Calcium in PDB 3wct: The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form

The structure of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form, PDB code: 3wct was solved by N.Numoto, T.Nakagawa, R.Ohara, T.Hasegawa, A.Kita, T.Yoshida, T.Maruyama, K.Imai, Y.Fukumori, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.02 / 2.40
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	108.556, 108.556, 193.552, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 26.4

The structure of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Calcium atom in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form (pdb code 3wct). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form, PDB code: 3wct:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


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 A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:47.8 occ:1.00 OD1 B:ASP135 2.4 42.9 1.0 O B:HOH316 2.4 43.6 1.0 O B:HOH320 2.4 47.6 1.0 OE2 B:GLU109 2.4 48.6 1.0 OD1 B:ASN106 2.4 48.7 1.0 OE1 B:GLU109 2.7 47.1 1.0 CD B:GLU109 2.9 47.2 1.0 CG B:ASN106 3.5 48.5 1.0 CG B:ASP135 3.6 44.2 1.0 O B:HOH308 4.3 55.0 1.0 OE1 B:GLN131 4.3 50.2 1.0 CA B:ASP135 4.3 42.0 1.0 OG1 B:THR138 4.4 43.2 1.0 CG B:GLU109 4.4 46.6 1.0 ND2 B:ASN106 4.4 46.8 1.0 CB B:ASP135 4.4 42.2 1.0 OD2 B:ASP135 4.4 46.5 1.0 CB B:ASN106 4.5 46.4 1.0 CA B:ASN106 4.6 44.8 1.0 N B:ASP135 5.0 42.0 1.0

Calcium binding site 2 out of 2 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


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 A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:42.1 occ:1.00 OD1 F:ASP135 2.3 38.3 1.0 O F:HOH328 2.4 45.1 1.0 OE2 F:GLU109 2.4 42.7 1.0 OD1 F:ASN106 2.4 45.8 1.0 O F:HOH327 2.4 42.4 1.0 O F:HOH313 2.4 36.7 1.0 OE1 F:GLU109 2.6 44.1 1.0 CD F:GLU109 2.8 43.3 1.0 CG F:ASN106 3.5 45.5 1.0 CG F:ASP135 3.6 36.4 1.0 OE1 F:GLN131 4.2 41.6 1.0 CG F:GLU109 4.3 40.5 1.0 OD2 F:ASP135 4.3 38.4 1.0 CB F:ASN106 4.4 43.7 1.0 OG1 F:THR138 4.4 42.5 1.0 CA F:ASP135 4.4 37.0 1.0 ND2 F:ASN106 4.4 47.2 1.0 CB F:ASP135 4.5 36.8 1.0 CA F:ASN106 4.6 42.2 1.0

N.Numoto, T.Nakagawa, R.Ohara, T.Hasegawa, A.Kita, T.Yoshida, T.Maruyama, K.Imai, Y.Fukumori, K.Miki. The Structure of A Deoxygenated 400 kDa Haemoglobin Reveals Ternary- and Quaternary-Structural Changes of Giant Haemoglobins Acta Crystallogr.,Sect.D V. 70 1823 2014.
ISSN: ISSN 0907-4449
PubMed: 25004960
DOI: 10.1107/S1399004714008475