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Copper in PDB 2xx1: Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite

Enzymatic activity of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite

All present enzymatic activity of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite:
1.7.2.1;

Protein crystallography data

The structure of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite, PDB code: 2xx1 was solved by S.V.Antonyuk, N.G.H.Leferink, C.Han, D.J.Heyes, S.E.J.Rigby, M.A.Hough, R.R.Eady, N.S.Scrutton, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.99 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 172.670, 174.650, 180.650, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.116

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite (pdb code 2xx1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite, PDB code: 2xx1:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 2xx1

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Copper binding site 1 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1337

b:77.4
occ:0.50
 SG A:CYS130 1.9 68.7 1.0
ND1 A:HIS89 2.3 67.0 1.0
ND1 A:HIS139 2.6 66.7 1.0
CB A:CYS130 2.8 68.5 1.0
SD A:MET144 3.1 67.9 1.0
CE1 A:HIS89 3.2 67.3 1.0
CG A:HIS89 3.3 66.1 1.0
CG A:HIS139 3.4 66.3 1.0
CB A:HIS139 3.4 64.8 1.0
CE1 A:HIS139 3.6 67.6 1.0
CB A:HIS89 3.7 65.0 1.0
CA A:HIS89 4.1 65.1 1.0
CE A:MET144 4.2 67.9 1.0
O A:PRO88 4.3 64.4 1.0
CA A:CYS130 4.3 68.7 1.0
NE2 A:HIS89 4.3 67.0 1.0
CG A:MET144 4.3 61.4 1.0
CD2 A:HIS89 4.4 67.4 1.0
CA A:HIS139 4.5 64.3 1.0
CD A:PRO132 4.5 81.0 1.0
CB A:MET144 4.5 58.8 1.0
SD A:MET56 4.6 58.0 1.0
CD2 A:HIS139 4.6 67.2 1.0
NE2 A:HIS139 4.7 67.0 1.0
N A:SER90 4.7 64.9 1.0
C A:CYS130 4.9 70.2 1.0
CG A:PRO132 4.9 81.7 1.0
O A:SER90 4.9 64.8 1.0
C A:HIS89 5.0 65.2 1.0
C A:HIS139 5.0 63.0 1.0

Copper binding site 2 out of 12 in 2xx1

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Copper binding site 2 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1338

b:53.7
occ:1.00
 NE2 A:HIS129 2.0 60.7 1.0
NE2 E:HIS300 2.0 55.7 1.0
NE2 A:HIS94 2.1 61.0 1.0
O2 E:NO21337 2.1 69.0 1.0
N E:NO21337 2.4 68.9 1.0
O1 E:NO21337 2.7 68.8 1.0
CE1 A:HIS129 2.9 60.3 1.0
CE1 E:HIS300 3.0 55.3 1.0
CE1 A:HIS94 3.0 59.8 1.0
CD2 E:HIS300 3.0 55.0 1.0
CD2 A:HIS129 3.1 61.1 1.0
CD2 A:HIS94 3.2 61.4 1.0
OD2 A:ASP92 3.5 64.8 1.0
ND1 A:HIS129 4.0 61.0 1.0
ND1 E:HIS300 4.1 55.3 1.0
NE2 E:HIS249 4.1 55.7 1.0
ND1 A:HIS94 4.1 60.5 1.0
CG A:HIS129 4.2 62.1 1.0
CG E:HIS300 4.2 54.8 1.0
CG A:HIS94 4.2 61.6 1.0
CG A:ASP92 4.3 63.5 1.0
CE1 E:HIS249 4.3 54.5 1.0
CD2 E:HIS249 4.5 55.4 1.0
OD1 A:ASP92 4.7 64.7 1.0
ND1 E:HIS249 4.8 54.9 1.0
CG E:HIS249 4.9 54.8 1.0
CD2 E:LEU302 5.0 50.6 1.0

