Atomistry » Calcium » PDB 3vyk-3whd » 3wcv
Atomistry »
  Calcium »
    PDB 3vyk-3whd »
      3wcv »

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

Protein crystallography data

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

Other elements in 3wcv:

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

Calcium Binding Sites:

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 3wcv

Go back to Calcium Binding Sites List in 3wcv
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 3wcv

Go back to Calcium Binding Sites List in 3wcv
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 3wcv

Go back to Calcium Binding Sites List in 3wcv
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 3wcv

Go back to Calcium Binding Sites List in 3wcv
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 3wcv

Go back to Calcium Binding Sites List in 3wcv
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 3wcv

Go back to Calcium Binding Sites List in 3wcv
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

Reference:

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
Page generated: Sat Dec 12 04:35:18 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy