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Copper in PDB 1qni: Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution

Protein crystallography data

The structure of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution, PDB code: 1qni was solved by K.Brown, M.Tegoni, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 211.290, 211.290, 166.457, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 26.1

Other elements in 1qni:

The structure of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Calcium (Ca) 12 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution (pdb code 1qni). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 36 binding sites of Copper where determined in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution, PDB code: 1qni:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 36 in 1qni

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Copper binding site 1 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:47.1
occ:1.00
CU1 A:CUA701 0.0 47.1 1.0
ND1 A:HIS526 2.0 46.4 1.0
SG A:CYS561 2.3 48.6 1.0
SG A:CYS565 2.3 45.8 1.0
SD A:MET572 2.5 45.3 1.0
CU2 A:CUA701 2.5 47.4 1.0
CE1 A:HIS526 2.8 48.2 1.0
CG A:HIS526 3.2 46.5 1.0
CE A:MET572 3.2 42.3 1.0
CB A:CYS561 3.3 44.1 1.0
CB A:CYS565 3.5 47.4 1.0
CB A:HIS526 3.8 45.2 1.0
O A:TRP563 3.8 46.6 1.0
NE2 A:HIS526 4.0 48.3 1.0
CG A:MET572 4.0 42.2 1.0
CA A:HIS526 4.1 44.1 1.0
CD2 A:HIS526 4.2 46.2 1.0
ND1 A:HIS569 4.4 49.9 1.0
CB A:MET572 4.5 45.6 1.0
O A:ALA495 4.6 55.9 1.0
O A:THR525 4.6 44.7 1.0
N A:GLY527 4.7 45.3 1.0
CA A:CYS561 4.7 43.5 1.0
CA A:CYS565 4.8 48.9 1.0
N A:CYS565 4.8 48.8 1.0
C A:TRP563 5.0 45.6 1.0

Copper binding site 2 out of 36 in 1qni

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Copper binding site 2 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:47.4
occ:1.00
CU2 A:CUA701 0.0 47.4 1.0
ND1 A:HIS569 2.0 49.9 1.0
SG A:CYS565 2.3 45.8 1.0
SG A:CYS561 2.4 48.6 1.0
CU1 A:CUA701 2.5 47.1 1.0
O A:TRP563 2.6 46.6 1.0
CE1 A:HIS569 2.7 49.9 1.0
CG A:HIS569 3.2 48.7 1.0
CB A:CYS561 3.4 44.1 1.0
N A:CYS565 3.4 48.8 1.0
C A:TRP563 3.5 45.6 1.0
CB A:CYS565 3.6 47.4 1.0
CB A:HIS569 3.8 48.0 1.0
NE2 A:HIS569 3.9 48.2 1.0
SD A:MET572 4.0 45.3 1.0
CA A:PHE564 4.0 46.9 1.0
CA A:HIS569 4.1 47.6 1.0
CA A:CYS565 4.1 48.9 1.0
N A:PHE564 4.1 45.9 1.0
C A:PHE564 4.1 47.8 1.0
CD2 A:HIS569 4.1 47.5 1.0
O A:HIS569 4.3 47.4 1.0
N A:TRP563 4.3 43.7 1.0
ND1 A:HIS526 4.3 46.4 1.0
O A:CYS561 4.4 42.9 1.0
C A:CYS561 4.5 43.4 1.0
CA A:TRP563 4.5 44.0 1.0
CA A:CYS561 4.5 43.5 1.0
C A:HIS569 4.6 46.5 1.0
CB A:MET572 4.7 45.6 1.0
N A:HIS566 4.8 49.3 1.0
C A:CYS565 4.9 49.3 1.0
CG A:MET572 4.9 42.2 1.0
CE1 A:HIS526 4.9 48.2 1.0

