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Iron in PDB 6kob: X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis

Protein crystallography data

The structure of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis, PDB code: 6kob was solved by J.Xu, Z.Ding, B.Liu, J.Li, R.B.Gennis, J.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.06 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 110.889, 158.070, 147.009, 90.00, 107.47, 90.00
R / Rfree (%) 32.1 / 35.1

Other elements in 6kob:

The structure of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis (pdb code 6kob). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis, PDB code: 6kob:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6kob

Go back to Iron Binding Sites List in 6kob
Iron binding site 1 out of 4 in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:0.1
occ:1.00
FE A:HEA1001 0.0 0.1 1.0
NA A:HEA1001 2.0 0.2 1.0
NC A:HEA1001 2.1 0.2 1.0
NB A:HEA1001 2.1 0.5 1.0
ND A:HEA1001 2.1 0.4 1.0
NE2 A:HIS102 2.2 0.0 1.0
NE2 A:HIS417 2.7 0.8 1.0
CD2 A:HIS102 2.9 0.7 1.0
C1A A:HEA1001 2.9 0.7 1.0
C4A A:HEA1001 2.9 0.4 1.0
C1C A:HEA1001 3.1 0.8 1.0
C1B A:HEA1001 3.1 0.9 1.0
C4B A:HEA1001 3.1 0.7 1.0
C4D A:HEA1001 3.1 0.2 1.0
C4C A:HEA1001 3.1 0.3 1.0
C1D A:HEA1001 3.1 0.1 1.0
CE1 A:HIS102 3.3 0.2 1.0
CHA A:HEA1001 3.4 0.1 1.0
CHB A:HEA1001 3.4 0.2 1.0
CHC A:HEA1001 3.4 0.8 1.0
CHD A:HEA1001 3.5 0.1 1.0
CD2 A:HIS417 3.6 0.8 1.0
CE1 A:HIS417 3.7 0.9 1.0
C3A A:HEA1001 4.1 0.3 1.0
C2A A:HEA1001 4.1 0.3 1.0
CG A:HIS102 4.1 0.1 1.0
ND1 A:HIS102 4.3 0.5 1.0
C3C A:HEA1001 4.4 0.3 1.0
C2B A:HEA1001 4.4 0.1 1.0
C3B A:HEA1001 4.4 0.5 1.0
C3D A:HEA1001 4.5 0.2 1.0
C2C A:HEA1001 4.5 0.4 1.0
C2D A:HEA1001 4.5 0.4 1.0
CG A:HIS417 4.8 0.6 1.0
ND1 A:HIS417 4.8 0.6 1.0

Iron binding site 2 out of 4 in 6kob

Go back to Iron Binding Sites List in 6kob
Iron binding site 2 out of 4 in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:0.4
occ:1.00
FE A:HEA1002 0.0 0.4 1.0
NA A:HEA1002 2.0 0.4 1.0
NC A:HEA1002 2.1 0.8 1.0
NB A:HEA1002 2.1 0.6 1.0
ND A:HEA1002 2.1 0.5 1.0
NE2 A:HIS415 2.9 0.1 1.0
C1A A:HEA1002 3.0 0.2 1.0
C4A A:HEA1002 3.0 0.6 1.0
C4C A:HEA1002 3.1 0.4 1.0
C4D A:HEA1002 3.1 1.0 1.0
C1C A:HEA1002 3.1 0.5 1.0
C4B A:HEA1002 3.1 0.0 1.0
C1B A:HEA1002 3.1 0.7 1.0
C1D A:HEA1002 3.2 0.1 1.0
CHA A:HEA1002 3.4 0.5 1.0
CHB A:HEA1002 3.5 0.2 1.0
CHC A:HEA1002 3.5 0.6 1.0
CHD A:HEA1002 3.5 0.8 1.0
CE1 A:HIS415 3.7 0.2 1.0
CD2 A:HIS415 4.0 0.1 1.0
C3A A:HEA1002 4.1 0.1 1.0
C2A A:HEA1002 4.1 0.2 1.0
C3C A:HEA1002 4.4 0.8 1.0
C3B A:HEA1002 4.5 0.8 1.0
C2B A:HEA1002 4.5 0.6 1.0
C3D A:HEA1002 4.5 0.8 1.0
C2C A:HEA1002 4.5 0.6 1.0
C2D A:HEA1002 4.5 0.6 1.0
ND1 A:HIS415 4.9 0.3 1.0
CU A:CU1003 4.9 0.5 1.0

