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Calcium in PDB 5djq: The Structure of CBB3 Cytochrome Oxidase.

Enzymatic activity of The Structure of CBB3 Cytochrome Oxidase.

All present enzymatic activity of The Structure of CBB3 Cytochrome Oxidase.:
1.9.3.1;

Protein crystallography data

The structure of The Structure of CBB3 Cytochrome Oxidase., PDB code: 5djq was solved by S.Buschmann, E.Warkentin, H.Xie, M.Kohlstaedt, J.D.Langer, U.Ermler, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.98 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.475, 279.933, 175.192, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.3

Other elements in 5djq:

The structure of The Structure of CBB3 Cytochrome Oxidase. also contains other interesting chemical elements:

Iron (Fe) 24 atoms
Copper (Cu) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of CBB3 Cytochrome Oxidase. (pdb code 5djq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structure of CBB3 Cytochrome Oxidase., PDB code: 5djq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5djq

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Calcium binding site 1 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:99.2
occ:1.00
 O A:ALA124 2.4 78.3 1.0
OD1 A:ASP131 2.6 0.7 1.0
O A:LEU126 2.6 57.5 1.0
OD2 A:ASP131 2.6 0.7 1.0
ND2 A:ASN179 2.9 92.2 1.0
CG A:ASP131 2.9 0.7 1.0
C A:ALA124 3.3 73.7 1.0
CG A:ASN179 3.4 83.1 1.0
C A:LEU126 3.7 61.2 1.0
OD1 A:ASN179 3.7 91.0 1.0
CA A:ALA124 3.9 67.3 1.0
N A:LEU126 3.9 64.7 1.0
OG A:SER119 4.0 74.6 1.0
CB A:ALA124 4.0 61.1 1.0
N A:GLU125 4.2 73.4 1.0
CB A:ASN179 4.2 69.1 1.0
CA A:LEU126 4.3 63.0 1.0
C A:GLU125 4.3 64.5 1.0
CB A:ASP131 4.4 88.8 1.0
CB A:LEU126 4.6 59.8 1.0
OE2 A:GLU181 4.7 94.3 1.0
CA A:GLU125 4.7 68.3 1.0
N A:GLU127 4.8 64.0 1.0
O A:GLU125 4.9 65.3 1.0
OE1 A:GLU181 4.9 0.3 1.0
CB A:SER119 4.9 65.2 1.0

Calcium binding site 2 out of 8 in 5djq

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Calcium binding site 2 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:84.5
occ:1.00
 OG B:SER102 2.1 53.5 1.0
O2D A:HEM502 2.3 83.8 1.0
O1D A:HEM501 2.4 46.5 1.0
O1D A:HEM502 2.5 82.3 1.0
CGD A:HEM502 2.7 75.5 1.0
OE2 A:GLU122 2.8 64.1 1.0
CGD A:HEM501 3.1 57.7 1.0
O2D A:HEM501 3.3 63.6 1.0
CB B:SER102 3.3 50.9 1.0
NH2 A:ARG57 3.5 54.2 1.0
CD A:GLU122 3.5 64.0 1.0
OE1 A:GLU122 3.6 64.1 1.0
C B:SER102 4.2 62.3 1.0
CBD A:HEM502 4.2 53.9 1.0
O B:SER102 4.3 77.0 1.0
CA B:SER102 4.4 52.2 1.0
CBD A:HEM501 4.5 58.3 1.0
OH A:TYR123 4.5 55.0 1.0
N B:LYS103 4.6 59.1 1.0
CAD A:HEM501 4.7 58.2 1.0
CZ A:ARG57 4.7 48.5 1.0
CB B:LYS103 4.9 56.7 1.0
CAD A:HEM502 4.9 47.4 1.0