Copper binding site 3 out of 36 in 1qni

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Copper binding site 3 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:44.9
occ:1.00
CU1 A:CUZ801 0.0 44.9 1.0
NE2 A:HIS128 1.9 44.4 1.0
ND1 A:HIS79 2.2 41.6 1.0
S1 A:CUZ801 2.2 45.8 1.0
CU3 A:CUZ801 2.5 45.0 1.0
CU4 A:CUZ801 2.6 43.4 1.0
CD2 A:HIS128 2.9 44.7 1.0
CE1 A:HIS128 3.0 45.2 1.0
CE1 A:HIS79 3.2 41.7 1.0
CG A:HIS79 3.2 42.2 1.0
ND1 A:HIS437 3.6 44.6 1.0
CB A:HIS79 3.6 40.8 1.0
O B:HOH2313 3.6 40.9 1.0
NE2 A:HIS80 3.6 44.4 1.0
CE1 A:HIS80 3.6 42.9 1.0
CE1 A:HIS437 4.0 43.8 1.0
CG A:HIS128 4.1 43.9 1.0
ND1 A:HIS128 4.1 44.0 1.0
CG A:HIS437 4.3 45.5 1.0
NE2 A:HIS79 4.3 41.8 1.0
CD2 A:HIS79 4.3 41.7 1.0
NE2 A:HIS376 4.4 42.0 1.0
CU2 A:CUZ801 4.4 48.3 1.0
CB A:HIS437 4.7 46.0 1.0
CE B:MET570 4.8 44.2 1.0
ND1 A:HIS80 4.8 44.2 1.0
CD2 A:HIS80 4.8 44.1 1.0
NE2 A:HIS437 4.8 43.7 1.0
O A:HOH2252 4.8 53.8 1.0
SD B:MET570 4.9 43.8 1.0
CD2 A:HIS437 4.9 45.0 1.0

Copper binding site 4 out of 36 in 1qni

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Copper binding site 4 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:48.3
occ:1.00
CU2 A:CUZ801 0.0 48.3 1.0
NE2 A:HIS270 2.1 45.7 1.0
NE2 A:HIS325 2.1 46.6 1.0
S1 A:CUZ801 2.3 45.8 1.0
O A:HOH2252 2.5 53.8 1.0
CE1 A:HIS325 3.1 47.0 1.0
CD2 A:HIS270 3.1 43.6 1.0
CE1 A:HIS270 3.1 45.0 1.0
CD2 A:HIS325 3.2 47.1 1.0
CU3 A:CUZ801 3.3 45.0 1.0
CU4 A:CUZ801 3.4 43.4 1.0
NE2 A:HIS376 3.4 42.0 1.0
CD2 A:HIS376 3.6 42.7 1.0
CE1 A:HIS376 4.2 42.1 1.0
ND1 A:HIS270 4.2 44.6 1.0
CG A:HIS270 4.2 44.0 1.0
ND1 A:HIS325 4.2 47.4 1.0
CG A:HIS325 4.3 48.1 1.0
CU1 A:CUZ801 4.4 44.9 1.0
CG A:HIS376 4.4 43.5 1.0
CE2 B:PHE564 4.6 40.9 1.0
OD1 A:ASN189 4.7 44.4 1.0
ND1 A:HIS376 4.7 42.4 1.0
N A:HIS376 4.9 46.2 1.0

Copper binding site 5 out of 36 in 1qni

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Copper binding site 5 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:45.0
occ:1.00
CU3 A:CUZ801 0.0 45.0 1.0
ND1 A:HIS437 1.9 44.6 1.0
S1 A:CUZ801 2.1 45.8 1.0
O A:HOH2252 2.5 53.8 1.0
CU1 A:CUZ801 2.5 44.9 1.0
CE1 A:HIS437 2.8 43.8 1.0
CG A:HIS437 3.0 45.5 1.0
CU4 A:CUZ801 3.0 43.4 1.0
CU2 A:CUZ801 3.3 48.3 1.0
CB A:HIS437 3.5 46.0 1.0
O B:HOH2313 3.6 40.9 1.0
ND1 A:HIS79 3.7 41.6 1.0
NE2 A:HIS376 3.7 42.0 1.0
CD2 A:HIS376 3.8 42.7 1.0
NE2 A:HIS437 4.0 43.7 1.0
CD2 A:HIS437 4.0 45.0 1.0
CE2 B:PHE564 4.3 40.9 1.0
NE2 A:HIS128 4.3 44.4 1.0
NZ A:LYS397 4.4 42.0 1.0
CE1 A:HIS79 4.4 41.7 1.0
CD2 B:PHE564 4.5 39.5 1.0
CA A:HIS437 4.5 48.2 1.0
CG A:HIS79 4.5 42.2 1.0
CB A:HIS79 4.8 40.8 1.0
NE2 A:HIS80 4.8 44.4 1.0
NE2 A:HIS270 4.8 45.7 1.0
CE A:LYS397 5.0 41.6 1.0

