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Iron in PDB 8zgp: Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis

Enzymatic activity of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis

All present enzymatic activity of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis:
1.7.99.7;

Other elements in 8zgp:

The structure of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis (pdb code 8zgp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis, PDB code: 8zgp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8zgp

Go back to Iron Binding Sites List in 8zgp
Iron binding site 1 out of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:16.5
occ:1.00
FE A:HEM801 0.0 16.5 1.0
ND A:HEM801 2.0 16.5 1.0
NA A:HEM801 2.0 16.5 1.0
NB A:HEM801 2.1 16.5 1.0
NC A:HEM801 2.1 16.5 1.0
NE2 A:HIS335 2.2 17.1 1.0
NE2 A:HIS635 2.4 14.0 1.0
C1D A:HEM801 3.0 16.5 1.0
C4D A:HEM801 3.0 16.5 1.0
C1A A:HEM801 3.0 16.5 1.0
C4A A:HEM801 3.0 16.5 1.0
C1B A:HEM801 3.0 16.5 1.0
C4C A:HEM801 3.1 16.5 1.0
CD2 A:HIS635 3.1 14.0 1.0
C1C A:HEM801 3.1 16.5 1.0
C4B A:HEM801 3.1 16.5 1.0
CD2 A:HIS335 3.1 17.1 1.0
CE1 A:HIS335 3.2 17.1 1.0
CHB A:HEM801 3.4 16.5 1.0
CHA A:HEM801 3.4 16.5 1.0
CHD A:HEM801 3.4 16.5 1.0
CE1 A:HIS635 3.4 14.0 1.0
CHC A:HEM801 3.5 16.5 1.0
C3D A:HEM801 4.2 16.5 1.0
C2D A:HEM801 4.2 16.5 1.0
CG A:HIS635 4.2 14.0 1.0
C2A A:HEM801 4.2 16.5 1.0
C3A A:HEM801 4.2 16.5 1.0
CG A:HIS335 4.3 17.1 1.0
C2B A:HEM801 4.3 16.5 1.0
C3C A:HEM801 4.3 16.5 1.0
ND1 A:HIS335 4.3 17.1 1.0
C2C A:HEM801 4.3 16.5 1.0
C3B A:HEM801 4.3 16.5 1.0
ND1 A:HIS635 4.4 14.0 1.0
NH2 A:ARG724 4.5 24.1 1.0
NE2 A:GLN294 4.9 17.6 1.0
O A:HOH935 4.9 30.0 1.0

Iron binding site 2 out of 6 in 8zgp

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Iron binding site 2 out of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:15.0
occ:1.00
FE A:HEM802 0.0 15.0 1.0
NC A:HEM802 2.0 15.0 1.0
NA A:HEM802 2.0 15.0 1.0
NB A:HEM802 2.1 15.0 1.0
ND A:HEM802 2.1 15.0 1.0
NE2 A:HIS633 2.5 13.3 1.0
O A:HOH905 2.5 30.0 1.0
C4C A:HEM802 3.0 15.0 1.0
C1C A:HEM802 3.1 15.0 1.0
C4A A:HEM802 3.1 15.0 1.0
C1D A:HEM802 3.1 15.0 1.0
C1A A:HEM802 3.1 15.0 1.0
C4B A:HEM802 3.1 15.0 1.0
C1B A:HEM802 3.1 15.0 1.0
C4D A:HEM802 3.1 15.0 1.0
CD2 A:HIS633 3.2 13.3 1.0
CHD A:HEM802 3.4 15.0 1.0
CHC A:HEM802 3.4 15.0 1.0
CHB A:HEM802 3.4 15.0 1.0
CHA A:HEM802 3.5 15.0 1.0
CE1 A:HIS633 3.6 13.3 1.0
FE A:FE803 3.9 22.2 1.0
C3C A:HEM802 4.3 15.0 1.0
C2C A:HEM802 4.3 15.0 1.0
C2A A:HEM802 4.3 15.0 1.0
C2D A:HEM802 4.3 15.0 1.0
C3A A:HEM802 4.3 15.0 1.0
C3B A:HEM802 4.3 15.0 1.0
C2B A:HEM802 4.3 15.0 1.0
C3D A:HEM802 4.3 15.0 1.0
OE1 A:GLU494 4.3 22.2 0.5
OE2 A:GLU494 4.3 22.2 0.5
OE2 A:GLU494 4.4 22.2 0.5
CD A:GLU494 4.4 22.2 0.5
CG A:HIS633 4.5 13.3 1.0
OE1 A:GLU494 4.5 22.2 0.5
CE1 A:HIS542 4.5 15.3 1.0
CD A:GLU494 4.5 22.2 0.5
ND1 A:HIS633 4.6 13.3 1.0
NE2 A:HIS542 4.8 15.3 1.0
NE2 A:HIS541 4.8 14.9 1.0

Iron binding site 3 out of 6 in 8zgp

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Iron binding site 3 out of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:22.2
occ:1.00
O A:HOH905 2.1 30.0 1.0
ND1 A:HIS490 2.1 18.2 1.0
NE2 A:HIS542 2.1 15.3 1.0
NE2 A:HIS541 2.3 14.9 1.0
OE1 A:GLU494 2.4 22.2 0.5
OE1 A:GLU494 2.6 22.2 0.5
CE1 A:HIS490 2.9 18.2 1.0
CE1 A:HIS542 3.1 15.3 1.0
CE1 A:HIS541 3.1 14.9 1.0
CD2 A:HIS542 3.1 15.3 1.0
CD A:GLU494 3.2 22.2 0.5
CG A:HIS490 3.2 18.2 1.0
OE2 A:GLU494 3.2 22.2 0.5
CD2 A:HIS541 3.4 14.9 1.0
CB A:HIS490 3.6 18.2 1.0
CD A:GLU494 3.7 22.2 0.5
FE A:HEM802 3.9 15.0 1.0
NC A:HEM802 4.1 15.0 1.0
NE2 A:HIS490 4.1 18.2 1.0
ND1 A:HIS542 4.2 15.3 1.0
CG A:HIS542 4.2 15.3 1.0
CD2 A:HIS490 4.2 18.2 1.0
ND A:HEM802 4.3 15.0 1.0
ND1 A:HIS541 4.3 14.9 1.0
OE2 A:GLU494 4.3 22.2 0.5
CA A:HIS490 4.4 18.2 1.0
C1D A:HEM802 4.4 15.0 1.0
C4C A:HEM802 4.4 15.0 1.0
CG A:HIS541 4.5 14.9 1.0
CHD A:HEM802 4.6 15.0 1.0
CG A:GLU494 4.6 22.2 0.5
C1C A:HEM802 4.7 15.0 1.0
CG A:GLU494 4.8 22.2 0.5
NB A:HEM802 4.8 15.0 1.0
NA A:HEM802 4.8 15.0 1.0
C4D A:HEM802 4.8 15.0 1.0
O A:GLY538 4.9 17.4 1.0
OE1 A:GLU563 4.9 19.5 1.0

Iron binding site 4 out of 6 in 8zgp

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Iron binding site 4 out of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis


Mono view


Stereo pair view

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

b:16.5
occ:1.00
FE B:HEM801 0.0 16.5 1.0
ND B:HEM801 2.0 16.5 1.0
NA B:HEM801 2.0 16.5 1.0
NB B:HEM801 2.1 16.5 1.0
NC B:HEM801 2.1 16.5 1.0
NE2 B:HIS335 2.2 17.1 1.0
NE2 B:HIS635 2.4 14.0 1.0
C1D B:HEM801 3.0 16.5 1.0
C4D B:HEM801 3.0 16.5 1.0
C1A B:HEM801 3.0 16.5 1.0
C4A B:HEM801 3.0 16.5 1.0
C1B B:HEM801 3.0 16.5 1.0
C4C B:HEM801 3.1 16.5 1.0
CD2 B:HIS635 3.1 14.0 1.0
C1C B:HEM801 3.1 16.5 1.0
C4B B:HEM801 3.1 16.5 1.0
CD2 B:HIS335 3.1 17.1 1.0
CE1 B:HIS335 3.2 17.1 1.0
CHB B:HEM801 3.4 16.5 1.0
CHA B:HEM801 3.4 16.5 1.0
CHD B:HEM801 3.4 16.5 1.0
CE1 B:HIS635 3.4 14.0 1.0
CHC B:HEM801 3.5 16.5 1.0
C3D B:HEM801 4.2 16.5 1.0
C2D B:HEM801 4.2 16.5 1.0
CG B:HIS635 4.2 14.0 1.0
C2A B:HEM801 4.2 16.5 1.0
C3A B:HEM801 4.2 16.5 1.0
CG B:HIS335 4.3 17.1 1.0
C2B B:HEM801 4.3 16.5 1.0
C3C B:HEM801 4.3 16.5 1.0
ND1 B:HIS335 4.3 17.1 1.0
C2C B:HEM801 4.3 16.5 1.0
C3B B:HEM801 4.3 16.5 1.0
ND1 B:HIS635 4.4 14.0 1.0
NH2 B:ARG724 4.5 24.1 1.0
NE2 B:GLN294 4.9 17.6 1.0
O B:HOH935 4.9 30.0 1.0

Iron binding site 5 out of 6 in 8zgp

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Iron binding site 5 out of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis


Mono view


Stereo pair view

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

b:15.0
occ:1.00
FE B:HEM802 0.0 15.0 1.0
NC B:HEM802 2.0 15.0 1.0
NA B:HEM802 2.0 15.0 1.0
NB B:HEM802 2.1 15.0 1.0
ND B:HEM802 2.1 15.0 1.0
NE2 B:HIS633 2.5 13.3 1.0
O B:HOH905 2.5 30.0 1.0
C4C B:HEM802 3.0 15.0 1.0
C1C B:HEM802 3.1 15.0 1.0
C4A B:HEM802 3.1 15.0 1.0
C1D B:HEM802 3.1 15.0 1.0
C1A B:HEM802 3.1 15.0 1.0
C4B B:HEM802 3.1 15.0 1.0
C1B B:HEM802 3.1 15.0 1.0
C4D B:HEM802 3.1 15.0 1.0
CD2 B:HIS633 3.2 13.3 1.0
CHD B:HEM802 3.4 15.0 1.0
CHC B:HEM802 3.4 15.0 1.0
CHB B:HEM802 3.4 15.0 1.0
CHA B:HEM802 3.5 15.0 1.0
CE1 B:HIS633 3.6 13.3 1.0
FE B:FE803 3.9 22.2 1.0
C3C B:HEM802 4.3 15.0 1.0
C2C B:HEM802 4.3 15.0 1.0
C2A B:HEM802 4.3 15.0 1.0
C2D B:HEM802 4.3 15.0 1.0
C3A B:HEM802 4.3 15.0 1.0
C3B B:HEM802 4.3 15.0 1.0
C2B B:HEM802 4.3 15.0 1.0
C3D B:HEM802 4.3 15.0 1.0
OE1 B:GLU494 4.3 22.2 0.5
OE2 B:GLU494 4.3 22.2 0.5
OE2 B:GLU494 4.4 22.2 0.5
CD B:GLU494 4.4 22.2 0.5
CG B:HIS633 4.5 13.3 1.0
OE1 B:GLU494 4.5 22.2 0.5
CE1 B:HIS542 4.5 15.3 1.0
CD B:GLU494 4.5 22.2 0.5
ND1 B:HIS633 4.6 13.3 1.0
NE2 B:HIS542 4.8 15.3 1.0
NE2 B:HIS541 4.8 14.9 1.0

Iron binding site 6 out of 6 in 8zgp

Go back to Iron Binding Sites List in 8zgp
Iron binding site 6 out of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis


Mono view


Stereo pair view

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

b:22.2
occ:1.00
O B:HOH905 2.1 30.0 1.0
ND1 B:HIS490 2.1 18.2 1.0
NE2 B:HIS542 2.1 15.3 1.0
NE2 B:HIS541 2.3 14.9 1.0
OE1 B:GLU494 2.4 22.2 0.5
OE1 B:GLU494 2.6 22.2 0.5
CE1 B:HIS490 2.9 18.2 1.0
CE1 B:HIS542 3.1 15.3 1.0
CE1 B:HIS541 3.1 14.9 1.0
CD2 B:HIS542 3.1 15.3 1.0
CD B:GLU494 3.2 22.2 0.5
CG B:HIS490 3.2 18.2 1.0
OE2 B:GLU494 3.2 22.2 0.5
CD2 B:HIS541 3.4 14.9 1.0
CB B:HIS490 3.6 18.2 1.0
CD B:GLU494 3.7 22.2 0.5
FE B:HEM802 3.9 15.0 1.0
NC B:HEM802 4.1 15.0 1.0
NE2 B:HIS490 4.1 18.2 1.0
ND1 B:HIS542 4.2 15.3 1.0
CG B:HIS542 4.2 15.3 1.0
CD2 B:HIS490 4.2 18.2 1.0
ND B:HEM802 4.3 15.0 1.0
ND1 B:HIS541 4.3 14.9 1.0
OE2 B:GLU494 4.3 22.2 0.5
CA B:HIS490 4.4 18.2 1.0
C1D B:HEM802 4.4 15.0 1.0
C4C B:HEM802 4.4 15.0 1.0
CG B:HIS541 4.5 14.9 1.0
CHD B:HEM802 4.6 15.0 1.0
CG B:GLU494 4.6 22.2 0.5
C1C B:HEM802 4.7 15.0 1.0
CG B:GLU494 4.8 22.2 0.5
NB B:HEM802 4.8 15.0 1.0
NA B:HEM802 4.8 15.0 1.0
C4D B:HEM802 4.8 15.0 1.0
O B:GLY538 4.9 17.4 1.0
OE1 B:GLU563 4.9 19.5 1.0

Reference:

C.C.Gopalasingam, Y.Shiro, T.Tosha. Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis To Be Published.
Page generated: Fri Aug 8 01:57:05 2025

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