Calcium binding site 3 out of 8 in 5djq

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Calcium binding site 3 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:0.2
occ:1.00
 OD2 D:ASP131 2.5 0.4 1.0
O D:ALA124 2.6 0.8 1.0
O D:LEU126 2.7 0.4 1.0
OD1 D:ASP131 3.1 0.7 1.0
CG D:ASP131 3.1 0.1 1.0
ND2 D:ASN179 3.3 1.0 1.0
CG D:ASN179 3.4 0.7 1.0
OG D:SER119 3.5 0.3 1.0
C D:ALA124 3.7 0.7 1.0
OD1 D:ASN179 3.7 0.6 1.0
C D:LEU126 4.0 0.1 1.0
OE2 D:GLU181 4.0 0.3 1.0
CB D:ASN179 4.0 0.0 1.0
OE1 D:GLU181 4.1 0.3 1.0
CB D:ALA124 4.2 0.0 1.0
CB D:SER119 4.2 0.6 1.0
CA D:ALA124 4.3 0.4 1.0
CD D:GLU181 4.4 0.0 1.0
N D:LEU126 4.5 0.8 1.0
CB D:ASP131 4.6 0.9 1.0
C D:GLU125 4.6 0.6 1.0
N D:GLU125 4.7 0.6 1.0
CA D:ASN179 4.7 0.6 1.0
CA D:LEU126 4.8 0.7 1.0
N D:GLU127 4.9 0.5 1.0
CA D:GLU127 5.0 0.5 1.0
O D:GLU125 5.0 0.2 1.0

Calcium binding site 4 out of 8 in 5djq

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Calcium binding site 4 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca507

b:96.8
occ:1.00
 OG E:SER102 2.2 87.4 1.0
O2D D:HEM502 2.3 0.7 1.0
O1D D:HEM501 2.4 96.5 1.0
O1D D:HEM502 2.5 0.3 1.0
CGD D:HEM502 2.7 0.2 1.0
OE2 D:GLU122 3.1 97.2 1.0
CGD D:HEM501 3.2 0.5 1.0
CB E:SER102 3.4 90.3 1.0
NH2 D:ARG57 3.4 94.0 1.0
O2D D:HEM501 3.5 0.8 1.0
OE1 D:GLU122 3.8 95.3 1.0
CD D:GLU122 3.8 0.2 1.0
C E:SER102 4.1 97.3 1.0
CBD D:HEM502 4.2 0.9 1.0
O E:SER102 4.3 0.8 1.0
CA E:SER102 4.4 95.5 1.0
CBD D:HEM501 4.5 0.7 1.0
N E:LYS103 4.5 95.6 1.0
CZ D:ARG57 4.6 92.9 1.0
CB E:LYS103 4.7 97.5 1.0
OH D:TYR123 4.7 0.9 1.0
CAD D:HEM501 4.7 1.0 1.0
CG2 D:THR342 4.9 0.5 1.0
CAD D:HEM502 4.9 0.0 1.0
NH1 D:ARG57 4.9 0.1 1.0
CD1 D:ILE343 5.0 0.3 1.0

Calcium binding site 5 out of 8 in 5djq

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Calcium binding site 5 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca504

b:88.0
occ:1.00
 O G:ALA124 2.4 81.6 1.0
OD2 G:ASP131 2.6 0.4 1.0
O G:LEU126 2.6 71.4 1.0
OD1 G:ASP131 2.7 0.2 1.0
CG G:ASP131 3.0 99.1 1.0
OG G:SER119 3.1 0.6 1.0
ND2 G:ASN179 3.1 0.7 1.0
C G:ALA124 3.4 80.5 1.0
CG G:ASN179 3.4 98.3 1.0
OD1 G:ASN179 3.7 0.2 1.0
C G:LEU126 3.7 74.0 1.0
CA G:ALA124 4.0 79.5 1.0
CB G:ALA124 4.1 85.1 1.0
N G:LEU126 4.1 72.9 1.0
CB G:SER119 4.1 0.1 1.0
CB G:ASN179 4.2 87.8 1.0
OE2 G:GLU181 4.4 0.2 1.0
N G:GLU125 4.4 77.7 1.0
C G:GLU125 4.4 71.6 1.0
CA G:LEU126 4.4 72.6 1.0
CB G:ASP131 4.4 83.7 1.0
OE1 G:GLU181 4.6 0.9 1.0
N G:GLU127 4.8 75.6 1.0
CA G:GLU125 4.8 73.7 1.0
CB G:LEU126 4.8 70.8 1.0
O G:GLU125 4.9 81.5 1.0
CD G:GLU181 4.9 0.1 1.0
CA G:GLU127 5.0 77.0 1.0

