Calcium in PDB 3mk7: The Structure of CBB3 Cytochrome Oxidase

The structure of The Structure of CBB3 Cytochrome Oxidase, PDB code: 3mk7 was solved by S.Buschmann, E.Warkentin, H.Michel, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 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 (%)	18.9 / 22.3

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

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

The binding sites of Calcium atom in the The Structure of CBB3 Cytochrome Oxidase (pdb code 3mk7). 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: 3mk7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

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 B:Ca504 b:51.8 occ:1.00 OG B:SER102 1.9 47.9 1.0 O1D A:HEM501 2.2 48.4 1.0 O2D A:HEM502 2.4 71.1 1.0 O1D A:HEM502 2.6 58.9 1.0 OE2 A:GLU122 2.7 58.4 1.0 CGD A:HEM502 2.9 59.1 1.0 CGD A:HEM501 3.1 53.9 1.0 CB B:SER102 3.3 47.1 1.0 O2D A:HEM501 3.3 57.5 1.0 NH2 A:ARG57 3.6 54.0 1.0 CD A:GLU122 3.6 64.1 1.0 OE1 A:GLU122 3.6 60.9 1.0 C B:SER102 4.1 53.7 1.0 CA B:SER102 4.2 49.0 1.0 O B:SER102 4.2 65.1 1.0 CBD A:HEM502 4.4 51.3 1.0 CBD A:HEM501 4.5 53.1 1.0 N B:LYS103 4.5 53.3 1.0 OH A:TYR123 4.6 46.9 1.0 CZ A:ARG57 4.7 48.1 1.0 CAD A:HEM501 4.8 51.6 1.0 CB B:LYS103 4.8 49.8 1.0 N B:SER102 4.9 52.4 1.0

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:Ca505 b:88.2 occ:1.00 O A:ALA124 2.4 71.4 1.0 O A:LEU126 2.7 59.0 1.0 OD2 A:ASP131 2.7 97.0 1.0 OD1 A:ASP131 2.8 0.8 1.0 ND2 A:ASN179 3.0 90.8 1.0 CG A:ASP131 3.1 91.6 1.0 C A:ALA124 3.3 62.1 1.0 CG A:ASN179 3.3 80.4 1.0 OD1 A:ASN179 3.6 89.0 1.0 C A:LEU126 3.8 60.2 1.0 CA A:ALA124 3.9 60.0 1.0 N A:LEU126 4.0 58.5 1.0 CB A:ALA124 4.0 58.2 1.0 OG A:SER119 4.1 62.0 1.0 CB A:ASN179 4.2 73.2 1.0 N A:GLU125 4.2 63.2 1.0 C A:GLU125 4.3 59.3 1.0 CA A:LEU126 4.3 60.5 1.0 CB A:ASP131 4.6 85.2 1.0 OE2 A:GLU181 4.6 80.0 1.0 CB A:SER119 4.6 57.6 1.0 OE1 A:GLU181 4.6 88.0 1.0 CA A:GLU125 4.7 59.2 1.0 CB A:LEU126 4.8 60.5 1.0 O A:GLU125 4.8 59.2 1.0 N A:GLU127 4.9 63.7 1.0

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 E:Ca504 b:0.7 occ:1.00 OG E:SER102 2.0 87.3 1.0 O1D D:HEM501 2.2 96.2 1.0 O2D D:HEM502 2.4 0.1 1.0 O1D D:HEM502 2.7 97.3 1.0 OE2 D:GLU122 2.9 0.6 1.0 CGD D:HEM502 2.9 96.4 1.0 CGD D:HEM501 3.1 0.6 1.0 CB E:SER102 3.3 91.2 1.0 O2D D:HEM501 3.4 0.5 1.0 NH2 D:ARG57 3.5 97.9 1.0 OE1 D:GLU122 3.6 0.1 1.0 CD D:GLU122 3.6 0.2 1.0 C E:SER102 4.1 91.7 1.0 O E:SER102 4.2 92.4 1.0 CA E:SER102 4.2 92.0 1.0 CBD D:HEM502 4.4 94.3 1.0 CBD D:HEM501 4.5 0.1 1.0 N E:LYS103 4.5 91.0 1.0 CZ D:ARG57 4.7 98.0 1.0 OH D:TYR123 4.7 0.4 1.0 CB E:LYS103 4.8 89.9 1.0 CAD D:HEM501 4.8 0.4 1.0 N E:SER102 5.0 91.8 1.0 CD1 D:ILE343 5.0 0.2 1.0

