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Copper in PDB 4ax3: Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution

Enzymatic activity of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution

All present enzymatic activity of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution:
1.7.2.1;

Protein crystallography data

The structure of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution, PDB code: 4ax3 was solved by S.V.Antonyuk, H.Cong, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.60
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 185.812, 185.812, 185.812, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.4

Other elements in 4ax3:

The structure of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution (pdb code 4ax3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution, PDB code: 4ax3:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 4ax3

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Copper binding site 1 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:18.0
occ:1.00
 ND1 A:HIS143 2.0 17.7 1.0
ND1 A:HIS94 2.1 13.5 1.0
SG A:CYS135 2.2 17.6 1.0
SD A:MET148 2.6 18.9 1.0
CE1 A:HIS143 2.9 16.9 1.0
CE1 A:HIS94 3.0 19.4 1.0
CG A:HIS143 3.1 17.5 1.0
CG A:HIS94 3.1 17.5 1.0
CB A:CYS135 3.2 16.8 1.0
CE A:MET148 3.3 14.1 1.0
CB A:HIS143 3.5 16.5 1.0
CB A:HIS94 3.5 16.2 1.0
CA A:HIS94 3.8 17.8 1.0
O A:PRO93 4.0 19.2 1.0
NE2 A:HIS143 4.1 17.7 1.0
NE2 A:HIS94 4.1 17.9 1.0
CD2 A:HIS143 4.1 18.8 1.0
CG A:MET148 4.1 16.7 1.0
CD2 A:HIS94 4.2 19.1 1.0
CB A:THR137 4.3 17.8 1.0
OG1 A:THR137 4.4 17.6 1.0
CE3 A:TRP61 4.6 17.3 1.0
CA A:HIS143 4.6 15.6 1.0
N A:ASN95 4.6 16.9 1.0
CA A:CYS135 4.6 16.0 1.0
CB A:MET148 4.7 15.8 1.0
N A:HIS94 4.8 18.0 1.0
C A:PRO93 4.8 18.8 1.0
C A:HIS94 4.8 17.8 1.0
CZ3 A:TRP61 5.0 16.6 1.0

Copper binding site 2 out of 8 in 4ax3

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Copper binding site 2 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:16.0
occ:1.00
 NE2 A:HIS134 2.0 13.0 1.0
NE2 A:HIS99 2.0 14.2 1.0
CD2 A:HIS134 2.9 14.3 1.0
CE1 A:HIS99 3.0 11.3 1.0
CD2 A:HIS99 3.1 14.2 1.0
CE1 A:HIS134 3.1 16.1 1.0
OD2 A:ASP97 3.9 15.7 1.0
CG A:HIS134 4.1 14.0 1.0
ND1 A:HIS99 4.1 12.3 1.0
ND1 A:HIS134 4.2 13.8 1.0
CG A:HIS99 4.2 11.8 1.0
CG A:ASP97 4.5 12.9 1.0
O A:HOH2255 4.7 10.4 0.3
OD1 A:ASP97 4.9 15.0 1.0

Copper binding site 3 out of 8 in 4ax3

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Copper binding site 3 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:17.4
occ:1.00
 ND1 B:HIS94 2.0 15.5 1.0
ND1 B:HIS143 2.1 18.3 1.0
SG B:CYS135 2.2 17.1 1.0
SD B:MET148 2.6 16.9 1.0
CE1 B:HIS143 2.9 15.8 1.0
CE1 B:HIS94 3.0 18.4 1.0
CG B:HIS94 3.1 15.7 1.0
CG B:HIS143 3.1 16.4 1.0
CB B:CYS135 3.3 15.9 1.0
CE B:MET148 3.3 15.9 1.0
CB B:HIS94 3.5 16.2 1.0
CB B:HIS143 3.5 15.3 1.0
CA B:HIS94 3.8 16.4 1.0
O B:PRO93 4.0 17.9 1.0
NE2 B:HIS143 4.1 15.6 1.0
NE2 B:HIS94 4.1 16.0 1.0
CD2 B:HIS143 4.2 18.8 1.0
CG B:MET148 4.2 15.5 1.0
CD2 B:HIS94 4.2 15.7 1.0
OG1 B:THR137 4.3 16.0 1.0
CB B:THR137 4.3 17.4 1.0
N B:ASN95 4.6 16.1 1.0
CE3 B:TRP61 4.6 16.5 1.0
CA B:CYS135 4.6 16.3 1.0
CA B:HIS143 4.7 15.3 1.0
CB B:MET148 4.7 16.1 1.0
C B:HIS94 4.8 17.2 1.0
N B:HIS94 4.8 17.0 1.0
C B:PRO93 4.8 17.9 1.0

Copper binding site 4 out of 8 in 4ax3

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Copper binding site 4 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:16.3
occ:1.00
 NE2 B:HIS99 2.0 12.7 1.0
NE2 B:HIS134 2.0 12.8 1.0
O B:HOH2230 2.1 17.6 1.0
CE1 B:HIS99 2.9 13.5 1.0
CD2 B:HIS134 2.9 13.1 1.0
CD2 B:HIS99 3.0 12.4 1.0
CE1 B:HIS134 3.1 17.3 1.0
OD2 B:ASP97 3.9 15.9 1.0
ND1 B:HIS99 4.1 13.3 1.0
CG B:HIS134 4.1 12.2 1.0
CG B:HIS99 4.1 13.2 1.0
ND1 B:HIS134 4.1 13.2 1.0
CG B:ASP97 4.5 15.9 1.0
OD1 B:ASP97 4.9 14.6 1.0

Copper binding site 5 out of 8 in 4ax3

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Copper binding site 5 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:14.8
occ:1.00
 ND1 C:HIS94 2.0 13.5 1.0
ND1 C:HIS143 2.1 16.0 1.0
SG C:CYS135 2.2 14.0 1.0
SD C:MET148 2.6 14.8 1.0
CE1 C:HIS143 2.9 13.0 1.0
CE1 C:HIS94 3.0 14.2 1.0
CG C:HIS143 3.1 13.1 1.0
CG C:HIS94 3.1 14.8 1.0
CB C:CYS135 3.2 12.3 1.0
CE C:MET148 3.3 13.1 1.0
CB C:HIS94 3.5 15.2 1.0
CB C:HIS143 3.5 11.9 1.0
CA C:HIS94 3.8 15.6 1.0
O C:PRO93 4.0 16.7 1.0
NE2 C:HIS143 4.0 14.7 1.0
NE2 C:HIS94 4.1 15.8 1.0
CD2 C:HIS143 4.1 14.6 1.0
CG C:MET148 4.2 12.9 1.0
CD2 C:HIS94 4.2 16.9 1.0
OG1 C:THR137 4.3 15.9 1.0
CB C:THR137 4.3 15.1 1.0
N C:ASN95 4.6 14.8 1.0
CA C:HIS143 4.6 11.9 1.0
CE3 C:TRP61 4.6 10.9 1.0
CA C:CYS135 4.6 12.1 1.0
CB C:MET148 4.6 11.8 1.0
C C:HIS94 4.8 17.2 1.0
N C:HIS94 4.8 16.6 1.0
C C:PRO93 4.8 16.2 1.0

Copper binding site 6 out of 8 in 4ax3

Go back to Copper Binding Sites List in 4ax3
Copper binding site 6 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:14.2
occ:1.00
 NE2 C:HIS134 2.0 11.9 1.0
NE2 C:HIS99 2.0 14.2 1.0
O C:HOH2244 2.1 15.9 1.0
CD2 C:HIS134 3.0 12.5 1.0
CE1 C:HIS99 3.0 13.1 1.0
CD2 C:HIS99 3.1 14.3 1.0
CE1 C:HIS134 3.1 13.9 1.0
OD2 C:ASP97 3.8 14.4 1.0
CG C:HIS134 4.1 10.3 1.0
ND1 C:HIS99 4.1 13.5 1.0
ND1 C:HIS134 4.2 11.2 1.0
CG C:HIS99 4.2 12.1 1.0
CG C:ASP97 4.5 13.3 1.0
OD1 C:ASP97 4.9 14.6 1.0

Copper binding site 7 out of 8 in 4ax3

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Copper binding site 7 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu501

b:19.4
occ:1.00
 ND1 D:HIS94 2.1 15.7 1.0
ND1 D:HIS143 2.1 21.0 1.0
SG D:CYS135 2.2 18.0 1.0
SD D:MET148 2.6 19.6 1.0
CE1 D:HIS94 3.0 21.0 1.0
CE1 D:HIS143 3.0 15.9 1.0
CG D:HIS94 3.1 19.5 1.0
CG D:HIS143 3.1 17.9 1.0
CB D:CYS135 3.2 17.7 1.0
CE D:MET148 3.4 18.5 1.0
CB D:HIS94 3.4 19.3 1.0
CB D:HIS143 3.5 17.3 1.0
CA D:HIS94 3.7 18.8 1.0
O D:PRO93 4.0 19.6 1.0
NE2 D:HIS94 4.1 20.2 1.0
NE2 D:HIS143 4.1 18.0 1.0
CG D:MET148 4.1 18.4 1.0
CD2 D:HIS94 4.2 19.9 1.0
CD2 D:HIS143 4.2 17.9 1.0
OG1 D:THR137 4.3 19.0 1.0
CB D:THR137 4.3 19.6 1.0
N D:ASN95 4.6 19.2 1.0
CE3 D:TRP61 4.6 17.8 1.0
CA D:HIS143 4.7 17.4 1.0
CB D:MET148 4.7 16.0 1.0
CA D:CYS135 4.7 17.5 1.0
C D:HIS94 4.7 19.8 1.0
N D:HIS94 4.7 18.7 1.0
C D:PRO93 4.8 19.3 1.0

Copper binding site 8 out of 8 in 4ax3

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Copper binding site 8 out of 8 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:19.3
occ:1.00
 NE2 D:HIS99 2.0 18.1 1.0
NE2 D:HIS134 2.0 16.0 1.0
O D:HOH2176 2.1 20.4 1.0
CD2 D:HIS134 2.9 16.6 1.0
CE1 D:HIS99 3.0 16.2 1.0
CD2 D:HIS99 3.1 16.4 1.0
CE1 D:HIS134 3.1 16.5 1.0
OD2 D:ASP97 3.9 17.9 1.0
CG D:HIS134 4.1 15.8 1.0
ND1 D:HIS99 4.1 16.9 1.0
ND1 D:HIS134 4.2 15.8 1.0
CG D:HIS99 4.2 17.6 1.0
CG D:ASP97 4.5 15.4 1.0
OD1 D:ASP97 4.9 17.2 1.0

Reference:

S.V.Antonyuk, C.Han, R.R.Eady, S.S.Hasnain. Structures of Protein-Protein Complexes Involved in Electron Transfer. Nature V. 496 123 2013.
ISSN: ESSN 1476-4687
PubMed: 23535590
DOI: 10.1038/NATURE11996
Page generated: Mon Jul 14 03:24:21 2025

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