Magnesium in PDB 3wcw: The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Mg 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: Mg Bound Form, PDB code: 3wcw 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)	43.44 / 2.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	109.273, 109.273, 195.599, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 25.9

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

Iron

(Fe)

8 atoms

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

Magnesium binding site 1 out of 3 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Mg Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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: Mg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:2.0 occ:0.33 O A:HOH341 2.1 20.9 1.0 O A:HOH328 2.1 20.5 1.0 O A:HOH330 4.1 27.2 1.0 O A:HOH308 4.2 21.5 1.0 OD2 A:ASP95 4.4 25.4 1.0 O A:HOH303 4.4 19.3 1.0 CG A:ASP95 4.6 25.4 1.0 CB A:ASP95 4.8 24.7 1.0 O A:HOH342 4.9 28.9 0.3

Magnesium binding site 2 out of 3 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Mg Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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: Mg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:58.0 occ:1.00 OE2 B:GLU109 2.1 55.4 1.0 OD1 B:ASN106 2.1 55.9 1.0 OD1 B:ASP135 2.1 58.9 1.0 OD2 B:ASP135 2.4 60.3 1.0 CG B:ASP135 2.6 58.7 1.0 CD B:GLU109 2.8 52.5 1.0 OE1 B:GLU109 2.8 53.1 1.0 CG B:ASN106 3.4 55.4 1.0 CB B:ASP135 4.1 53.6 1.0 ND2 B:ASN106 4.2 56.3 1.0 CG B:GLU109 4.2 50.3 1.0 CB B:ASN106 4.4 53.5 1.0 CA B:ASN106 4.5 53.6 1.0 CA B:ASP135 4.6 48.9 1.0 OG1 B:THR138 4.7 47.9 1.0 CB B:GLU109 4.8 48.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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: Mg Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:59.7 occ:1.00 OD1 F:ASP135 2.1 57.7 1.0 OD1 F:ASN106 2.1 59.9 1.0 OE2 F:GLU109 2.1 58.1 1.0 CD F:GLU109 2.8 54.4 1.0 OE1 F:GLU109 2.9 55.5 1.0 CG F:ASP135 3.0 54.6 1.0 OD2 F:ASP135 3.4 59.9 1.0 CG F:ASN106 3.4 58.4 1.0 ND2 F:ASN106 4.2 59.1 1.0 CB F:ASP135 4.2 51.3 1.0 OG1 F:THR138 4.2 50.0 1.0 CG F:GLU109 4.3 51.1 1.0 CB F:ASN106 4.4 55.5 1.0 CA F:ASN106 4.5 53.1 1.0 CA F:ASP135 4.5 48.4 1.0 CB F:GLU109 5.0 47.4 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