Iron binding site 3 out of 4 in 6kob

Go back to Iron Binding Sites List in 6kob
Iron binding site 3 out of 4 in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:0.1
occ:1.00
FE E:HEA1001 0.0 0.1 1.0
NA E:HEA1001 2.0 0.5 1.0
NC E:HEA1001 2.1 0.8 1.0
NB E:HEA1001 2.1 77.0 1.0
ND E:HEA1001 2.1 84.7 1.0
NE2 E:HIS102 2.1 0.2 1.0
NE2 E:HIS417 2.7 79.8 1.0
CD2 E:HIS102 2.9 0.7 1.0
C4A E:HEA1001 2.9 0.4 1.0
C1A E:HEA1001 2.9 0.7 1.0
C1B E:HEA1001 3.1 93.1 1.0
C4C E:HEA1001 3.1 0.3 1.0
C1C E:HEA1001 3.1 0.4 1.0
C4B E:HEA1001 3.1 95.1 1.0
C4D E:HEA1001 3.1 98.4 1.0
C1D E:HEA1001 3.1 86.3 1.0
CE1 E:HIS102 3.2 0.6 1.0
CHA E:HEA1001 3.4 0.7 1.0
CHB E:HEA1001 3.4 0.4 1.0
CHC E:HEA1001 3.4 0.3 1.0
CHD E:HEA1001 3.5 0.8 1.0
CD2 E:HIS417 3.6 98.4 1.0
CE1 E:HIS417 3.6 87.6 1.0
C3A E:HEA1001 4.0 0.9 1.0
C2A E:HEA1001 4.1 0.1 1.0
CG E:HIS102 4.1 0.0 1.0
ND1 E:HIS102 4.2 0.5 1.0
C3C E:HEA1001 4.4 0.0 1.0
C2B E:HEA1001 4.4 86.2 1.0
C3B E:HEA1001 4.4 97.0 1.0
C2D E:HEA1001 4.5 89.8 1.0
C3D E:HEA1001 4.5 90.8 1.0
C2C E:HEA1001 4.5 0.5 1.0
ND1 E:HIS417 4.8 0.1 1.0
CG E:HIS417 4.8 0.6 1.0

Iron binding site 4 out of 4 in 6kob

Go back to Iron Binding Sites List in 6kob
Iron binding site 4 out of 4 in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1002

b:0.7
occ:1.00
FE E:HEA1002 0.0 0.7 1.0
NA E:HEA1002 2.0 0.7 1.0
NC E:HEA1002 2.1 0.7 1.0
NB E:HEA1002 2.1 0.0 1.0
ND E:HEA1002 2.1 0.5 1.0
NE2 E:HIS415 2.9 93.4 1.0
C1A E:HEA1002 3.0 0.3 1.0
C4A E:HEA1002 3.0 0.3 1.0
C1C E:HEA1002 3.1 0.6 1.0
C4C E:HEA1002 3.1 0.9 1.0
C4D E:HEA1002 3.1 0.1 1.0
C4B E:HEA1002 3.1 0.8 1.0
C1B E:HEA1002 3.1 0.8 1.0
C1D E:HEA1002 3.2 1.0 1.0
CHA E:HEA1002 3.4 0.2 1.0
CHB E:HEA1002 3.5 0.4 1.0
CHC E:HEA1002 3.5 0.1 1.0
CHD E:HEA1002 3.5 0.1 1.0
CE1 E:HIS415 3.7 87.5 1.0
CD2 E:HIS415 4.0 93.4 1.0
C3A E:HEA1002 4.1 0.8 1.0
C2A E:HEA1002 4.1 0.1 1.0
CU E:CU1003 4.3 0.2 1.0
C3C E:HEA1002 4.4 0.1 1.0
C3B E:HEA1002 4.5 0.1 1.0
C2B E:HEA1002 4.5 0.6 1.0
C2C E:HEA1002 4.5 0.2 1.0
C3D E:HEA1002 4.5 0.1 1.0
C2D E:HEA1002 4.5 1.0 1.0
ND1 E:HIS415 4.9 93.8 1.0

Reference:

J.Xu, Z.Ding, B.Liu, S.M.Yi, J.Li, Z.Zhang, Y.Liu, J.Li, L.Liu, A.Zhou, R.B.Gennis, J.Zhu. Structure of the Cytochrome AA3-600 Heme-Copper Menaquinol Oxidase Bound to Inhibitor Hqno Shows TM0 Is Part of the Quinol Binding Site Proc.Natl.Acad.Sci.Usa 2010.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1915013117
Page generated: Sun Dec 13 16:37:26 2020

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