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:Ca505 b:0.8 occ:1.00 O D:ALA124 2.4 0.7 1.0 OD2 D:ASP131 2.6 0.6 1.0 O D:LEU126 2.6 0.5 1.0 OD1 D:ASP131 2.8 0.0 1.0 CG D:ASP131 3.1 0.8 1.0 ND2 D:ASN179 3.1 0.3 1.0 C D:ALA124 3.4 0.8 1.0 CG D:ASN179 3.4 0.8 1.0 OD1 D:ASN179 3.7 0.4 1.0 C D:LEU126 3.8 0.3 1.0 OG D:SER119 4.0 0.7 1.0 CA D:ALA124 4.0 0.9 1.0 N D:LEU126 4.1 0.5 1.0 CB D:ALA124 4.1 0.2 1.0 CB D:ASN179 4.2 0.2 1.0 N D:GLU125 4.3 0.8 1.0 C D:GLU125 4.3 0.8 1.0 OE2 D:GLU181 4.4 0.7 1.0 CA D:LEU126 4.4 0.9 1.0 OE1 D:GLU181 4.5 0.5 1.0 CB D:SER119 4.5 0.8 1.0 CB D:ASP131 4.5 0.1 1.0 O D:GLU125 4.8 1.0 1.0 CA D:GLU125 4.8 0.3 1.0 N D:GLU127 4.9 0.7 1.0 CD D:GLU181 4.9 0.8 1.0 CB D:LEU126 4.9 0.9 1.0

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:74.2 occ:1.00 OG H:SER102 2.0 60.1 1.0 O1D G:HEM501 2.2 56.9 1.0 O2D G:HEM502 2.3 71.0 1.0 OE2 G:GLU122 2.7 75.5 1.0 O1D G:HEM502 2.8 59.9 1.0 CGD G:HEM502 2.9 63.1 1.0 CGD G:HEM501 3.1 60.4 1.0 CB H:SER102 3.3 61.8 1.0 O2D G:HEM501 3.3 61.8 1.0 NH2 G:ARG57 3.5 64.0 1.0 CD G:GLU122 3.5 79.3 1.0 OE1 G:GLU122 3.5 80.7 1.0 C H:SER102 4.1 67.3 1.0 CA H:SER102 4.3 63.2 1.0 O H:SER102 4.3 80.8 1.0 CBD G:HEM502 4.4 58.6 1.0 CBD G:HEM501 4.5 61.3 1.0 N H:LYS103 4.5 68.9 1.0 OH G:TYR123 4.6 60.0 1.0 CZ G:ARG57 4.6 61.9 1.0 CB H:LYS103 4.8 62.1 1.0 CAD G:HEM501 4.8 60.9 1.0 CG G:GLU122 5.0 74.5 1.0 N H:SER102 5.0 66.6 1.0