Copper binding site 6 out of 36 in 1qni

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Copper binding site 6 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu801

b:43.4
occ:1.00
CU4 A:CUZ801 0.0 43.4 1.0
NE2 A:HIS376 2.1 42.0 1.0
NE2 A:HIS80 2.1 44.4 1.0
S1 A:CUZ801 2.2 45.8 1.0
CU1 A:CUZ801 2.6 44.9 1.0
CE1 A:HIS376 2.9 42.1 1.0
CU3 A:CUZ801 3.0 45.0 1.0
CE1 A:HIS80 3.0 42.9 1.0
CD2 A:HIS80 3.2 44.1 1.0
CD2 A:HIS376 3.2 42.7 1.0
CU2 A:CUZ801 3.4 48.3 1.0
NE2 A:HIS128 3.6 44.4 1.0
ND2 A:ASN189 3.8 45.2 1.0
ND1 A:HIS376 4.1 42.4 1.0
CE1 A:HIS128 4.1 45.2 1.0
ND1 A:HIS80 4.2 44.2 1.0
CB A:HIS79 4.2 40.8 1.0
O A:HOH2252 4.2 53.8 1.0
CE1 A:HIS325 4.2 47.0 1.0
O A:HOH2120 4.2 31.9 1.0
NE2 A:HIS325 4.2 46.6 1.0
CG A:HIS80 4.3 43.5 1.0
ND1 A:HIS79 4.3 41.6 1.0
CG A:HIS376 4.3 43.5 1.0
CB A:HIS437 4.3 46.0 1.0
ND1 A:HIS437 4.3 44.6 1.0
OD1 A:ASN189 4.5 44.4 1.0
NE2 A:HIS270 4.6 45.7 1.0
CG A:ASN189 4.6 44.7 1.0
CD2 A:HIS128 4.6 44.7 1.0
CG A:HIS437 4.7 45.5 1.0
CG A:HIS79 4.7 42.2 1.0
CE1 A:HIS270 4.9 45.0 1.0

Copper binding site 7 out of 36 in 1qni

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Copper binding site 7 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:38.4
occ:1.00
CU1 B:CUA701 0.0 38.4 1.0
ND1 B:HIS526 2.1 42.7 1.0
SG B:CYS561 2.2 35.9 1.0
SG B:CYS565 2.4 36.6 1.0
SD B:MET572 2.4 41.0 1.0
CU2 B:CUA701 2.5 37.7 1.0
CE1 B:HIS526 3.0 42.5 1.0
CB B:CYS561 3.2 38.7 1.0
CE B:MET572 3.2 39.4 1.0
CG B:HIS526 3.2 42.2 1.0
CB B:CYS565 3.4 38.5 1.0
CB B:HIS526 3.7 40.9 1.0
O B:TRP563 3.8 40.4 1.0
CG B:MET572 3.9 39.5 1.0
CA B:HIS526 4.1 40.4 1.0
NE2 B:HIS526 4.1 43.1 1.0
CD2 B:HIS526 4.3 42.4 1.0
CB B:MET572 4.4 40.7 1.0
ND1 B:HIS569 4.5 38.3 1.0
CA B:CYS561 4.6 39.2 1.0
O B:THR525 4.7 38.4 1.0
N B:GLY527 4.7 41.7 1.0
CA B:CYS565 4.7 40.3 1.0
N B:CYS565 4.8 40.9 1.0
O B:ALA495 4.8 53.4 1.0
C B:TRP563 4.9 40.8 1.0
C B:HIS526 5.0 41.0 1.0

Copper binding site 8 out of 36 in 1qni

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Copper binding site 8 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:37.7
occ:1.00
CU2 B:CUA701 0.0 37.7 1.0
ND1 B:HIS569 2.0 38.3 1.0
SG B:CYS565 2.2 36.6 1.0
SG B:CYS561 2.4 35.9 1.0
CU1 B:CUA701 2.5 38.4 1.0
O B:TRP563 2.6 40.4 1.0
CE1 B:HIS569 2.7 38.1 1.0
CG B:HIS569 3.2 39.9 1.0
N B:CYS565 3.3 40.9 1.0
CB B:CYS565 3.4 38.5 1.0
CB B:CYS561 3.4 38.7 1.0
C B:TRP563 3.5 40.8 1.0
CB B:HIS569 3.8 42.0 1.0
NE2 B:HIS569 3.9 38.5 1.0
CA B:CYS565 4.0 40.3 1.0
CA B:PHE564 4.0 41.9 1.0
C B:PHE564 4.0 41.8 1.0
SD B:MET572 4.0 41.0 1.0
CA B:HIS569 4.1 43.3 1.0
N B:PHE564 4.1 41.2 1.0
CD2 B:HIS569 4.2 38.5 1.0
ND1 B:HIS526 4.3 42.7 1.0
O B:CYS561 4.4 38.8 1.0
N B:TRP563 4.4 41.2 1.0
O B:HIS569 4.5 43.6 1.0
C B:CYS561 4.6 39.5 1.0
CB B:MET572 4.6 40.7 1.0
CA B:TRP563 4.6 40.8 1.0
CA B:CYS561 4.6 39.2 1.0
N B:HIS566 4.7 41.4 1.0
C B:HIS569 4.7 43.5 1.0
C B:CYS565 4.7 40.9 1.0
O B:HOH2307 4.9 35.1 1.0
CG B:MET572 4.9 39.5 1.0
CE1 B:HIS526 5.0 42.5 1.0

