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Iron in PDB 6l3h: Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis

Enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis

All present enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis:
1.7.99.7;

Other elements in 6l3h:

The structure of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis (pdb code 6l3h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis, PDB code: 6l3h:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6l3h

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Iron binding site 1 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis


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 Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:31.2
occ:1.00
 FE A:HEM801 0.0 31.2 1.0
NC A:HEM801 2.0 31.2 1.0
NB A:HEM801 2.0 31.2 1.0
ND A:HEM801 2.0 31.2 1.0
NA A:HEM801 2.0 31.2 1.0
NE2 A:HIS335 2.5 31.6 1.0
NE2 A:HIS635 2.5 28.0 1.0
CE1 A:HIS335 3.0 31.6 1.0
CD2 A:HIS635 3.0 28.0 1.0
C1C A:HEM801 3.0 31.2 1.0
C4B A:HEM801 3.0 31.2 1.0
C4D A:HEM801 3.0 31.2 1.0
C1D A:HEM801 3.0 31.2 1.0
C1A A:HEM801 3.1 31.2 1.0
C4C A:HEM801 3.1 31.2 1.0
C1B A:HEM801 3.1 31.2 1.0
C4A A:HEM801 3.1 31.2 1.0
CHC A:HEM801 3.4 31.2 1.0
CHA A:HEM801 3.4 31.2 1.0
CHD A:HEM801 3.4 31.2 1.0
CHB A:HEM801 3.4 31.2 1.0
CE1 A:HIS635 3.7 28.0 1.0
CD2 A:HIS335 3.8 31.6 1.0
C2C A:HEM801 4.2 31.2 1.0
C2D A:HEM801 4.2 31.2 1.0
C3D A:HEM801 4.2 31.2 1.0
ND1 A:HIS335 4.2 31.6 1.0
C3B A:HEM801 4.3 31.2 1.0
CG A:HIS635 4.3 28.0 1.0
C3C A:HEM801 4.3 31.2 1.0
C2B A:HEM801 4.3 31.2 1.0
C2A A:HEM801 4.3 31.2 1.0
C3A A:HEM801 4.3 31.2 1.0
ND1 A:HIS635 4.6 28.0 1.0
CG A:HIS335 4.6 31.6 1.0
NH2 A:ARG724 5.0 43.5 1.0
NE2 A:GLN294 5.0 34.2 1.0

Iron binding site 2 out of 6 in 6l3h

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Iron binding site 2 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis


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 Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:31.2
occ:1.00
 FE A:HEM802 0.0 31.2 1.0
NA A:HEM802 2.0 31.2 1.0
NB A:HEM802 2.0 31.2 1.0
ND A:HEM802 2.0 31.2 1.0
NC A:HEM802 2.1 31.2 1.0
NE2 A:HIS633 2.5 27.5 1.0
C4D A:HEM802 3.0 31.2 1.0
C1C A:HEM802 3.0 31.2 1.0
C1A A:HEM802 3.0 31.2 1.0
C4A A:HEM802 3.1 31.2 1.0
C1B A:HEM802 3.1 31.2 1.0
C4B A:HEM802 3.1 31.2 1.0
C1D A:HEM802 3.1 31.2 1.0
C4C A:HEM802 3.1 31.2 1.0
CD2 A:HIS633 3.4 27.5 1.0
CHA A:HEM802 3.4 31.2 1.0
CHC A:HEM802 3.4 31.2 1.0
CHB A:HEM802 3.4 31.2 1.0
CHD A:HEM802 3.5 31.2 1.0
CE1 A:HIS633 3.5 27.5 1.0
OE1 A:GLU494 3.8 37.7 1.0
FE A:FE803 3.9 35.2 1.0
C3D A:HEM802 4.2 31.2 1.0
CD A:GLU494 4.2 37.7 1.0
C2A A:HEM802 4.2 31.2 1.0
C2C A:HEM802 4.2 31.2 1.0
C2D A:HEM802 4.3 31.2 1.0
C3A A:HEM802 4.3 31.2 1.0
C2B A:HEM802 4.3 31.2 1.0
C3B A:HEM802 4.3 31.2 1.0
C3C A:HEM802 4.3 31.2 1.0
OE2 A:GLU494 4.4 37.7 1.0
CG A:HIS633 4.5 27.5 1.0
ND1 A:HIS633 4.6 27.5 1.0
CE1 A:HIS542 4.7 30.6 1.0
NE2 A:HIS542 4.9 30.6 1.0
NE2 A:HIS541 4.9 31.1 1.0

