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Copper in PDB 1ar1: Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment

Enzymatic activity of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment

All present enzymatic activity of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment:
1.9.3.1;

Protein crystallography data

The structure of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment, PDB code: 1ar1 was solved by C.Ostermeier, A.Harrenga, U.Ermler, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.500, 151.000, 156.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26.1

Other elements in 1ar1:

The structure of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 2 atoms
Calcium (Ca) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment (pdb code 1ar1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment, PDB code: 1ar1:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 1ar1

Go back to Copper Binding Sites List in 1ar1
Copper binding site 1 out of 3 in the Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu559

b:47.1
occ:1.00
 ND1 A:HIS276 2.2 79.3 1.0
NE2 A:HIS326 2.2 52.0 1.0
NE2 A:HIS325 2.2 55.3 1.0
CE1 A:HIS276 2.9 82.6 1.0
CE1 A:HIS325 3.0 60.7 1.0
CE1 A:HIS326 3.2 52.5 1.0
CD2 A:HIS326 3.2 43.6 1.0
CG A:HIS276 3.3 78.8 1.0
CD2 A:HIS325 3.4 62.5 1.0
CB A:HIS276 3.8 67.4 1.0
NA A:HEA563 4.0 49.1 1.0
CA A:HIS276 4.1 57.6 1.0
NE2 A:HIS276 4.1 90.7 1.0
ND1 A:HIS325 4.2 63.2 1.0
C1A A:HEA563 4.2 48.8 1.0
ND1 A:HIS326 4.3 56.3 1.0
ND A:HEA563 4.3 58.8 1.0
CD2 A:HIS276 4.3 86.9 1.0
CG A:HIS326 4.3 50.9 1.0
C4A A:HEA563 4.4 47.7 1.0
CG A:HIS325 4.4 59.8 1.0
CG2 A:VAL279 4.4 56.9 1.0
FE A:HEA563 4.5 46.9 1.0
CHA A:HEA563 4.5 50.0 1.0
C4D A:HEA563 4.5 57.1 1.0
NB A:HEA563 4.7 54.7 1.0
C2A A:HEA563 4.8 51.8 1.0
C3A A:HEA563 4.8 47.1 1.0
CHB A:HEA563 4.8 53.4 1.0
NC A:HEA563 4.9 59.1 1.0
N A:HIS276 4.9 55.5 1.0
C1D A:HEA563 5.0 57.9 1.0
CG1 A:VAL279 5.0 52.2 1.0
C1B A:HEA563 5.0 56.9 1.0

Copper binding site 2 out of 3 in 1ar1

Go back to Copper Binding Sites List in 1ar1
Copper binding site 2 out of 3 in the Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu270

b:40.4
occ:1.00
 ND1 B:HIS224 2.1 39.4 1.0
SG B:CYS220 2.2 52.3 1.0
SG B:CYS216 2.2 56.7 1.0
CU B:CU271 2.5 44.8 1.0
O B:GLU218 2.8 51.6 1.0
CB B:CYS216 2.9 45.8 1.0
CG B:HIS224 3.0 48.5 1.0
CE1 B:HIS224 3.2 48.2 1.0
CB B:HIS224 3.2 50.5 1.0
CB B:CYS220 3.3 44.1 1.0
O B:HIS224 3.4 56.1 1.0
CA B:HIS224 3.4 53.4 1.0
N B:CYS220 3.7 49.7 1.0
C B:GLU218 3.7 51.2 1.0
C B:HIS224 3.8 52.2 1.0
CA B:CYS220 4.1 50.3 1.0
SD B:MET227 4.1 35.9 1.0
CD2 B:HIS224 4.2 51.9 1.0
CA B:CYS216 4.2 47.6 1.0
NE2 B:HIS224 4.2 55.7 1.0
C B:LEU219 4.3 53.5 1.0
C B:CYS216 4.3 49.8 1.0
N B:GLU218 4.3 54.3 1.0
O B:CYS216 4.4 49.2 1.0
N B:LEU219 4.5 50.2 1.0
CA B:LEU219 4.5 50.5 1.0
ND1 B:HIS181 4.5 38.2 1.0
CA B:GLU218 4.7 53.4 1.0
CG B:MET227 4.7 29.4 1.0
N B:HIS224 4.7 56.7 1.0
N B:SER217 4.8 51.9 1.0
CA B:HIS181 4.9 46.6 1.0
CB B:HIS181 4.9 44.9 1.0

Copper binding site 3 out of 3 in 1ar1

Go back to Copper Binding Sites List in 1ar1
Copper binding site 3 out of 3 in the Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu271

b:44.8
occ:1.00
 ND1 B:HIS181 2.1 38.2 1.0
SG B:CYS220 2.2 52.3 1.0
SG B:CYS216 2.2 56.7 1.0
CU B:CU270 2.5 40.4 1.0
SD B:MET227 2.6 35.9 1.0
CB B:CYS220 3.0 44.1 1.0
CG B:HIS181 3.0 48.5 1.0
CE1 B:HIS181 3.1 45.1 1.0
CE B:MET227 3.2 14.5 1.0
CB B:HIS181 3.3 44.9 1.0
CB B:CYS216 3.5 45.8 1.0
CA B:HIS181 3.9 46.6 1.0
CG B:MET227 3.9 29.4 1.0
O B:GLU218 4.2 51.6 1.0
CD2 B:HIS181 4.2 49.5 1.0
NE2 B:HIS181 4.3 51.8 1.0
CA B:CYS220 4.5 50.3 1.0
ND1 B:HIS224 4.6 39.4 1.0
CA B:HIS224 4.8 53.4 1.0
O B:HIS119 4.8 39.0 1.0
O B:ILE180 4.8 46.0 1.0
N B:CYS220 4.9 49.7 1.0
O B:HIS224 4.9 56.1 1.0
N B:HIS181 4.9 45.8 1.0
CA B:CYS216 4.9 47.6 1.0
N B:ALA182 5.0 49.5 1.0
C B:HIS181 5.0 47.6 1.0

Reference:

C.Ostermeier, A.Harrenga, U.Ermler, H.Michel. Structure at 2.7 A Resolution of the Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed with An Antibody Fv Fragment. Proc.Natl.Acad.Sci.Usa V. 94 10547 1997.
ISSN: ISSN 0027-8424
PubMed: 9380672
DOI: 10.1073/PNAS.94.20.10547
Page generated: Tue Jul 30 21:30:23 2024

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