Copper binding site 9 out of 36 in 1qni

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Copper binding site 9 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu801

b:46.1
occ:1.00
CU1 B:CUZ801 0.0 46.1 1.0
ND1 B:HIS437 1.9 47.0 1.0
O B:HOH2201 2.3 50.8 1.0
S1 B:CUZ801 2.4 47.8 1.0
CU2 B:CUZ801 2.6 44.3 1.0
CE1 B:HIS437 2.9 47.9 1.0
CG B:HIS437 3.0 48.0 1.0
CU4 B:CUZ801 3.0 44.4 1.0
CU3 B:CUZ801 3.3 50.0 1.0
CB B:HIS437 3.4 48.5 1.0
ND1 B:HIS79 3.8 42.4 1.0
CD2 B:HIS376 3.9 46.2 1.0
NE2 B:HIS376 3.9 45.9 1.0
NE2 B:HIS437 4.0 48.7 1.0
CD2 B:HIS437 4.0 48.7 1.0
NZ B:LYS397 4.2 46.9 1.0
CE2 A:PHE564 4.2 44.9 1.0
CA B:HIS437 4.4 47.8 1.0
CD2 A:PHE564 4.4 44.9 1.0
CE1 B:HIS79 4.5 42.4 1.0
NE2 B:HIS128 4.5 42.6 1.0
CG B:HIS79 4.6 41.8 1.0
NE2 B:HIS80 4.8 44.7 1.0
CE B:LYS397 4.9 47.4 1.0
NE2 B:HIS270 4.9 49.9 1.0
CB B:HIS79 4.9 41.2 1.0

Copper binding site 10 out of 36 in 1qni

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Copper binding site 10 out of 36 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu801

b:44.3
occ:1.00
CU2 B:CUZ801 0.0 44.3 1.0
S1 B:CUZ801 1.9 47.8 1.0
NE2 B:HIS128 2.1 42.6 1.0
ND1 B:HIS79 2.2 42.4 1.0
CU1 B:CUZ801 2.6 46.1 1.0
CU4 B:CUZ801 2.6 44.4 1.0
CD2 B:HIS128 3.1 42.5 1.0
CE1 B:HIS79 3.1 42.4 1.0
CE1 B:HIS128 3.1 43.3 1.0
ND1 B:HIS437 3.2 47.0 1.0
CG B:HIS79 3.2 41.8 1.0
NE2 B:HIS80 3.4 44.7 1.0
CB B:HIS79 3.6 41.2 1.0
CE1 B:HIS437 3.8 47.9 1.0
CE1 B:HIS80 3.9 44.8 1.0
CG B:HIS437 4.1 48.0 1.0
CG B:HIS128 4.2 42.7 1.0
ND1 B:HIS128 4.3 41.7 1.0
NE2 B:HIS79 4.3 43.0 1.0
CD2 B:HIS79 4.3 42.2 1.0
CU3 B:CUZ801 4.5 50.0 1.0
NE2 B:HIS376 4.5 45.9 1.0
CB B:HIS437 4.5 48.5 1.0
CD2 B:HIS80 4.5 44.5 1.0
O B:HOH2201 4.6 50.8 1.0
NE2 B:HIS437 4.8 48.7 1.0
CD2 B:HIS437 4.9 48.7 1.0
CE A:MET570 4.9 47.3 1.0
SD A:MET570 5.0 48.9 1.0

Reference:

K.Brown, M.Tegoni, M.Prudencio, A.S.Pereira, S.Besson, J.J.Moura, I.Moura, C.Cambillau. A Novel Type of Catalytic Copper Cluster in Nitrous Oxide Reductase. Nat.Struct.Biol. V. 7 191 2000.
ISSN: ISSN 1072-8368
PubMed: 10700275
DOI: 10.1038/73288
Page generated: Sun Dec 13 11:01:37 2020

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