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

The structure of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Deoxygenated Form, PDB code: 3wcu 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)	42.45 / 2.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	108.872, 108.872, 195.157, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 29.2

The structure of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Deoxygenated 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: Deoxygenated Form (pdb code 3wcu). 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: Deoxygenated Form, PDB code: 3wcu:
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: Deoxygenated 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: Deoxygenated Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:67.8 occ:1.00 ND2 B:ASN106 2.9 93.1 1.0 OE1 B:GLU109 3.1 0.4 1.0 OD1 B:ASN106 3.1 93.1 1.0 OE2 B:GLU109 3.1 0.4 1.0 CG B:ASN106 3.2 93.1 1.0 OD1 B:ASP135 3.2 71.9 1.0 OD2 B:ASP135 3.2 71.9 1.0 CG B:ASP135 3.3 71.9 1.0 CD B:GLU109 3.4 0.4 1.0 CB B:ASP135 4.3 71.9 1.0 OE1 B:GLN131 4.3 79.3 1.0 CB B:ASN106 4.3 93.1 1.0 CA B:ASP135 4.6 0.4 1.0 OG1 B:THR138 4.8 78.3 1.0 CA B:ASN106 4.8 70.6 1.0 CG B:GLU109 4.9 0.4 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: Deoxygenated 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: Deoxygenated Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca202 b:67.8 occ:1.00 ND2 F:ASN106 2.9 93.1 1.0 OE1 F:GLU109 3.1 0.4 1.0 OD1 F:ASN106 3.1 93.1 1.0 OE2 F:GLU109 3.1 0.4 1.0 CG F:ASN106 3.2 93.1 1.0 OD1 F:ASP135 3.2 71.9 1.0 OD2 F:ASP135 3.2 71.9 1.0 CG F:ASP135 3.3 71.9 1.0 CD F:GLU109 3.4 0.4 1.0 CB F:ASP135 4.3 71.9 1.0 OE1 F:GLN131 4.3 79.3 1.0 CB F:ASN106 4.3 93.1 1.0 CA F:ASP135 4.6 0.4 1.0 OG1 F:THR138 4.8 78.3 1.0 CA F:ASN106 4.8 70.6 1.0 CG F:GLU109 4.9 0.4 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