Iron binding site 3 out of 6 in 6l3h

Go back to Iron Binding Sites List in 6l3h
Iron binding site 3 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis


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 Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:35.2
occ:1.00
 ND1 A:HIS490 2.0 34.5 1.0
OE1 A:GLU494 2.2 37.7 1.0
NE2 A:HIS542 2.4 30.6 1.0
NE2 A:HIS541 2.5 31.1 1.0
CE1 A:HIS490 2.7 34.5 1.0
CE1 A:HIS541 2.8 31.1 1.0
CD A:GLU494 2.9 37.7 1.0
OE2 A:GLU494 3.0 37.7 1.0
CG A:HIS490 3.3 34.5 1.0
CD2 A:HIS542 3.3 30.6 1.0
CE1 A:HIS542 3.4 30.6 1.0
CD2 A:HIS541 3.8 31.1 1.0
CB A:HIS490 3.9 34.5 1.0
NE2 A:HIS490 3.9 34.5 1.0
FE A:HEM802 3.9 31.2 1.0
ND1 A:HIS541 4.0 31.1 1.0
CD2 A:HIS490 4.2 34.5 1.0
NC A:HEM802 4.2 31.2 1.0
ND A:HEM802 4.3 31.2 1.0
CG A:GLU494 4.4 37.7 1.0
CG A:HIS542 4.4 30.6 1.0
ND1 A:HIS542 4.5 30.6 1.0
C1D A:HEM802 4.5 31.2 1.0
C4C A:HEM802 4.5 31.2 1.0
CG A:HIS541 4.6 31.1 1.0
CA A:HIS490 4.7 34.5 1.0
CHD A:HEM802 4.7 31.2 1.0
C1C A:HEM802 4.7 31.2 1.0
C4D A:HEM802 4.8 31.2 1.0
CB A:GLU494 4.8 37.7 1.0
OE2 A:GLU563 4.9 37.8 1.0
O A:GLY538 4.9 36.1 1.0
NA A:HEM802 4.9 31.2 1.0
NB A:HEM802 5.0 31.2 1.0

Iron binding site 4 out of 6 in 6l3h

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:31.1
occ:1.00
 FE B:HEM801 0.0 31.1 1.0
NC B:HEM801 2.0 31.1 1.0
NB B:HEM801 2.0 31.1 1.0
ND B:HEM801 2.0 31.1 1.0
NA B:HEM801 2.0 31.1 1.0
NE2 B:HIS335 2.5 31.5 1.0
NE2 B:HIS635 2.5 28.0 1.0
CE1 B:HIS335 3.0 31.5 1.0
CD2 B:HIS635 3.0 28.0 1.0
C1C B:HEM801 3.0 31.1 1.0
C4B B:HEM801 3.0 31.1 1.0
C4D B:HEM801 3.0 31.1 1.0
C1D B:HEM801 3.0 31.1 1.0
C1A B:HEM801 3.1 31.1 1.0
C4C B:HEM801 3.1 31.1 1.0
C1B B:HEM801 3.1 31.1 1.0
C4A B:HEM801 3.1 31.1 1.0
CHC B:HEM801 3.4 31.1 1.0
CHA B:HEM801 3.4 31.1 1.0
CHD B:HEM801 3.4 31.1 1.0
CHB B:HEM801 3.4 31.1 1.0
CE1 B:HIS635 3.7 28.0 1.0
CD2 B:HIS335 3.8 31.5 1.0
C2C B:HEM801 4.2 31.1 1.0
C2D B:HEM801 4.2 31.1 1.0
C3D B:HEM801 4.2 31.1 1.0
ND1 B:HIS335 4.2 31.5 1.0
C3B B:HEM801 4.3 31.1 1.0
CG B:HIS635 4.3 28.0 1.0
C3C B:HEM801 4.3 31.1 1.0
C2B B:HEM801 4.3 31.1 1.0
C2A B:HEM801 4.3 31.1 1.0
C3A B:HEM801 4.3 31.1 1.0
ND1 B:HIS635 4.6 28.0 1.0
CG B:HIS335 4.6 31.5 1.0
NH2 B:ARG724 5.0 43.7 1.0
NE2 B:GLN294 5.0 34.1 1.0

