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Iron in PDB 6l1x: Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex.

Enzymatic activity of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex.

All present enzymatic activity of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex.:
1.7.99.7;

Protein crystallography data

The structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex., PDB code: 6l1x was solved by M.M.A.Jamali, S.V.Antonyuk, T.Tosha, K.Muramoto, S.S.Hasnain, Y.Shiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.92 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.120, 116.680, 123.550, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 30.3

Other elements in 6l1x:

The structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex. also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex. (pdb code 6l1x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex., PDB code: 6l1x:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 6l1x

Go back to Iron Binding Sites List in 6l1x
Iron binding site 1 out of 3 in the Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:73.6
occ:1.00
 FE A:HEM801 0.0 73.6 1.0
NE2 A:HIS635 1.9 79.4 1.0
ND A:HEM801 1.9 70.4 1.0
NE2 A:HIS335 1.9 77.2 1.0
NA A:HEM801 2.0 69.2 1.0
NC A:HEM801 2.1 71.5 1.0
NB A:HEM801 2.1 73.3 1.0
CE1 A:HIS635 2.7 84.2 1.0
CE1 A:HIS335 2.9 75.9 1.0
C4D A:HEM801 2.9 69.1 1.0
C1D A:HEM801 2.9 65.4 1.0
C1A A:HEM801 2.9 72.5 1.0
CD2 A:HIS335 2.9 77.2 1.0
CD2 A:HIS635 2.9 77.1 1.0
C4A A:HEM801 3.0 71.0 1.0
C4C A:HEM801 3.1 68.9 1.0
C1B A:HEM801 3.1 73.3 1.0
C4B A:HEM801 3.1 74.0 1.0
C1C A:HEM801 3.2 71.9 1.0
CHA A:HEM801 3.3 70.6 1.0
CHD A:HEM801 3.4 65.0 1.0
CHB A:HEM801 3.5 70.7 1.0
CHC A:HEM801 3.5 73.8 1.0
ND1 A:HIS635 3.8 81.9 1.0
CG A:HIS635 4.0 74.3 1.0
ND1 A:HIS335 4.0 73.8 1.0
CG A:HIS335 4.0 76.5 1.0
C2A A:HEM801 4.1 75.7 1.0
C3A A:HEM801 4.1 75.2 1.0
C3D A:HEM801 4.1 65.1 1.0
C2D A:HEM801 4.2 63.7 1.0
C3C A:HEM801 4.3 71.3 1.0
C2B A:HEM801 4.3 77.0 1.0
C2C A:HEM801 4.3 69.4 1.0
C3B A:HEM801 4.4 74.1 1.0
NH2 A:ARG724 4.6 0.8 1.0

Iron binding site 2 out of 3 in 6l1x

Go back to Iron Binding Sites List in 6l1x
Iron binding site 2 out of 3 in the Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:75.3
occ:1.00
 FE A:HEM802 0.0 75.3 1.0
ND A:HEM802 1.9 76.3 1.0
NE2 A:HIS633 1.9 67.8 1.0
NA A:HEM802 2.0 82.0 1.0
O A:HOH901 2.0 65.9 1.0
NC A:HEM802 2.1 80.1 1.0
NB A:HEM802 2.1 85.9 1.0
C1D A:HEM802 2.9 76.9 1.0
CD2 A:HIS633 2.9 64.3 1.0
C4D A:HEM802 2.9 74.4 1.0
CE1 A:HIS633 2.9 64.2 1.0
C1A A:HEM802 3.0 77.1 1.0
C4C A:HEM802 3.0 83.4 1.0
C4A A:HEM802 3.1 83.3 1.0
C1B A:HEM802 3.1 87.5 1.0
C4B A:HEM802 3.1 91.7 1.0
C1C A:HEM802 3.1 85.4 1.0
CHD A:HEM802 3.3 81.7 1.0
CHA A:HEM802 3.3 75.9 1.0
CHB A:HEM802 3.5 86.2 1.0
CHC A:HEM802 3.5 90.4 1.0
FE A:FE803 3.8 62.2 1.0
ND1 A:HIS633 4.0 63.5 1.0
CG A:HIS633 4.0 63.9 1.0
C2D A:HEM802 4.1 74.1 1.0
C3D A:HEM802 4.1 71.6 1.0
C2A A:HEM802 4.2 76.2 1.0
C3A A:HEM802 4.2 77.2 1.0
C3C A:HEM802 4.3 85.1 1.0
C2C A:HEM802 4.3 84.1 1.0
C2B A:HEM802 4.3 91.6 1.0
C3B A:HEM802 4.4 95.1 1.0
NE2 A:HIS541 4.5 75.7 1.0
CE1 A:HIS542 4.5 61.5 1.0
NE2 A:HIS542 4.8 63.0 1.0

Iron binding site 3 out of 3 in 6l1x

Go back to Iron Binding Sites List in 6l1x
Iron binding site 3 out of 3 in the Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Neisseria Meningitidis in the Monomeric Oxidized State with Zinc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:62.2
occ:1.00
 NE2 A:HIS541 1.9 75.7 1.0
ND1 A:HIS490 1.9 66.1 1.0
NE2 A:HIS542 1.9 63.0 1.0
O A:HOH901 2.0 65.9 1.0
CE1 A:HIS490 2.4 62.3 1.0
CE1 A:HIS542 2.8 61.5 1.0
CE1 A:HIS541 2.8 79.4 1.0
CD2 A:HIS542 3.0 65.6 1.0
CD2 A:HIS541 3.0 75.7 1.0
CG A:HIS490 3.2 67.4 1.0
NE2 A:HIS490 3.7 60.5 1.0
FE A:HEM802 3.8 75.3 1.0
ND A:HEM802 3.8 76.3 1.0
ND1 A:HIS542 3.9 65.1 1.0
CB A:HIS490 3.9 76.2 1.0
ND1 A:HIS541 4.0 75.4 1.0
C1D A:HEM802 4.0 76.9 1.0
CG A:HIS542 4.0 66.1 1.0
NC A:HEM802 4.0 80.1 1.0
CD2 A:HIS490 4.0 60.3 1.0
CG A:HIS541 4.0 69.2 1.0
CHD A:HEM802 4.2 81.7 1.0
C4C A:HEM802 4.3 83.4 1.0
C4D A:HEM802 4.4 74.4 1.0
NA A:HEM802 4.5 82.0 1.0
NB A:HEM802 4.7 85.9 1.0
C2D A:HEM802 4.8 74.1 1.0
C1C A:HEM802 4.9 85.4 1.0
CA A:HIS490 4.9 78.5 1.0
CHA A:HEM802 4.9 75.9 1.0
C3D A:HEM802 5.0 71.6 1.0
O A:THR539 5.0 76.3 1.0

Reference:

M.M.A.Jamali, C.C.Gopalasingam, R.M.Johnson, T.Tosha, K.Muramoto, S.P.Muench, S.V.Antonyuk, Y.Shiro, S.S.Hasnain. The Active Form of Quinol-Dependent Nitric Oxide Reductase From Neisseria Meningitidis Is A Dimer Iucrj V. 7 2020.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252520003656
Page generated: Wed Aug 7 00:29:50 2024

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