Calcium binding site 6 out of 8 in 5djq

Go back to Calcium Binding Sites List in 5djq
Calcium binding site 6 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca507

b:73.0
occ:1.00
 OG H:SER102 2.2 64.0 1.0
OE2 G:GLU122 2.3 84.6 1.0
O2D G:HEM502 2.4 76.7 1.0
O1D G:HEM501 2.4 57.4 1.0
O1D G:HEM502 2.7 67.2 1.0
CGD G:HEM502 2.8 69.8 1.0
CGD G:HEM501 3.0 66.5 1.0
O2D G:HEM501 3.1 71.5 1.0
CB H:SER102 3.3 67.5 1.0
CD G:GLU122 3.5 86.5 1.0
NH2 G:ARG57 3.6 60.7 1.0
OE1 G:GLU122 4.0 82.6 1.0
C H:SER102 4.2 77.0 1.0
O H:SER102 4.2 88.7 1.0
CBD G:HEM502 4.3 58.4 1.0
CA H:SER102 4.3 67.4 1.0
CBD G:HEM501 4.4 64.1 1.0
N H:LYS103 4.6 77.6 1.0
OH G:TYR123 4.6 76.5 1.0
CAD G:HEM501 4.6 58.3 1.0
CG G:GLU122 4.7 84.3 1.0
CZ G:ARG57 4.7 63.7 1.0
CB H:LYS103 4.8 71.2 1.0
CG2 G:THR342 4.9 79.6 1.0
CAD G:HEM502 5.0 54.2 1.0

Calcium binding site 7 out of 8 in 5djq

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Calcium binding site 7 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca504

b:95.9
occ:1.00
 O1D K:HEM502 2.3 0.6 1.0
OG L:SER102 2.3 1.0 1.0
O2D K:HEM502 2.4 0.9 1.0
O1D K:HEM501 2.5 0.0 1.0
CGD K:HEM502 2.6 0.8 1.0
OE2 K:GLU122 3.1 95.5 1.0
CGD K:HEM501 3.4 0.6 1.0
NH2 K:ARG57 3.4 0.9 1.0
CB L:SER102 3.5 0.0 1.0
O2D K:HEM501 3.7 0.0 1.0
OE1 K:GLU122 3.8 92.4 1.0
CD K:GLU122 3.9 0.7 1.0
CBD K:HEM502 4.1 0.5 1.0
C L:SER102 4.2 0.0 1.0
O L:SER102 4.2 0.6 1.0
CA L:SER102 4.5 0.1 1.0
CZ K:ARG57 4.5 90.6 1.0
N L:LYS103 4.5 0.5 1.0
CB L:LYS103 4.6 95.3 1.0
CBD K:HEM501 4.6 0.1 1.0
OH K:TYR123 4.7 0.0 1.0
CAD K:HEM501 4.8 0.9 1.0
CAD K:HEM502 4.8 0.9 1.0
NH1 K:ARG57 4.8 93.0 1.0
CD1 K:ILE343 4.9 0.7 1.0

Calcium binding site 8 out of 8 in 5djq

Go back to Calcium Binding Sites List in 5djq
Calcium binding site 8 out of 8 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca505

b:0.1
occ:1.00
 O K:ALA124 2.5 0.1 1.0
OD2 K:ASP131 2.7 0.4 1.0
O K:LEU126 2.9 1.0 1.0
ND2 K:ASN179 2.9 0.2 1.0
OD1 K:ASP131 3.1 1.0 1.0
CG K:ASN179 3.1 0.8 1.0
CG K:ASP131 3.2 1.0 1.0
OD1 K:ASN179 3.4 0.7 1.0
C K:ALA124 3.4 0.6 1.0
CB K:ASN179 3.8 0.4 1.0
CB K:ALA124 3.9 0.6 1.0
CA K:ALA124 4.0 0.3 1.0
C K:LEU126 4.1 0.6 1.0
OE2 K:GLU181 4.2 0.3 1.0
OG K:SER119 4.3 0.9 1.0
CB K:SER119 4.4 1.0 1.0
N K:LEU126 4.4 0.7 1.0
OE1 K:GLU181 4.4 0.8 1.0
N K:GLU125 4.5 0.5 1.0
CA K:ASN179 4.6 0.4 1.0
CB K:ASP131 4.6 0.9 1.0
C K:GLU125 4.7 0.6 1.0
CD K:GLU181 4.7 0.1 1.0
CA K:LEU126 4.8 0.3 1.0
CA K:GLU125 5.0 0.2 1.0

Reference:

S.Buschmann, E.Warkentin, H.Xie, J.D.Langer, U.Ermler, H.Michel. The Structure of CBB3 Cytochrome Oxidase Provides Insights Into Proton Pumping. Science V. 329 327 2010.
ISSN: ESSN 1095-9203
PubMed: 20576851
DOI: 10.1126/SCIENCE.1187303
Page generated: Sun Jul 14 18:01:29 2024

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