Iron in PDB 7ddu: Elephant Seal Myoglobin Esmb

Protein crystallography data

The structure of Elephant Seal Myoglobin Esmb, PDB code: 7ddu was solved by Y.Isogai, H.Imamura, S.Nakae, T.Sumi, K.Takahashi, T.Shirai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.82 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.09, 29.35, 75.36, 90, 96.2, 90
R / Rfree (%) 19.9 / 20.5

Iron Binding Sites:

The binding sites of Iron atom in the Elephant Seal Myoglobin Esmb (pdb code 7ddu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Elephant Seal Myoglobin Esmb, PDB code: 7ddu:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 7ddu

Go back to Iron Binding Sites List in 7ddu
Iron binding site 1 out of 2 in the Elephant Seal Myoglobin Esmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Elephant Seal Myoglobin Esmb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:17.3
occ:1.00
FE A:HEM201 0.0 17.3 1.0
NA A:HEM201 1.9 15.1 1.0
ND A:HEM201 2.0 21.4 1.0
NB A:HEM201 2.0 15.2 1.0
NC A:HEM201 2.1 15.1 1.0
NE2 A:HIS93 2.2 17.6 1.0
O A:HOH331 2.2 20.0 1.0
C1A A:HEM201 3.0 22.5 1.0
C4A A:HEM201 3.0 17.3 1.0
C4D A:HEM201 3.0 20.1 1.0
C1D A:HEM201 3.0 15.5 1.0
C4B A:HEM201 3.1 15.1 1.0
C1B A:HEM201 3.1 14.6 1.0
C4C A:HEM201 3.1 12.3 1.0
CE1 A:HIS93 3.1 18.2 1.0
C1C A:HEM201 3.1 13.4 1.0
CD2 A:HIS93 3.2 12.0 1.0
HE1 A:HIS93 3.2 21.9 1.0
CHA A:HEM201 3.4 21.1 1.0
CHB A:HEM201 3.4 17.1 1.0
HD2 A:HIS93 3.4 14.4 1.0
CHD A:HEM201 3.4 16.2 1.0
CHC A:HEM201 3.5 12.5 1.0
HG22 A:VAL68 3.8 20.3 1.0
HE1 A:HIS64 4.1 21.2 1.0
C2A A:HEM201 4.2 19.9 1.0
C3A A:HEM201 4.2 20.1 1.0
C3D A:HEM201 4.2 21.6 1.0
C2D A:HEM201 4.2 21.6 1.0
ND1 A:HIS93 4.2 15.5 1.0
C3B A:HEM201 4.3 14.8 1.0
C2B A:HEM201 4.3 15.8 1.0
CG A:HIS93 4.3 17.9 1.0
C2C A:HEM201 4.3 14.0 1.0
C3C A:HEM201 4.3 15.6 1.0
NE2 A:HIS64 4.3 15.3 1.0
HD11 A:LEU89 4.5 35.5 1.0
CE1 A:HIS64 4.6 17.6 1.0
HZ A:PHE43 4.6 26.1 1.0
HG13 A:ILE99 4.6 17.2 1.0
CG2 A:VAL68 4.7 16.9 1.0
HE1 A:PHE43 4.7 20.0 1.0
HD2 A:HIS97 4.7 34.1 1.0
HG21 A:VAL68 4.8 20.3 1.0
HG23 A:VAL68 5.0 20.3 1.0

Iron binding site 2 out of 2 in 7ddu

Go back to Iron Binding Sites List in 7ddu
Iron binding site 2 out of 2 in the Elephant Seal Myoglobin Esmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Elephant Seal Myoglobin Esmb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:13.3
occ:1.00
FE C:HEM201 0.0 13.3 1.0
NC C:HEM201 2.0 9.4 1.0
NB C:HEM201 2.0 11.4 1.0
ND C:HEM201 2.0 14.4 1.0
NA C:HEM201 2.0 13.2 1.0
NE2 C:HIS93 2.1 13.7 1.0
O C:HOH324 2.2 18.2 1.0
C4C C:HEM201 3.0 10.8 1.0
C1D C:HEM201 3.0 15.0 1.0
C1C C:HEM201 3.0 9.8 1.0
C4B C:HEM201 3.0 11.7 1.0
C1B C:HEM201 3.0 17.1 1.0
C4A C:HEM201 3.1 12.3 1.0
C4D C:HEM201 3.1 16.0 1.0
C1A C:HEM201 3.1 12.7 1.0
CD2 C:HIS93 3.1 12.9 1.0
CE1 C:HIS93 3.1 13.1 1.0
HD2 C:HIS93 3.2 15.5 1.0
HE1 C:HIS93 3.3 15.8 1.0
CHD C:HEM201 3.3 9.7 1.0
CHC C:HEM201 3.4 13.8 1.0
CHB C:HEM201 3.4 13.6 1.0
CHA C:HEM201 3.5 17.5 1.0
HG22 C:VAL68 3.8 18.7 1.0
ND1 C:HIS93 4.2 16.4 1.0
C3C C:HEM201 4.2 10.5 1.0
CG C:HIS93 4.2 11.5 1.0
C2D C:HEM201 4.2 15.1 1.0
C2C C:HEM201 4.2 14.2 1.0
C2B C:HEM201 4.3 12.4 1.0
C3D C:HEM201 4.3 13.7 1.0
C3B C:HEM201 4.3 12.7 1.0
NE2 C:HIS64 4.3 13.7 1.0
C3A C:HEM201 4.3 13.6 1.0
C2A C:HEM201 4.3 9.7 1.0
HE1 C:HIS64 4.4 26.0 1.0
HZ C:PHE43 4.5 16.1 1.0
HD11 C:LEU89 4.5 20.5 1.0
HG13 C:ILE99 4.6 14.1 1.0
CG2 C:VAL68 4.6 15.6 1.0
HG21 C:VAL68 4.6 18.7 1.0
CE1 C:HIS64 4.7 21.6 1.0
HD2 C:HIS97 4.8 33.7 1.0
HE1 C:PHE43 4.8 20.1 1.0
HG23 C:VAL68 5.0 18.7 1.0
HD1 C:HIS93 5.0 19.7 1.0

Reference:

Y.Isogai, H.Imamura, S.Nakae, T.Sumi, K.I.Takahashi, T.Shirai. Common and Unique Strategies of Myoglobin Evolution For Deep-Sea Adaptation of Diving Mammals. Iscience V. 24 02920 2021.
ISSN: ESSN 2589-0042
PubMed: 34430810
DOI: 10.1016/J.ISCI.2021.102920
Page generated: Fri Sep 24 14:04:17 2021

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