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Iron in PDB 6ls8: The Monomeric Structure of G80A/H81A/H82A Myoglobin

Protein crystallography data

The structure of The Monomeric Structure of G80A/H81A/H82A Myoglobin, PDB code: 6ls8 was solved by S.Nagao, A.Suda, H.Kobayashi, N.Shibata, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.41 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.147, 61.490, 70.323, 78.83, 81.14, 63.12
R / Rfree (%) 21.6 / 27.4

Iron Binding Sites:

The binding sites of Iron atom in the The Monomeric Structure of G80A/H81A/H82A Myoglobin (pdb code 6ls8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the The Monomeric Structure of G80A/H81A/H82A Myoglobin, PDB code: 6ls8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6ls8

Go back to Iron Binding Sites List in 6ls8
Iron binding site 1 out of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:27.9
occ:1.00
FE A:HEM201 0.0 27.9 1.0
O A:HOH307 1.8 22.3 1.0
ND A:HEM201 2.0 24.4 1.0
NC A:HEM201 2.0 26.1 1.0
NB A:HEM201 2.0 21.6 1.0
NE2 A:HIS93 2.1 29.0 1.0
NA A:HEM201 2.1 24.1 1.0
C1C A:HEM201 3.0 21.8 1.0
C4B A:HEM201 3.0 22.5 1.0
C4D A:HEM201 3.0 25.2 1.0
CE1 A:HIS93 3.0 28.2 1.0
C1D A:HEM201 3.1 28.8 1.0
C1A A:HEM201 3.1 25.1 1.0
CD2 A:HIS93 3.1 29.3 1.0
C4C A:HEM201 3.1 25.3 1.0
C1B A:HEM201 3.1 23.7 1.0
C4A A:HEM201 3.2 25.3 1.0
CHC A:HEM201 3.3 22.0 1.0
CHA A:HEM201 3.4 25.3 1.0
CHD A:HEM201 3.5 27.6 1.0
CHB A:HEM201 3.6 26.5 1.0
ND1 A:HIS93 4.2 30.8 1.0
C2C A:HEM201 4.2 27.6 1.0
CG A:HIS93 4.2 32.7 1.0
C3D A:HEM201 4.2 32.3 1.0
C3B A:HEM201 4.3 23.6 1.0
C2D A:HEM201 4.3 28.2 1.0
C3C A:HEM201 4.3 22.6 1.0
C2A A:HEM201 4.3 25.4 1.0
C2B A:HEM201 4.3 27.1 1.0
C3A A:HEM201 4.3 22.3 1.0
NE2 A:HIS64 4.4 20.9 1.0
CG2 A:VAL68 4.7 19.2 1.0
CE1 A:HIS64 4.7 24.8 1.0
CD2 A:HIS97 5.0 30.5 1.0

Iron binding site 2 out of 6 in 6ls8

Go back to Iron Binding Sites List in 6ls8
Iron binding site 2 out of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:21.6
occ:1.00
FE C:HEM201 0.0 21.6 1.0
ND C:HEM201 2.0 26.2 1.0
O C:HOH304 2.0 26.5 1.0
NA C:HEM201 2.0 23.5 1.0
NE2 C:HIS93 2.0 28.2 1.0
NC C:HEM201 2.1 23.3 1.0
NB C:HEM201 2.1 25.4 1.0
CE1 C:HIS93 2.9 26.3 1.0
C4D C:HEM201 3.0 28.1 1.0
C1A C:HEM201 3.0 23.3 1.0
C1D C:HEM201 3.0 23.3 1.0
C4C C:HEM201 3.1 25.7 1.0
C4A C:HEM201 3.1 24.7 1.0
C1C C:HEM201 3.1 26.2 1.0
CD2 C:HIS93 3.1 24.8 1.0
C1B C:HEM201 3.2 30.0 1.0
C4B C:HEM201 3.2 27.7 1.0
CHA C:HEM201 3.4 26.4 1.0
CHD C:HEM201 3.4 21.7 1.0
CHB C:HEM201 3.5 24.9 1.0
CHC C:HEM201 3.5 26.7 1.0
ND1 C:HIS93 4.1 25.6 1.0
C2D C:HEM201 4.2 25.1 1.0
CG C:HIS93 4.2 26.2 1.0
C3D C:HEM201 4.2 27.8 1.0
C2A C:HEM201 4.2 27.1 1.0
C3A C:HEM201 4.3 27.9 1.0
C3C C:HEM201 4.3 23.8 1.0
C2C C:HEM201 4.3 27.5 1.0
NE2 C:HIS64 4.4 25.5 1.0
C2B C:HEM201 4.4 26.0 1.0
C3B C:HEM201 4.4 24.0 1.0
CG2 C:VAL68 4.5 22.5 1.0
CE1 C:HIS64 4.7 24.0 1.0
CD2 C:HIS97 4.9 31.0 1.0

Iron binding site 3 out of 6 in 6ls8

Go back to Iron Binding Sites List in 6ls8
Iron binding site 3 out of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:32.0
occ:1.00
FE E:HEM201 0.0 32.0 1.0
NE2 E:HIS93 2.0 38.1 1.0
ND E:HEM201 2.0 29.8 1.0
NC E:HEM201 2.0 29.9 1.0
NB E:HEM201 2.1 24.4 1.0
NA E:HEM201 2.1 31.7 1.0
O E:HOH304 2.1 30.9 1.0
CE1 E:HIS93 2.9 32.4 1.0
C1D E:HEM201 3.0 35.8 1.0
C4C E:HEM201 3.0 33.0 1.0
C4D E:HEM201 3.0 28.8 1.0
C1C E:HEM201 3.1 27.5 1.0
CD2 E:HIS93 3.1 29.5 1.0
C4B E:HEM201 3.1 25.2 1.0
C1A E:HEM201 3.1 28.6 1.0
C1B E:HEM201 3.1 26.8 1.0
C4A E:HEM201 3.1 25.9 1.0
CHD E:HEM201 3.3 29.5 1.0
CHA E:HEM201 3.4 33.0 1.0
CHC E:HEM201 3.5 24.1 1.0
CHB E:HEM201 3.5 26.5 1.0
ND1 E:HIS93 4.0 30.6 1.0
CG E:HIS93 4.2 33.2 1.0
C2D E:HEM201 4.2 31.2 1.0
C3C E:HEM201 4.2 29.0 1.0
C3D E:HEM201 4.2 34.6 1.0
C2C E:HEM201 4.3 29.4 1.0
C3B E:HEM201 4.3 26.4 1.0
C2A E:HEM201 4.3 28.0 1.0
C2B E:HEM201 4.3 23.9 1.0
C3A E:HEM201 4.3 22.3 1.0
NE2 E:HIS64 4.4 24.9 1.0
CE1 E:HIS64 4.6 31.9 1.0
CD2 E:HIS97 4.8 32.6 1.0
CG2 E:VAL68 4.8 24.3 1.0

Iron binding site 4 out of 6 in 6ls8

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Iron binding site 4 out of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:33.9
occ:1.00
FE G:HEM201 0.0 33.9 1.0
O G:HOH303 2.0 31.6 1.0
NC G:HEM201 2.0 24.6 1.0
ND G:HEM201 2.0 39.4 1.0
NA G:HEM201 2.0 30.0 1.0
NE2 G:HIS93 2.1 37.8 1.0
NB G:HEM201 2.1 26.6 1.0
CE1 G:HIS93 2.9 41.3 1.0
C4C G:HEM201 3.0 29.4 1.0
C1D G:HEM201 3.0 28.0 1.0
C4A G:HEM201 3.0 30.4 1.0
C1B G:HEM201 3.1 29.8 1.0
C1C G:HEM201 3.1 28.8 1.0
C4D G:HEM201 3.1 36.1 1.0
C4B G:HEM201 3.1 25.3 1.0
C1A G:HEM201 3.1 34.1 1.0
CD2 G:HIS93 3.2 36.7 1.0
CHD G:HEM201 3.4 32.7 1.0
CHB G:HEM201 3.4 33.2 1.0
CHC G:HEM201 3.5 20.6 1.0
CHA G:HEM201 3.5 29.5 1.0
ND1 G:HIS93 4.1 43.6 1.0
C2D G:HEM201 4.2 31.1 1.0
CG G:HIS93 4.2 41.0 1.0
C3C G:HEM201 4.2 29.9 1.0
C3D G:HEM201 4.3 37.1 1.0
C3A G:HEM201 4.3 26.9 1.0
C2C G:HEM201 4.3 24.5 1.0
C2B G:HEM201 4.3 29.4 1.0
C2A G:HEM201 4.3 34.1 1.0
C3B G:HEM201 4.3 30.4 1.0
NE2 G:HIS64 4.4 27.4 1.0
CG2 G:VAL68 4.5 27.4 1.0
CE1 G:HIS64 4.5 27.4 1.0
CD2 G:HIS97 4.9 38.9 1.0
CZ G:PHE43 5.0 28.3 1.0

Iron binding site 5 out of 6 in 6ls8

Go back to Iron Binding Sites List in 6ls8
Iron binding site 5 out of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:25.5
occ:1.00
FE I:HEM201 0.0 25.5 1.0
ND I:HEM201 2.0 27.5 1.0
NC I:HEM201 2.0 26.4 1.0
NE2 I:HIS93 2.1 34.0 1.0
NB I:HEM201 2.1 22.8 1.0
NA I:HEM201 2.1 29.7 1.0
O I:HOH301 2.3 35.7 1.0
CE1 I:HIS93 2.9 33.0 1.0
C1D I:HEM201 3.0 35.9 1.0
C4D I:HEM201 3.0 32.6 1.0
C4C I:HEM201 3.0 29.7 1.0
C1C I:HEM201 3.1 26.6 1.0
C4B I:HEM201 3.1 26.1 1.0
C1A I:HEM201 3.1 28.4 1.0
CD2 I:HIS93 3.1 30.8 1.0
C1B I:HEM201 3.2 28.8 1.0
C4A I:HEM201 3.2 30.8 1.0
CHD I:HEM201 3.4 34.2 1.0
CHA I:HEM201 3.4 31.8 1.0
CHC I:HEM201 3.4 18.7 1.0
CHB I:HEM201 3.6 29.6 1.0
ND1 I:HIS93 4.1 32.9 1.0
C3D I:HEM201 4.2 36.9 1.0
C2D I:HEM201 4.2 31.3 1.0
CG I:HIS93 4.2 35.7 1.0
C3C I:HEM201 4.2 27.4 1.0
C2C I:HEM201 4.3 28.9 1.0
NE2 I:HIS64 4.3 42.4 1.0
C3B I:HEM201 4.3 27.4 1.0
C2B I:HEM201 4.4 29.5 1.0
C2A I:HEM201 4.4 31.0 1.0
C3A I:HEM201 4.4 28.6 1.0
CE1 I:HIS64 4.5 37.7 1.0
CG2 I:VAL68 4.7 29.7 1.0
CZ I:PHE43 4.8 28.7 1.0
CD2 I:HIS97 4.9 33.0 1.0

Iron binding site 6 out of 6 in 6ls8

Go back to Iron Binding Sites List in 6ls8
Iron binding site 6 out of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe201

b:27.9
occ:1.00
FE K:HEM201 0.0 27.9 1.0
NE2 K:HIS93 2.0 36.8 1.0
NB K:HEM201 2.0 30.9 1.0
O K:HOH301 2.0 32.4 1.0
NC K:HEM201 2.0 41.1 1.0
ND K:HEM201 2.1 35.8 1.0
NA K:HEM201 2.1 36.3 1.0
CE1 K:HIS93 2.8 32.3 1.0
C4B K:HEM201 3.0 34.9 1.0
C1B K:HEM201 3.0 33.3 1.0
C1C K:HEM201 3.0 34.4 1.0
C1D K:HEM201 3.0 40.2 1.0
CD2 K:HIS93 3.0 35.8 1.0
C4C K:HEM201 3.0 36.5 1.0
C4A K:HEM201 3.0 37.2 1.0
C4D K:HEM201 3.1 38.1 1.0
C1A K:HEM201 3.1 31.3 1.0
CHB K:HEM201 3.4 36.8 1.0
CHC K:HEM201 3.4 33.9 1.0
CHD K:HEM201 3.4 35.6 1.0
CHA K:HEM201 3.5 34.6 1.0
ND1 K:HIS93 4.0 34.0 1.0
CG K:HIS93 4.1 35.5 1.0
NE2 K:HIS64 4.2 44.5 1.0
C3B K:HEM201 4.2 34.8 1.0
C2B K:HEM201 4.2 28.6 1.0
C2C K:HEM201 4.3 38.6 1.0
C3C K:HEM201 4.3 42.9 1.0
C2D K:HEM201 4.3 38.3 1.0
C3A K:HEM201 4.3 34.7 1.0
C3D K:HEM201 4.3 41.2 1.0
C2A K:HEM201 4.3 31.6 1.0
CE1 K:HIS64 4.5 46.9 1.0
CG2 K:VAL68 4.6 33.6 1.0
CD2 K:HIS97 4.9 31.6 1.0

Reference:

S.Nagao, A.Suda, H.Kobayashi, N.Shibata, Y.Higuchi, S.Hirota. Thermodynamic Control of Domain Swapping By Modulating Helical Propensity in the Hinge Region of Myoglobin. Chem Asian J 2020.
ISSN: ESSN 1861-471X
PubMed: 32329228
DOI: 10.1002/ASIA.202000307
Page generated: Sun Dec 13 16:40:21 2020

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