Atomistry » Iron » PDB 3vtj-3wg7 » 3wct
Atomistry »
  Iron »
    PDB 3vtj-3wg7 »
      3wct »

Iron in PDB 3wct: The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated 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: Oxygenated Form, PDB code: 3wct 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) 43.02 / 2.40
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 108.556, 108.556, 193.552, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 26.4

Other elements in 3wct:

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

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form (pdb code 3wct). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form, PDB code: 3wct:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 1 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:38.3
occ:1.00
FE A:HEM200 0.0 38.3 1.0
O1 A:OXY201 1.8 50.8 1.0
NA A:HEM200 2.0 36.0 1.0
NC A:HEM200 2.0 34.8 1.0
NB A:HEM200 2.0 35.3 1.0
ND A:HEM200 2.0 37.0 1.0
NE2 A:HIS94 2.1 46.1 1.0
O2 A:OXY201 2.8 56.5 1.0
C4C A:HEM200 3.0 35.5 1.0
C1D A:HEM200 3.0 34.6 1.0
C1B A:HEM200 3.0 34.4 1.0
C1C A:HEM200 3.0 35.9 1.0
C4A A:HEM200 3.0 35.5 1.0
C4D A:HEM200 3.0 39.5 1.0
C1A A:HEM200 3.0 37.3 1.0
CE1 A:HIS94 3.1 48.0 1.0
C4B A:HEM200 3.1 32.6 1.0
CD2 A:HIS94 3.2 44.8 1.0
CHB A:HEM200 3.4 34.0 1.0
CHD A:HEM200 3.4 33.8 1.0
CHA A:HEM200 3.4 38.3 1.0
CHC A:HEM200 3.4 35.1 1.0
ND1 A:HIS94 4.2 45.6 1.0
C3A A:HEM200 4.2 35.1 1.0
C2A A:HEM200 4.3 36.7 1.0
CG A:HIS94 4.3 45.3 1.0
C2B A:HEM200 4.3 33.7 1.0
C3B A:HEM200 4.3 32.1 1.0
C2C A:HEM200 4.3 35.2 1.0
C3D A:HEM200 4.3 39.1 1.0
C2D A:HEM200 4.3 37.1 1.0
C3C A:HEM200 4.3 35.4 1.0
CG2 A:VAL66 4.5 37.6 1.0
CE1 A:HIS62 4.7 33.2 1.0

Iron binding site 2 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 2 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:40.4
occ:1.00
FE B:HEM201 0.0 40.4 1.0
O1 B:OXY202 1.8 50.9 1.0
NA B:HEM201 2.0 38.0 1.0
NC B:HEM201 2.0 39.0 1.0
ND B:HEM201 2.0 40.9 1.0
NB B:HEM201 2.0 38.0 1.0
NE2 B:HIS95 2.1 51.3 1.0
O2 B:OXY202 2.8 54.3 1.0
C1D B:HEM201 3.0 41.2 1.0
C4C B:HEM201 3.0 41.1 1.0
C1C B:HEM201 3.0 40.6 1.0
C4D B:HEM201 3.0 39.8 1.0
C1B B:HEM201 3.0 37.2 1.0
C1A B:HEM201 3.0 39.1 1.0
C4A B:HEM201 3.0 37.4 1.0
CE1 B:HIS95 3.0 52.9 1.0
C4B B:HEM201 3.1 39.9 1.0
CD2 B:HIS95 3.1 53.1 1.0
CHB B:HEM201 3.4 36.1 1.0
CHD B:HEM201 3.4 40.1 1.0
CHA B:HEM201 3.4 38.9 1.0
CHC B:HEM201 3.4 39.3 1.0
ND1 B:HIS95 4.2 54.4 1.0
CG B:HIS95 4.2 56.4 1.0
C3A B:HEM201 4.3 36.9 1.0
C2A B:HEM201 4.3 37.5 1.0
C2C B:HEM201 4.3 39.5 1.0
C2B B:HEM201 4.3 38.5 1.0
C3D B:HEM201 4.3 39.5 1.0
C3B B:HEM201 4.3 40.5 1.0
C2D B:HEM201 4.3 40.5 1.0
C3C B:HEM201 4.3 41.1 1.0
CG2 B:VAL67 4.6 35.4 1.0
CE1 B:HIS63 4.7 32.4 1.0

