxin From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Novel Purple Cupredoxin From Nitrosopumilus Maritimus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu4401

b:16.3
occ:0.98
 ND1 D:HIS4043 2.0 16.1 1.0
ND1 D:HIS4086 2.1 14.9 1.0
O D:HOH4504 2.2 18.1 1.0
SG D:CYS4083 2.2 16.9 1.0
CE1 D:HIS4043 2.9 17.1 1.0
CE1 D:HIS4086 3.0 17.9 1.0
CB D:CYS4083 3.1 14.2 1.0
CG D:HIS4086 3.1 14.7 1.0
CG D:HIS4043 3.1 16.9 1.0
CB D:HIS4086 3.5 14.1 1.0
CB D:HIS4043 3.6 17.1 1.0
CA D:HIS4043 3.9 14.0 1.0
OD1 D:ASN4011 3.9 17.7 1.0
N D:HIS4086 3.9 14.2 1.0
NE2 D:HIS4043 4.1 16.3 1.0
NE2 D:HIS4086 4.1 15.3 1.0
CD2 D:HIS4043 4.2 16.6 1.0
CD2 D:HIS4086 4.2 16.0 1.0
O D:PRO4042 4.3 18.5 1.0
CB D:PHE4085 4.3 14.6 1.0
CA D:HIS4086 4.3 14.6 1.0
N D:ASN4044 4.5 16.7 1.0
CA D:CYS4083 4.5 15.4 1.0
C D:PHE4085 4.6 14.5 1.0
C D:HIS4043 4.8 18.8 1.0
O D:HIS4086 4.8 15.0 1.0
OH D:TYR4020 4.8 17.7 1.0
CA D:PHE4085 4.9 15.5 1.0
N D:PHE4085 4.9 15.5 1.0
N D:HIS4043 4.9 18.3 1.0
CD2 D:PHE4085 5.0 18.5 1.0
C D:CYS4083 5.0 15.9 1.0
O D:ASN4044 5.0 16.6 1.0

Reference:

P.Hosseinzadeh, S.Tian, N.M.Marshall, J.Hemp, T.Mullen, M.J.Nilges, Y.G.Gao, H.Robinson, D.A.Stahl, R.B.Gennis, Y.Lu. A Purple Cupredoxin From Nitrosopumilus Maritimus Containing A Mononuclear Type 1 Copper Center with An Open Binding Site. J.Am.Chem.Soc. V. 138 6324 2016.
ISSN: ESSN 1520-5126
PubMed: 27120678
DOI: 10.1021/JACS.5B13128
Page generated: Sun Dec 13 11:17:32 2020

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