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Iron in PDB 6rko: Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution

Enzymatic activity of Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution

All present enzymatic activity of Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution:
7.1.1.7;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution (pdb code 6rko). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution, PDB code: 6rko:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 6rko

Go back to Iron Binding Sites List in 6rko
Iron binding site 1 out of 3 in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:0.4
occ:1.00
FE A:HDD603 0.0 0.4 1.0
ND A:HDD603 1.8 0.4 1.0
NA A:HDD603 2.1 0.4 1.0
NC A:HDD603 2.1 0.4 1.0
NB A:HDD603 2.1 0.4 1.0
NE2 A:HIS19 2.6 0.4 1.0
C4D A:HDD603 2.8 0.4 1.0
C1D A:HDD603 2.8 0.4 1.0
C4C A:HDD603 3.0 0.4 1.0
C1A A:HDD603 3.0 0.4 1.0
C1B A:HDD603 3.1 0.4 1.0
C4B A:HDD603 3.1 0.4 1.0
C4A A:HDD603 3.1 0.4 1.0
C1C A:HDD603 3.1 0.4 1.0
CHA A:HDD603 3.3 0.4 1.0
CHD A:HDD603 3.3 0.4 1.0
O1 A:OXY606 3.3 0.5 1.0
CHC A:HDD603 3.4 0.4 1.0
CHB A:HDD603 3.5 0.4 1.0
CD2 A:HIS19 3.5 0.4 1.0
CE1 A:HIS19 3.6 0.4 1.0
O2 A:OXY606 3.7 0.5 1.0
C3D A:HDD603 4.1 0.4 1.0
C2D A:HDD603 4.1 0.4 1.0
C3C A:HDD603 4.3 0.4 1.0
C2A A:HDD603 4.3 0.4 1.0
CZ A:PHE104 4.4 1.7 1.0
C2B A:HDD603 4.4 0.4 1.0
C3B A:HDD603 4.4 0.4 1.0
C3A A:HDD603 4.4 0.4 1.0
C2C A:HDD603 4.4 0.4 1.0
CG2 A:VAL23 4.4 2.1 1.0
OND A:HDD603 4.7 0.4 1.0
CE1 A:PHE104 4.7 1.7 1.0
CG A:HIS19 4.7 0.4 1.0
ND1 A:HIS19 4.7 0.4 1.0
CAD A:HDD603 4.7 0.4 1.0
CA A:GLY70 4.8 1.2 1.0

Iron binding site 2 out of 3 in 6rko

Go back to Iron Binding Sites List in 6rko
Iron binding site 2 out of 3 in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:0.4
occ:1.00
FE A:HEB604 0.0 0.4 1.0
NA A:HEB604 2.1 0.4 1.0
NC A:HEB604 2.1 0.4 1.0
NB A:HEB604 2.1 0.4 1.0
ND A:HEB604 2.1 0.4 1.0
OE1 A:GLU445 2.2 0.9 1.0
CD A:GLU445 3.1 0.9 1.0
C1A A:HEB604 3.1 0.4 1.0
C4A A:HEB604 3.1 0.4 1.0
C4B A:HEB604 3.1 0.4 1.0
C1C A:HEB604 3.1 0.4 1.0
C1D A:HEB604 3.1 0.4 1.0
C4C A:HEB604 3.1 0.4 1.0
C4D A:HEB604 3.1 0.4 1.0
C1B A:HEB604 3.2 0.4 1.0
CHC A:HEB604 3.4 0.4 1.0
CHA A:HEB604 3.5 0.4 1.0
CHD A:HEB604 3.5 0.4 1.0
CHB A:HEB604 3.5 0.4 1.0
CG A:GLU445 3.6 0.9 1.0
CE2 A:PHE12 3.8 0.4 1.0
OE2 A:GLU445 4.0 0.9 1.0
CD2 A:PHE12 4.1 0.4 1.0
CB A:GLU445 4.2 0.9 1.0
NH1 A:ARG448 4.2 1.0 1.0
C2A A:HEB604 4.4 0.4 1.0
C3A A:HEB604 4.4 0.4 1.0
C3C A:HEB604 4.4 0.4 1.0
C3B A:HEB604 4.4 0.4 1.0
C2D A:HEB604 4.4 0.4 1.0
C2C A:HEB604 4.5 0.4 1.0
C3D A:HEB604 4.5 0.4 1.0
C2B A:HEB604 4.5 0.4 1.0
CB A:ALA16 4.8 0.4 1.0
ND2 A:ASN148 4.9 1.7 1.0
CZ A:PHE12 5.0 0.4 1.0

Iron binding site 3 out of 3 in 6rko

Go back to Iron Binding Sites List in 6rko
Iron binding site 3 out of 3 in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:2.8
occ:1.00
FE A:HEB605 0.0 2.8 1.0
NA A:HEB605 2.1 2.8 1.0
NB A:HEB605 2.1 2.8 1.0
NC A:HEB605 2.2 2.8 1.0
ND A:HEB605 2.4 2.8 1.0
NE2 A:HIS186 2.4 1.9 1.0
SD A:MET393 2.7 2.8 1.0
C1B A:HEB605 3.2 2.8 1.0
C1A A:HEB605 3.2 2.8 1.0
C4A A:HEB605 3.2 2.8 1.0
C4B A:HEB605 3.2 2.8 1.0
C1C A:HEB605 3.2 2.8 1.0
CD2 A:HIS186 3.3 1.9 1.0
C4C A:HEB605 3.3 2.8 1.0
C4D A:HEB605 3.4 2.8 1.0
C1D A:HEB605 3.4 2.8 1.0
CE1 A:HIS186 3.5 1.9 1.0
CHB A:HEB605 3.6 2.8 1.0
CE A:MET393 3.6 2.8 1.0
CHC A:HEB605 3.6 2.8 1.0
CHA A:HEB605 3.7 2.8 1.0
CG A:MET393 3.7 2.8 1.0
CHD A:HEB605 3.8 2.8 1.0
C2B A:HEB605 4.1 2.8 1.0
C2A A:HEB605 4.1 2.8 1.0
C2C A:HEB605 4.2 2.8 1.0
C3A A:HEB605 4.2 2.8 1.0
C3B A:HEB605 4.2 2.8 1.0
C3C A:HEB605 4.4 2.8 1.0
C2D A:HEB605 4.4 2.8 1.0
CG A:HIS186 4.4 1.9 1.0
ND1 A:HIS186 4.5 1.9 1.0
OD2 A:ASP239 4.5 4.7 1.0
C3D A:HEB605 4.6 2.8 1.0

Reference:

S.Safarian, A.Hahn, D.J.Mills, M.Radloff, M.L.Eisinger, A.Nikolaev, J.Meier-Credo, F.Melin, H.Miyoshi, R.B.Gennis, J.Sakamoto, J.D.Langer, P.Hellwig, W.Kuhlbrandt, H.Michel. Active Site Rearrangement and Structural Divergence in Prokaryotic Respiratory Oxidases. Science V. 366 100 2019.
ISSN: ESSN 1095-9203
PubMed: 31604309
DOI: 10.1126/SCIENCE.AAY0967
Page generated: Sun Dec 13 17:02:28 2020

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