Iron binding site 3 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 3 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:42.8
occ:1.00
FE C:HEM200 0.0 42.8 1.0
O1 C:OXY201 1.8 46.2 1.0
NA C:HEM200 2.0 42.1 1.0
NC C:HEM200 2.0 43.3 1.0
ND C:HEM200 2.0 44.2 1.0
NB C:HEM200 2.0 43.8 1.0
NE2 C:HIS99 2.1 47.6 1.0
CD2 C:HIS99 2.9 48.8 1.0
O2 C:OXY201 2.9 50.5 1.0
C4C C:HEM200 3.0 45.3 1.0
C1D C:HEM200 3.0 42.4 1.0
C4D C:HEM200 3.0 42.7 1.0
C1C C:HEM200 3.0 45.1 1.0
C1B C:HEM200 3.0 41.4 1.0
C4A C:HEM200 3.0 40.2 1.0
C1A C:HEM200 3.0 42.7 1.0
C4B C:HEM200 3.1 42.6 1.0
CE1 C:HIS99 3.2 49.2 1.0
CHD C:HEM200 3.4 43.1 1.0
CHB C:HEM200 3.4 39.1 1.0
CHA C:HEM200 3.4 42.9 1.0
CHC C:HEM200 3.4 44.2 1.0
CG C:HIS99 4.1 50.3 1.0
ND1 C:HIS99 4.2 48.8 1.0
C3A C:HEM200 4.3 41.6 1.0
C2A C:HEM200 4.3 42.5 1.0
C3D C:HEM200 4.3 45.2 1.0
C2C C:HEM200 4.3 44.0 1.0
C2B C:HEM200 4.3 43.6 1.0
C3B C:HEM200 4.3 43.6 1.0
C2D C:HEM200 4.3 45.4 1.0
C3C C:HEM200 4.3 46.6 1.0
CG2 C:VAL71 4.8 34.8 1.0
CE1 C:HIS67 4.9 36.2 1.0

Iron binding site 4 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 4 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:49.9
occ:1.00
FE D:HEM201 0.0 49.9 1.0
O1 D:OXY202 1.8 53.4 1.0
NA D:HEM201 2.0 51.4 1.0
ND D:HEM201 2.0 53.2 1.0
NC D:HEM201 2.0 52.3 1.0
NB D:HEM201 2.0 51.3 1.0
NE2 D:HIS99 2.1 55.3 1.0
O2 D:OXY202 2.7 59.1 1.0
CE1 D:HIS99 3.0 59.2 1.0
C1D D:HEM201 3.0 53.0 1.0
C4C D:HEM201 3.0 52.0 1.0
C4D D:HEM201 3.0 54.2 1.0
C4A D:HEM201 3.0 48.7 1.0
C1B D:HEM201 3.0 49.6 1.0
C1A D:HEM201 3.0 50.9 1.0
C1C D:HEM201 3.0 51.1 1.0
C4B D:HEM201 3.1 50.5 1.0
CD2 D:HIS99 3.1 58.0 1.0
CHB D:HEM201 3.3 48.6 1.0
CHD D:HEM201 3.4 52.8 1.0
CHA D:HEM201 3.4 52.5 1.0
CHC D:HEM201 3.4 50.3 1.0
ND1 D:HIS99 4.1 57.7 1.0
CG D:HIS99 4.2 58.4 1.0
C3A D:HEM201 4.2 48.6 1.0
C2A D:HEM201 4.2 50.6 1.0
C3D D:HEM201 4.3 55.8 1.0
C2B D:HEM201 4.3 51.2 1.0
C2D D:HEM201 4.3 55.5 1.0
C3B D:HEM201 4.3 51.3 1.0
C2C D:HEM201 4.3 51.5 1.0
C3C D:HEM201 4.3 53.2 1.0
CG2 D:VAL71 4.7 38.9 1.0
CE1 D:HIS67 4.9 39.0 1.0

Iron binding site 5 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 5 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:44.3
occ:1.00
FE E:HEM200 0.0 44.3 1.0
O1 E:OXY201 1.8 53.2 1.0
NC E:HEM200 2.0 41.5 1.0
NB E:HEM200 2.0 43.5 1.0
NA E:HEM200 2.0 44.2 1.0
ND E:HEM200 2.0 44.9 1.0
NE2 E:HIS94 2.1 48.9 1.0
O2 E:OXY201 2.8 57.9 1.0
C4C E:HEM200 3.0 42.8 1.0
C1C E:HEM200 3.0 43.0 1.0
C1D E:HEM200 3.0 44.0 1.0
C1B E:HEM200 3.0 43.4 1.0
C4D E:HEM200 3.0 43.5 1.0
C1A E:HEM200 3.1 45.5 1.0
C4B E:HEM200 3.1 43.2 1.0
C4A E:HEM200 3.1 44.8 1.0
CD2 E:HIS94 3.1 49.9 1.0
CE1 E:HIS94 3.1 50.5 1.0
CHD E:HEM200 3.4 42.5 1.0
CHB E:HEM200 3.4 44.2 1.0
CHA E:HEM200 3.4 45.4 1.0
CHC E:HEM200 3.4 43.9 1.0
ND1 E:HIS94 4.2 51.4 1.0
CG E:HIS94 4.2 51.0 1.0
C3A E:HEM200 4.3 47.1 1.0
C2A E:HEM200 4.3 46.7 1.0
C3B E:HEM200 4.3 43.5 1.0
C2C E:HEM200 4.3 43.0 1.0
C2B E:HEM200 4.3 44.7 1.0
C3D E:HEM200 4.3 43.2 1.0
C3C E:HEM200 4.3 44.5 1.0
C2D E:HEM200 4.3 43.7 1.0
CG2 E:VAL66 4.6 41.3 1.0
CE1 E:HIS62 4.8 35.6 1.0

Iron binding site 6 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 6 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:39.4
occ:1.00
FE F:HEM201 0.0 39.4 1.0
O1 F:OXY202 1.8 48.2 1.0
NC F:HEM201 2.0 35.4 1.0
NA F:HEM201 2.0 36.9 1.0
NB F:HEM201 2.0 37.0 1.0
ND F:HEM201 2.0 38.3 1.0
NE2 F:HIS95 2.1 45.8 1.0
O2 F:OXY202 2.9 48.3 1.0
C4C F:HEM201 3.0 36.1 1.0
CE1 F:HIS95 3.0 45.8 1.0
C1D F:HEM201 3.0 37.0 1.0
C1C F:HEM201 3.0 37.3 1.0
C1B F:HEM201 3.0 39.0 1.0
C4D F:HEM201 3.0 37.9 1.0
C4A F:HEM201 3.0 36.6 1.0
C1A F:HEM201 3.0 38.0 1.0
C4B F:HEM201 3.1 38.1 1.0
CD2 F:HIS95 3.1 46.8 1.0
CHB F:HEM201 3.4 35.5 1.0
CHD F:HEM201 3.4 35.8 1.0
CHA F:HEM201 3.4 38.5 1.0
CHC F:HEM201 3.4 36.7 1.0
ND1 F:HIS95 4.1 47.2 1.0
CG F:HIS95 4.2 48.6 1.0
C3A F:HEM201 4.3 36.4 1.0
C2C F:HEM201 4.3 37.0 1.0
C2A F:HEM201 4.3 37.6 1.0
C3D F:HEM201 4.3 37.7 1.0
C2B F:HEM201 4.3 38.6 1.0
C3B F:HEM201 4.3 39.0 1.0
C3C F:HEM201 4.3 36.3 1.0
C2D F:HEM201 4.3 39.0 1.0
CG2 F:VAL67 4.7 26.7 1.0
CE1 F:HIS63 4.9 27.2 1.0

Iron binding site 7 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 7 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe200

b:40.0
occ:1.00
FE G:HEM200 0.0 40.0 1.0
O1 G:OXY201 1.8 47.8 1.0
ND G:HEM200 2.0 43.5 1.0
NC G:HEM200 2.0 41.0 1.0
NA G:HEM200 2.0 40.3 1.0
NB G:HEM200 2.0 40.7 1.0
NE2 G:HIS99 2.1 48.7 1.0
O2 G:OXY201 2.8 50.1 1.0
CE1 G:HIS99 3.0 50.8 1.0
C1D G:HEM200 3.0 42.6 1.0
C4C G:HEM200 3.0 41.7 1.0
C4D G:HEM200 3.0 43.9 1.0
C1C G:HEM200 3.0 41.4 1.0
C1B G:HEM200 3.0 38.9 1.0
C1A G:HEM200 3.1 41.5 1.0
C4A G:HEM200 3.1 37.9 1.0
C4B G:HEM200 3.1 40.6 1.0
CD2 G:HIS99 3.1 50.9 1.0
CHD G:HEM200 3.4 41.2 1.0
CHB G:HEM200 3.4 39.1 1.0
CHA G:HEM200 3.4 43.7 1.0
CHC G:HEM200 3.4 40.3 1.0
ND1 G:HIS99 4.1 49.7 1.0
CG G:HIS99 4.2 50.8 1.0
C3A G:HEM200 4.3 41.3 1.0
C3D G:HEM200 4.3 42.7 1.0
C2A G:HEM200 4.3 40.3 1.0
C2C G:HEM200 4.3 40.2 1.0
C2D G:HEM200 4.3 43.7 1.0
C2B G:HEM200 4.3 38.3 1.0
C3B G:HEM200 4.3 39.1 1.0
C3C G:HEM200 4.3 42.4 1.0
CE1 G:HIS67 4.6 35.2 1.0
CG2 G:VAL71 4.7 38.3 1.0

Iron binding site 8 out of 8 in 3wct

Go back to Iron Binding Sites List in 3wct
Iron binding site 8 out of 8 in the The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of A Deoxygenated 400 kDa Hemoglobin Provides A More Accurate Description of the Cooperative Mechanism of Giant Hemoglobins: Oxygenated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:47.8
occ:1.00
FE H:HEM201 0.0 47.8 1.0
O1 H:OXY202 1.8 52.0 1.0
NA H:HEM201 2.0 48.9 1.0
NC H:HEM201 2.0 46.7 1.0
ND H:HEM201 2.0 48.4 1.0
NB H:HEM201 2.0 48.0 1.0
NE2 H:HIS99 2.1 55.4 1.0
O2 H:OXY202 2.8 55.4 1.0
C1D H:HEM201 3.0 47.1 1.0
C4C H:HEM201 3.0 46.5 1.0
CE1 H:HIS99 3.0 56.1 1.0
C4D H:HEM201 3.0 48.6 1.0
C1C H:HEM201 3.0 46.2 1.0
C4A H:HEM201 3.0 48.2 1.0
C1B H:HEM201 3.0 45.6 1.0
C1A H:HEM201 3.1 49.6 1.0
C4B H:HEM201 3.1 46.6 1.0
CD2 H:HIS99 3.1 59.1 1.0
CHD H:HEM201 3.4 46.7 1.0
CHB H:HEM201 3.4 46.2 1.0
CHA H:HEM201 3.4 49.5 1.0
CHC H:HEM201 3.4 46.7 1.0
ND1 H:HIS99 4.1 58.0 1.0
CG H:HIS99 4.2 60.5 1.0
C3A H:HEM201 4.3 49.5 1.0
C2A H:HEM201 4.3 50.9 1.0
C3D H:HEM201 4.3 49.0 1.0
C2C H:HEM201 4.3 45.9 1.0
C2D H:HEM201 4.3 49.1 1.0
C3B H:HEM201 4.3 46.1 1.0
C2B H:HEM201 4.3 46.7 1.0
C3C H:HEM201 4.3 46.5 1.0
CG2 H:VAL71 4.6 40.9 1.0
CE1 H:HIS67 5.0 37.8 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: Sun Dec 13 15:25:42 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