Copper binding site 3 out of 12 in 2xx1

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Copper binding site 3 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1337

b:66.4
occ:0.50
 SG B:CYS130 2.0 61.8 1.0
ND1 B:HIS89 2.1 60.4 1.0
ND1 B:HIS139 2.4 63.3 1.0
CE1 B:HIS89 3.0 60.6 1.0
CB B:CYS130 3.0 61.9 1.0
SD B:MET144 3.1 67.9 1.0
CG B:HIS89 3.2 61.0 1.0
CG B:HIS139 3.2 62.4 1.0
CB B:HIS139 3.4 61.5 1.0
CE1 B:HIS139 3.4 64.3 1.0
CB B:HIS89 3.6 61.5 1.0
CA B:HIS89 3.8 61.8 1.0
O B:PRO88 4.0 61.8 1.0
NE2 B:HIS89 4.1 61.1 1.0
CD2 B:HIS89 4.2 61.6 1.0
CG B:MET144 4.2 60.9 1.0
CA B:CYS130 4.4 62.0 1.0
CD2 B:HIS139 4.4 63.7 1.0
NE2 B:HIS139 4.5 64.1 1.0
N B:SER90 4.6 62.4 1.0
CE B:MET144 4.6 67.3 1.0
CA B:HIS139 4.6 61.0 1.0
SD B:MET56 4.7 58.6 1.0
CB B:MET144 4.8 57.7 1.0
C B:HIS89 4.8 62.1 1.0
N B:HIS89 4.8 61.9 1.0
C B:PRO88 4.8 61.6 1.0
O B:SER90 4.9 63.8 1.0

Copper binding site 4 out of 12 in 2xx1

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Copper binding site 4 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1338

b:55.4
occ:1.00
 O2 F:NO21337 1.8 59.2 1.0
NE2 B:HIS129 2.0 56.2 1.0
NE2 B:HIS94 2.0 62.6 1.0
NE2 F:HIS300 2.1 53.4 1.0
O1 F:NO21337 2.4 59.1 1.0
N F:NO21337 2.4 58.9 1.0
CE1 B:HIS129 2.9 56.6 1.0
CE1 B:HIS94 2.9 62.9 1.0
CE1 F:HIS300 3.0 53.0 1.0
CD2 B:HIS94 3.1 63.9 1.0
CD2 F:HIS300 3.1 53.3 1.0
CD2 B:HIS129 3.1 57.1 1.0
OD2 B:ASP92 3.8 65.9 1.0
ND1 B:HIS129 4.0 57.1 1.0
NE2 F:HIS249 4.1 57.1 1.0
ND1 B:HIS94 4.1 63.7 1.0
ND1 F:HIS300 4.1 52.8 1.0
CG B:HIS94 4.2 63.9 1.0
CG B:HIS129 4.2 57.8 1.0
CG F:HIS300 4.2 53.1 1.0
CG B:ASP92 4.3 64.4 1.0
CE1 F:HIS249 4.4 56.6 1.0
CD2 F:HIS249 4.5 56.1 1.0
OD1 B:ASP92 4.6 64.2 1.0
ND1 F:HIS249 5.0 55.6 1.0

Copper binding site 5 out of 12 in 2xx1

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Copper binding site 5 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1336

b:65.1
occ:0.50
 SG C:CYS130 1.8 63.2 1.0
ND1 C:HIS89 2.2 63.3 1.0
ND1 C:HIS139 2.5 60.7 1.0
CB C:CYS130 2.9 62.3 1.0
CE1 C:HIS89 3.1 63.1 1.0
SD C:MET144 3.2 67.2 1.0
CG C:HIS89 3.2 62.9 1.0
CG C:HIS139 3.3 60.5 1.0
CE1 C:HIS139 3.5 60.6 1.0
CB C:HIS139 3.5 59.6 1.0
CB C:HIS89 3.6 62.8 1.0
CA C:HIS89 3.8 63.1 1.0
O C:PRO88 4.0 63.4 1.0
NE2 C:HIS89 4.2 62.8 1.0
CG C:MET144 4.2 62.1 1.0
CA C:CYS130 4.3 62.8 1.0
CD2 C:HIS89 4.3 63.1 1.0
N C:SER90 4.4 63.3 1.0
CD2 C:HIS139 4.5 61.0 1.0
NE2 C:HIS139 4.6 60.6 1.0
C C:HIS89 4.7 63.4 1.0
CB C:MET144 4.7 59.5 1.0
CE C:MET144 4.7 67.6 1.0
O C:SER90 4.8 63.5 1.0
CA C:HIS139 4.8 59.3 1.0
N C:HIS89 4.8 63.1 1.0
SD C:MET56 4.8 59.4 1.0
C C:PRO88 4.9 63.3 1.0
C C:CYS130 4.9 64.2 1.0

Copper binding site 6 out of 12 in 2xx1

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Copper binding site 6 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1337

b:60.4
occ:1.00
 NE2 C:HIS94 2.0 65.6 1.0
O1 B:NO21339 2.0 49.4 1.0
NE2 B:HIS300 2.1 54.3 1.0
NE2 C:HIS129 2.1 54.9 1.0
O2 B:NO21339 2.4 50.9 1.0
N B:NO21339 2.5 49.8 1.0
CE1 C:HIS94 2.8 65.6 1.0
CE1 B:HIS300 3.0 53.9 1.0
CD2 C:HIS129 3.0 55.9 1.0
CD2 C:HIS94 3.1 66.3 1.0
CD2 B:HIS300 3.1 53.6 1.0
CE1 C:HIS129 3.2 55.4 1.0
OD2 C:ASP92 3.7 62.8 1.0
ND1 C:HIS94 3.9 65.9 1.0
CG C:HIS94 4.1 65.6 1.0
ND1 B:HIS300 4.1 55.0 1.0
NE2 B:HIS249 4.1 57.2 1.0
CG C:HIS129 4.2 57.6 1.0
CG B:HIS300 4.2 53.2 1.0
ND1 C:HIS129 4.3 56.1 1.0
CG C:ASP92 4.3 62.9 1.0
CE1 B:HIS249 4.3 57.6 1.0
OD1 C:ASP92 4.6 63.2 1.0
CD2 B:HIS249 4.6 57.1 1.0
ND1 B:HIS249 4.8 56.6 1.0
CG B:HIS249 5.0 55.9 1.0

Copper binding site 7 out of 12 in 2xx1

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Copper binding site 7 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1337

b:85.8
occ:0.50
 SG D:CYS130 1.9 63.3 1.0
ND1 D:HIS89 2.2 67.7 1.0
ND1 D:HIS139 2.4 62.8 1.0
SD D:MET144 2.9 70.8 1.0
CB D:CYS130 3.0 62.6 1.0
CE1 D:HIS89 3.2 67.1 1.0
CG D:HIS89 3.2 66.5 1.0
CG D:HIS139 3.4 61.7 1.0
CE1 D:HIS139 3.4 64.5 1.0
CB D:HIS89 3.5 65.9 1.0
CB D:HIS139 3.5 59.6 1.0
CG D:MET144 3.9 62.8 1.0
CA D:HIS89 4.0 66.1 1.0
O D:PRO88 4.1 65.8 1.0
NE2 D:HIS89 4.3 66.8 1.0
CD2 D:HIS89 4.3 67.0 1.0
CA D:CYS130 4.4 62.8 1.0
CD D:PRO132 4.4 62.4 0.5
CB D:MET144 4.5 59.6 1.0
SD D:MET56 4.5 57.8 1.0
CD2 D:HIS139 4.5 62.9 1.0
NE2 D:HIS139 4.5 64.0 1.0
CE D:MET144 4.6 67.9 1.0
CA D:HIS139 4.7 58.7 1.0
N D:SER90 4.8 66.4 1.0
CG D:PRO132 4.8 62.1 0.5
N D:HIS89 5.0 65.9 1.0
C D:HIS89 5.0 66.4 1.0
O D:SER90 5.0 67.5 1.0
C D:PRO88 5.0 65.6 1.0
N D:ALA131 5.0 63.0 0.5
N D:ALA131 5.0 64.2 0.5
C D:CYS130 5.0 63.3 1.0

Copper binding site 8 out of 12 in 2xx1

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Copper binding site 8 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1338

b:58.6
occ:1.00
 O2 A:NO21339 1.9 64.2 1.0
NE2 D:HIS129 2.0 56.0 1.0
NE2 A:HIS300 2.0 57.8 1.0
NE2 D:HIS94 2.0 65.8 1.0
N A:NO21339 2.3 63.8 1.0
O1 A:NO21339 2.7 64.3 1.0
CE1 D:HIS94 2.9 66.1 1.0
CD2 D:HIS129 2.9 56.5 1.0
CE1 A:HIS300 3.0 57.5 1.0
CE1 D:HIS129 3.0 56.0 1.0
CD2 A:HIS300 3.1 57.0 1.0
CD2 D:HIS94 3.2 66.7 1.0
OD2 D:ASP92 3.7 69.6 1.0
ND1 D:HIS94 4.1 66.5 1.0
NE2 A:HIS249 4.1 56.1 1.0
CG D:HIS129 4.1 58.2 1.0
ND1 D:HIS129 4.1 56.2 1.0
ND1 A:HIS300 4.1 58.0 1.0
CG A:HIS300 4.2 56.9 1.0
CG D:HIS94 4.2 66.7 1.0
CE1 A:HIS249 4.3 55.4 1.0
CG D:ASP92 4.3 68.8 1.0
CD2 A:HIS249 4.5 56.0 1.0
OD1 D:ASP92 4.7 71.4 1.0
ND1 A:HIS249 4.9 55.8 1.0

Copper binding site 9 out of 12 in 2xx1

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Copper binding site 9 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu1338

b:49.4
occ:0.50
 SG E:CYS130 1.9 61.8 1.0
ND1 E:HIS89 2.2 59.8 1.0
ND1 E:HIS139 2.4 61.2 1.0
CB E:CYS130 2.9 62.8 1.0
CG E:HIS89 3.2 59.3 1.0
SD E:MET144 3.2 66.6 1.0
CE1 E:HIS89 3.2 59.4 1.0
CG E:HIS139 3.3 60.8 1.0
CB E:HIS89 3.4 60.5 1.0
CB E:HIS139 3.4 60.2 1.0
CE1 E:HIS139 3.5 62.7 1.0
CA E:HIS89 3.6 60.8 1.0
O E:PRO88 3.9 62.0 1.0
CA E:CYS130 4.3 63.2 1.0
CD2 E:HIS89 4.3 58.6 1.0
NE2 E:HIS89 4.3 59.3 1.0
CG E:MET144 4.3 61.0 1.0
N E:SER90 4.4 61.5 1.0
CD2 E:HIS139 4.5 62.0 1.0
NE2 E:HIS139 4.5 63.3 1.0
C E:HIS89 4.6 61.1 1.0
CE E:MET144 4.6 66.2 1.0
N E:HIS89 4.7 61.3 1.0
O E:SER90 4.7 61.6 1.0
CB E:MET144 4.7 58.8 1.0
C E:PRO88 4.7 61.4 1.0
CA E:HIS139 4.8 59.7 1.0
C E:CYS130 4.9 64.8 1.0
SD E:MET56 5.0 57.0 1.0

Copper binding site 10 out of 12 in 2xx1

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Copper binding site 10 out of 12 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans Complexed with Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu1339

b:57.5
occ:1.00
 O2 E:NO21340 2.0 57.2 1.0
NE2 E:HIS94 2.0 60.0 1.0
NE2 E:HIS129 2.0 55.9 1.0
NE2 D:HIS300 2.1 51.4 1.0
N E:NO21340 2.3 56.6 1.0
O1 E:NO21340 2.4 56.4 1.0
CE1 E:HIS94 2.9 60.6 1.0
CE1 E:HIS129 3.0 56.4 1.0
CD2 E:HIS129 3.0 56.9 1.0
CD2 E:HIS94 3.0 60.6 1.0
CE1 D:HIS300 3.1 50.7 1.0
CD2 D:HIS300 3.1 51.4 1.0
OD2 E:ASP92 3.6 63.1 1.0
NE2 D:HIS249 4.1 59.7 1.0
ND1 E:HIS94 4.1 61.0 1.0
ND1 E:HIS129 4.1 56.9 1.0
CG E:HIS94 4.2 61.2 1.0
CG E:HIS129 4.2 57.9 1.0
ND1 D:HIS300 4.2 51.5 1.0
CG D:HIS300 4.2 51.2 1.0
CE1 D:HIS249 4.2 58.4 1.0
CG E:ASP92 4.3 61.7 1.0
CD2 D:HIS249 4.6 59.1 1.0
OD1 E:ASP92 4.7 61.9 1.0
ND1 D:HIS249 4.8 58.5 1.0

Reference:

N.G.H.Leferink, C.Han, S.V.Antonyuk, D.J.Heyes, S.E.J.Rigby, M.A.Hough, R.R.Eady, N.S.Scrutton, S.S.Hasnain. Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry V. 50 4121 2011.
ISSN: ISSN 0006-2960
PubMed: 21469743
DOI: 10.1021/BI200246F
Page generated: Wed Jul 31 00:17:32 2024

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