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:Ca505 b:91.3 occ:1.00 O G:ALA124 2.3 74.6 1.0 O G:LEU126 2.6 72.4 1.0 OD2 G:ASP131 2.7 96.7 1.0 OD1 G:ASP131 2.7 100.0 1.0 CG G:ASP131 3.0 92.2 1.0 ND2 G:ASN179 3.0 90.8 1.0 C G:ALA124 3.3 72.5 1.0 CG G:ASN179 3.4 88.8 1.0 OD1 G:ASN179 3.7 92.0 1.0 C G:LEU126 3.8 72.1 1.0 CA G:ALA124 3.9 70.2 1.0 N G:LEU126 4.0 68.6 1.0 CB G:ALA124 4.0 70.5 1.0 OG G:SER119 4.1 75.6 1.0 CB G:ASN179 4.2 85.5 1.0 N G:GLU125 4.2 72.6 1.0 CA G:LEU126 4.3 71.1 1.0 C G:GLU125 4.3 66.5 1.0 CB G:ASP131 4.5 85.4 1.0 OE2 G:GLU181 4.6 91.5 1.0 OE1 G:GLU181 4.7 0.1 1.0 CB G:SER119 4.7 73.6 1.0 CA G:GLU125 4.7 67.2 1.0 CB G:LEU126 4.8 70.9 1.0 O G:GLU125 4.8 70.8 1.0 N G:GLU127 4.9 74.4 1.0

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:99.2 occ:1.00 OG L:SER102 2.2 0.3 1.0 O1D K:HEM501 2.3 0.8 1.0 O2D K:HEM502 2.3 0.9 1.0 O1D K:HEM502 2.5 0.9 1.0 CGD K:HEM502 2.7 0.9 1.0 OE2 K:GLU122 3.0 0.1 1.0 CGD K:HEM501 3.2 0.6 1.0 CB L:SER102 3.4 0.5 1.0 O2D K:HEM501 3.5 0.2 1.0 NH2 K:ARG57 3.5 86.9 1.0 OE1 K:GLU122 3.8 0.7 1.0 CD K:GLU122 3.8 0.5 1.0 C L:SER102 4.2 0.2 1.0 CBD K:HEM502 4.2 0.2 1.0 O L:SER102 4.2 0.2 1.0 CA L:SER102 4.4 0.6 1.0 CBD K:HEM501 4.5 0.1 1.0 N L:LYS103 4.5 0.8 1.0 CZ K:ARG57 4.6 84.5 1.0 OH K:TYR123 4.7 0.5 1.0 CB L:LYS103 4.7 96.8 1.0 CAD K:HEM501 4.8 1.0 1.0 CD1 K:ILE343 4.8 93.1 1.0 CAD K:HEM502 4.9 0.9 1.0 NH1 K:ARG57 5.0 85.3 1.0

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:0.9 occ:1.00 O K:ALA124 2.3 0.0 1.0 O K:LEU126 2.7 0.9 1.0 OD2 K:ASP131 2.7 0.7 1.0 OD1 K:ASP131 2.9 0.9 1.0 ND2 K:ASN179 3.2 0.2 1.0 CG K:ASP131 3.2 0.2 1.0 C K:ALA124 3.2 0.8 1.0 CG K:ASN179 3.4 0.2 1.0 OD1 K:ASN179 3.7 0.5 1.0 C K:LEU126 3.8 0.5 1.0 CA K:ALA124 3.9 0.7 1.0 OG K:SER119 3.9 0.5 1.0 CB K:ALA124 3.9 0.7 1.0 N K:LEU126 4.0 0.6 1.0 CB K:ASN179 4.2 0.4 1.0 N K:GLU125 4.2 0.8 1.0 C K:GLU125 4.3 0.8 1.0 CA K:LEU126 4.4 0.6 1.0 CB K:SER119 4.4 0.1 1.0 OE2 K:GLU181 4.5 0.1 1.0 OE1 K:GLU181 4.5 0.1 1.0 CB K:ASP131 4.6 0.9 1.0 CA K:GLU125 4.7 0.8 1.0 O K:GLU125 4.9 0.1 1.0 CB K:LEU126 4.9 0.8 1.0 N K:GLU127 4.9 0.9 1.0 CD K:GLU181 4.9 0.1 1.0

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: ISSN 0036-8075
PubMed: 20576851
DOI: 10.1126/SCIENCE.1187303