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

The structure of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form, PDB code: 3wcv 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)	36.33 / 2.60
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	108.944, 108.944, 195.016, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 26.7

The structure of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound 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: Ca Bound Form (pdb code 3wcv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 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: Ca Bound Form, PDB code: 3wcv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound 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: Ca Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:56.0 occ:0.33 O A:ASP95 4.6 40.2 1.0

Calcium binding site 2 out of 6 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound 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: Ca Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:77.7 occ:1.00 OD1 B:ASP135 2.4 71.4 1.0 OD1 B:ASN106 2.4 82.3 1.0 OE2 B:GLU109 2.4 79.5 1.0 OE1 B:GLU109 2.7 77.9 1.0 CD B:GLU109 2.9 77.8 1.0 CG B:ASN106 3.5 84.4 1.0 CG B:ASP135 3.6 68.6 1.0 OE1 B:GLN131 4.3 59.1 1.0 OG1 B:THR138 4.3 69.6 1.0 CA B:ASP135 4.3 67.1 1.0 ND2 B:ASN106 4.4 85.4 1.0 CG B:GLU109 4.4 76.5 1.0 OD2 B:ASP135 4.4 66.5 1.0 CB B:ASN106 4.5 83.8 1.0 CB B:ASP135 4.5 67.8 1.0 CA B:ASN106 4.6 83.5 1.0

Calcium binding site 3 out of 6 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form


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 A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:91.2 occ:1.00 OE2 B:GLU119 2.6 67.1 1.0 CD B:GLU119 3.5 63.3 1.0 CG B:GLU119 3.6 62.9 1.0 OE1 B:GLU119 4.6 61.3 1.0 O B:GLU119 4.7 59.2 1.0 O B:ALA18 4.9 56.1 1.0 CB B:GLU119 4.9 61.4 1.0

Calcium binding site 4 out of 6 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form


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 A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:60.6 occ:1.00 OD1 F:ASN106 2.4 66.8 1.0 OD1 F:ASP135 2.4 57.4 1.0 OE2 F:GLU109 2.5 60.4 1.0 OE1 F:GLU109 2.5 59.6 1.0 CD F:GLU109 2.8 59.1 1.0 CG F:ASN106 3.4 67.9 1.0 CG F:ASP135 3.6 57.4 1.0 CB F:ASN106 4.2 67.0 1.0 OE1 F:GLN131 4.3 60.5 1.0 CG F:GLU109 4.3 58.4 1.0 ND2 F:ASN106 4.4 67.9 1.0 OD2 F:ASP135 4.4 59.7 1.0 OG1 F:THR138 4.5 68.9 1.0 CA F:ASN106 4.5 67.0 1.0 CA F:ASP135 4.6 58.9 1.0 CB F:ASP135 4.6 58.5 1.0

Calcium binding site 5 out of 6 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form


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 A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca204 b:83.0 occ:1.00 OE2 F:GLU119 2.3 70.8 1.0 CG F:GLU119 3.1 62.4 1.0 CD F:GLU119 3.2 65.3 1.0 O F:GLU119 4.0 50.8 1.0 CB F:GLU119 4.3 55.8 1.0 OE1 F:GLU119 4.3 68.3 1.0 CA F:GLU119 4.5 52.7 1.0 O F:ALA18 4.6 46.6 1.0 C F:GLU119 4.7 50.7 1.0 O F:GLU17 4.8 48.1 1.0

Calcium binding site 6 out of 6 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form


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 A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Ca Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca205 b:81.9 occ:1.00 O F:GLY99 2.4 78.2 1.0 C F:GLY99 3.3 77.8 1.0 N F:SER101 3.9 75.6 1.0 CA F:GLY99 4.1 78.1 1.0 N F:VAL100 4.1 77.6 1.0 C F:VAL100 4.2 76.4 1.0 CA F:VAL100 4.3 76.7 1.0 OE1 F:GLN104 4.4 77.1 1.0 CB F:SER101 4.5 75.5 1.0 CA F:SER101 4.6 76.0 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