Atomistry » Calcium » PDB 7uww-7vmj » 7vld
Atomistry »
  Calcium »
    PDB 7uww-7vmj »
      7vld »

Calcium in PDB 7vld: Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation

Protein crystallography data

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation, PDB code: 7vld was solved by N.Numoto, S.Onoda, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 2.10
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 110.263, 110.263, 196.968, 90, 90, 120
R / Rfree (%) 19 / 22.1

Other elements in 7vld:

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation (pdb code 7vld). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation, PDB code: 7vld:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7vld

Go back to Calcium Binding Sites List in 7vld
Calcium binding site 1 out of 2 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:44.5
occ:1.00
OD1 B:ASP135 2.4 37.9 1.0
O B:HOH352 2.4 42.0 1.0
O B:HOH371 2.4 45.8 1.0
OD1 B:ASN106 2.4 37.4 1.0
OE1 B:GLU109 2.5 40.9 1.0
OE2 B:GLU109 2.5 38.1 1.0
O B:HOH396 2.5 47.5 1.0
CD B:GLU109 2.8 37.4 1.0
CG B:ASN106 3.5 45.8 1.0
CG B:ASP135 3.5 39.6 1.0
O B:HOH325 4.0 44.5 1.0
OE1 B:GLN131 4.1 41.3 1.0
OG1 B:THR138 4.2 36.9 1.0
OD2 B:ASP135 4.2 41.6 1.0
O B:HOH349 4.2 38.2 1.0
ND2 B:ASN106 4.2 39.9 1.0
CG B:GLU109 4.3 36.9 1.0
CA B:ASP135 4.5 35.6 1.0
CB B:ASP135 4.5 33.7 1.0
CB B:ASN106 4.5 34.3 1.0
CA B:ASN106 4.6 35.6 1.0

Calcium binding site 2 out of 2 in 7vld

Go back to Calcium Binding Sites List in 7vld
Calcium binding site 2 out of 2 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca203

b:41.6
occ:1.00
OD1 F:ASP135 2.4 33.3 1.0
OE1 F:GLU109 2.4 37.2 1.0
O F:HOH356 2.4 44.8 1.0
OD1 F:ASN106 2.4 40.4 1.0
O F:HOH386 2.4 42.7 1.0
O F:HOH392 2.5 41.7 1.0
OE2 F:GLU109 2.5 42.8 1.0
CD F:GLU109 2.8 40.5 1.0
CG F:ASN106 3.4 41.4 1.0
CG F:ASP135 3.5 35.2 1.0
NE2 F:GLN131 4.1 44.7 1.0
O F:HOH360 4.1 43.8 1.0
ND2 F:ASN106 4.2 40.4 1.0
O F:HOH368 4.2 35.4 1.0
OD2 F:ASP135 4.3 37.2 1.0
OG1 F:THR138 4.3 34.2 1.0
CG F:GLU109 4.3 37.1 1.0
CB F:ASN106 4.4 41.2 1.0
CA F:ASN106 4.5 36.3 1.0
CA F:ASP135 4.5 36.3 1.0
CB F:ASP135 4.5 30.4 1.0
O F:HOH394 4.8 54.2 1.0
CB F:GLU109 5.0 36.4 1.0
N F:ASN106 5.0 39.4 1.0

Reference:

N.Numoto, S.Onoda, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito. Structures of Oxygen Dissociation Intermediates of 400 kDa V2 Hemoglobin Provide Coarse Snapshots of the Protein Allostery. Biophys Physicobio. V. 19 1 2022.
ISSN: ESSN 2189-4779
PubMed: 35797404
DOI: 10.2142/BIOPHYSICO.BPPB-V19.0019
Page generated: Thu Jul 10 01:59:35 2025

Last articles

Zn in 3MPG
Zn in 3MP2
Zn in 3MKV
Zn in 3MNU
Zn in 3MNK
Zn in 3MNJ
Zn in 3MMK
Zn in 3MND
Zn in 3MNI
Zn in 3MNH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy