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Iron in PDB 2w72: Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe

Protein crystallography data

The structure of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe, PDB code: 2w72 was solved by A.E.Miele, F.Draghi, G.Sciara, K.A.Johnson, F.Renzi, B.Vallone, M.Brunori, C.Savino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.32 / 1.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.957, 82.447, 53.531, 90.00, 99.60, 90.00
R / Rfree (%) 12.9 / 15.3

Other elements in 2w72:

The structure of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe also contains other interesting chemical elements:

Potassium (K) 3 atoms
Xenon (Xe) 23 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe (pdb code 2w72). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe, PDB code: 2w72:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2w72

Go back to Iron Binding Sites List in 2w72
Iron binding site 1 out of 4 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1142

b:7.4
occ:1.00
FE A:HEM1142 0.0 7.4 1.0
ND A:HEM1142 2.1 7.7 1.0
NB A:HEM1142 2.1 7.6 1.0
NC A:HEM1142 2.1 7.3 1.0
NA A:HEM1142 2.1 8.4 1.0
NE2 A:HIS87 2.2 7.3 1.0
CE1 A:HIS87 3.0 7.4 1.0
C1B A:HEM1142 3.1 8.5 1.0
C1D A:HEM1142 3.1 8.0 1.0
C4B A:HEM1142 3.1 7.8 1.0
C1C A:HEM1142 3.1 7.4 1.0
C4A A:HEM1142 3.1 8.6 1.0
C4C A:HEM1142 3.1 7.3 1.0
C4D A:HEM1142 3.1 8.2 1.0
C1A A:HEM1142 3.1 8.6 1.0
CD2 A:HIS87 3.3 7.7 1.0
CHB A:HEM1142 3.4 8.6 1.0
CHD A:HEM1142 3.4 7.8 1.0
CHC A:HEM1142 3.5 7.6 1.0
CHA A:HEM1142 3.5 9.0 1.0
NE2 A:GLN58 3.9 11.4 1.0
OH A:TYR29 3.9 10.8 1.0
ND1 A:HIS87 4.2 7.8 1.0
C2D A:HEM1142 4.3 8.8 1.0
C3B A:HEM1142 4.3 8.0 1.0
C2B A:HEM1142 4.3 8.9 1.0
C3D A:HEM1142 4.3 9.5 1.0
C2C A:HEM1142 4.3 7.5 1.0
C3C A:HEM1142 4.3 7.7 1.0
C3A A:HEM1142 4.3 9.3 1.0
C2A A:HEM1142 4.4 9.2 1.0
CG A:HIS87 4.4 7.2 1.0
CD1 A:LEU91 4.4 9.0 1.0
CG2 A:VAL62 4.7 11.9 1.0

Iron binding site 2 out of 4 in 2w72

Go back to Iron Binding Sites List in 2w72
Iron binding site 2 out of 4 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1147

b:7.9
occ:1.00
FE B:HEM1147 0.0 7.9 1.0
NA B:HEM1147 2.0 8.2 1.0
ND B:HEM1147 2.1 8.0 1.0
NB B:HEM1147 2.1 8.2 1.0
NC B:HEM1147 2.1 7.7 1.0
NE2 B:HIS92 2.1 7.7 1.0
CE1 B:HIS92 3.1 7.7 1.0
C1D B:HEM1147 3.1 7.8 1.0
C4A B:HEM1147 3.1 8.7 1.0
C1B B:HEM1147 3.1 8.3 1.0
C4D B:HEM1147 3.1 8.9 1.0
C1A B:HEM1147 3.1 9.0 1.0
C4B B:HEM1147 3.1 7.7 1.0
C4C B:HEM1147 3.1 7.5 1.0
C1C B:HEM1147 3.1 7.6 1.0
CD2 B:HIS92 3.2 8.0 1.0
CHD B:HEM1147 3.4 8.4 1.0
CHB B:HEM1147 3.4 9.0 1.0
CHA B:HEM1147 3.4 9.4 1.0
CHC B:HEM1147 3.5 7.9 1.0
CG2 B:VAL67 4.1 9.9 1.0
NE2 B:GLN63 4.1 12.9 1.0
ND1 B:HIS92 4.2 8.4 1.0
C2B B:HEM1147 4.3 8.7 1.0
C2D B:HEM1147 4.3 9.2 1.0
C3B B:HEM1147 4.3 9.6 1.0
C3A B:HEM1147 4.3 10.1 1.0
C2A B:HEM1147 4.3 9.8 1.0
C3C B:HEM1147 4.3 7.4 1.0
C3D B:HEM1147 4.3 9.0 1.0
C2C B:HEM1147 4.3 8.0 1.0
CG B:HIS92 4.3 7.8 1.0
OH B:TYR28 4.7 15.7 1.0
CD1 B:LEU96 4.8 10.2 1.0

Iron binding site 3 out of 4 in 2w72

Go back to Iron Binding Sites List in 2w72
Iron binding site 3 out of 4 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1142

b:8.3
occ:1.00
FE C:HEM1142 0.0 8.3 1.0
NB C:HEM1142 2.1 8.5 1.0
NA C:HEM1142 2.1 9.2 1.0
ND C:HEM1142 2.1 8.8 1.0
NC C:HEM1142 2.1 7.9 1.0
CE1 C:HIS87 2.2 9.3 0.8
NE2 C:HIS87 2.2 4.4 0.2
NE2 C:HIS87 3.0 13.6 0.8
C1D C:HEM1142 3.1 8.3 1.0
C1B C:HEM1142 3.1 9.1 1.0
C4B C:HEM1142 3.1 8.6 1.0
C4A C:HEM1142 3.1 10.1 1.0
C1C C:HEM1142 3.1 8.3 1.0
C4C C:HEM1142 3.1 7.6 1.0
C1A C:HEM1142 3.1 9.6 1.0
C4D C:HEM1142 3.1 8.8 1.0
CE1 C:HIS87 3.2 4.6 0.2
CD2 C:HIS87 3.3 3.7 0.2
ND1 C:HIS87 3.4 12.3 0.8
CHB C:HEM1142 3.4 9.7 1.0
CHC C:HEM1142 3.4 9.1 1.0
CHD C:HEM1142 3.4 9.0 1.0
CHA C:HEM1142 3.5 9.9 1.0
OH C:TYR29 3.9 10.3 1.0
NE2 C:GLN58 3.9 11.0 1.0
CD2 C:HIS87 4.2 9.6 0.8
C3B C:HEM1142 4.3 9.9 1.0
C2D C:HEM1142 4.3 9.0 1.0
ND1 C:HIS87 4.3 5.0 0.2
C3A C:HEM1142 4.3 11.2 1.0
C2B C:HEM1142 4.3 9.7 1.0
C2C C:HEM1142 4.3 8.1 1.0
C2A C:HEM1142 4.3 10.9 1.0
C3C C:HEM1142 4.3 8.1 1.0
C3D C:HEM1142 4.4 9.5 1.0
CG C:HIS87 4.4 5.6 0.2
CG C:HIS87 4.4 9.6 0.8
CD1 C:LEU91 4.4 11.1 1.0
CG2 C:VAL62 4.9 11.9 1.0

Iron binding site 4 out of 4 in 2w72

Go back to Iron Binding Sites List in 2w72
Iron binding site 4 out of 4 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1147

b:7.2
occ:1.00
FE D:HEM1147 0.0 7.2 1.0
NA D:HEM1147 2.1 7.7 1.0
ND D:HEM1147 2.1 7.3 1.0
NB D:HEM1147 2.1 7.2 1.0
NC D:HEM1147 2.1 7.1 1.0
NE2 D:HIS92 2.1 7.5 1.0
CE1 D:HIS92 3.1 8.4 1.0
C1B D:HEM1147 3.1 7.4 1.0
C4A D:HEM1147 3.1 7.7 1.0
C1D D:HEM1147 3.1 7.5 1.0
C4D D:HEM1147 3.1 7.6 1.0
C1A D:HEM1147 3.1 7.8 1.0
C1C D:HEM1147 3.1 7.5 1.0
C4C D:HEM1147 3.1 7.6 1.0
C4B D:HEM1147 3.1 7.3 1.0
CD2 D:HIS92 3.2 7.6 1.0
CHB D:HEM1147 3.4 7.9 1.0
CHD D:HEM1147 3.4 7.8 1.0
CHC D:HEM1147 3.4 8.0 1.0
CHA D:HEM1147 3.4 8.4 1.0
CG2 D:VAL67 4.0 8.9 1.0
NE2 D:GLN63 4.1 9.3 1.0
ND1 D:HIS92 4.2 8.2 1.0
C3B D:HEM1147 4.3 7.9 1.0
C2D D:HEM1147 4.3 8.0 1.0
C2B D:HEM1147 4.3 7.7 1.0
C3C D:HEM1147 4.3 7.8 1.0
C3A D:HEM1147 4.3 8.8 1.0
C2C D:HEM1147 4.3 8.1 1.0
C2A D:HEM1147 4.3 9.0 1.0
C3D D:HEM1147 4.3 7.9 1.0
CG D:HIS92 4.3 7.5 1.0
CD1 D:LEU96 4.8 9.9 1.0
OH D:TYR28 5.0 11.2 1.0

Reference:

C.Savino, A.E.Miele, F.Draghi, K.A.Johnson, G.Sciara, M.Brunori, B.Vallone. Pattern of Cavities in Globins: the Case of Human Hemoglobin. Biopolymers V. 91 1097 2009.
ISSN: ISSN 0006-3525
PubMed: 19365817
DOI: 10.1002/BIP.21201
Page generated: Sun Dec 13 14:55:09 2020

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