Iron binding site 5 out of 6 in 6l3h

Go back to Iron Binding Sites List in 6l3h
Iron binding site 5 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:31.2
occ:1.00
 FE B:HEM802 0.0 31.2 1.0
NA B:HEM802 2.0 31.2 1.0
NB B:HEM802 2.0 31.2 1.0
ND B:HEM802 2.0 31.2 1.0
NC B:HEM802 2.0 31.2 1.0
NE2 B:HIS633 2.5 27.5 1.0
C4D B:HEM802 3.0 31.2 1.0
C1C B:HEM802 3.0 31.2 1.0
C1A B:HEM802 3.0 31.2 1.0
C4A B:HEM802 3.1 31.2 1.0
C1B B:HEM802 3.1 31.2 1.0
C4B B:HEM802 3.1 31.2 1.0
C1D B:HEM802 3.1 31.2 1.0
C4C B:HEM802 3.1 31.2 1.0
CD2 B:HIS633 3.4 27.5 1.0
CHA B:HEM802 3.4 31.2 1.0
CHC B:HEM802 3.4 31.2 1.0
CHB B:HEM802 3.4 31.2 1.0
CHD B:HEM802 3.5 31.2 1.0
CE1 B:HIS633 3.5 27.5 1.0
OE1 B:GLU494 3.8 37.7 1.0
FE B:FE803 3.9 35.2 1.0
C3D B:HEM802 4.2 31.2 1.0
CD B:GLU494 4.2 37.7 1.0
C2A B:HEM802 4.2 31.2 1.0
C2C B:HEM802 4.2 31.2 1.0
C2D B:HEM802 4.3 31.2 1.0
C3A B:HEM802 4.3 31.2 1.0
C2B B:HEM802 4.3 31.2 1.0
C3B B:HEM802 4.3 31.2 1.0
C3C B:HEM802 4.3 31.2 1.0
OE2 B:GLU494 4.4 37.7 1.0
CG B:HIS633 4.5 27.5 1.0
ND1 B:HIS633 4.6 27.5 1.0
CE1 B:HIS542 4.7 30.7 1.0
NE2 B:HIS542 4.9 30.7 1.0
NE2 B:HIS541 4.9 31.2 1.0

Iron binding site 6 out of 6 in 6l3h

Go back to Iron Binding Sites List in 6l3h
Iron binding site 6 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From the Pathogen Neisseria Meninigitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:35.2
occ:1.00
 ND1 B:HIS490 2.0 34.5 1.0
OE1 B:GLU494 2.2 37.7 1.0
NE2 B:HIS542 2.4 30.7 1.0
NE2 B:HIS541 2.5 31.2 1.0
CE1 B:HIS490 2.7 34.5 1.0
CE1 B:HIS541 2.8 31.2 1.0
CD B:GLU494 2.9 37.7 1.0
OE2 B:GLU494 3.0 37.7 1.0
CG B:HIS490 3.3 34.5 1.0
CD2 B:HIS542 3.3 30.7 1.0
CE1 B:HIS542 3.4 30.7 1.0
CD2 B:HIS541 3.8 31.2 1.0
CB B:HIS490 3.9 34.5 1.0
NE2 B:HIS490 3.9 34.5 1.0
FE B:HEM802 3.9 31.2 1.0
ND1 B:HIS541 4.0 31.2 1.0
CD2 B:HIS490 4.2 34.5 1.0
NC B:HEM802 4.2 31.2 1.0
ND B:HEM802 4.3 31.2 1.0
CG B:GLU494 4.4 37.7 1.0
CG B:HIS542 4.4 30.7 1.0
ND1 B:HIS542 4.5 30.7 1.0
C1D B:HEM802 4.5 31.2 1.0
C4C B:HEM802 4.5 31.2 1.0
CG B:HIS541 4.6 31.2 1.0
CA B:HIS490 4.7 34.5 1.0
CHD B:HEM802 4.7 31.2 1.0
C1C B:HEM802 4.7 31.2 1.0
C4D B:HEM802 4.8 31.2 1.0
CB B:GLU494 4.8 37.7 1.0
OE2 B:GLU563 4.9 37.9 1.0
O B:GLY538 4.9 36.1 1.0
NA B:HEM802 4.9 31.2 1.0
NB B:HEM802 5.0 31.2 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 00:39:58 2024

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