Iron in PDB 6vk5: Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex

Protein crystallography data

The structure of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex, PDB code: 6vk5 was solved by J.C.Jones, R.Banerjee, K.Shi, H.Aihara, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.54 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.615, 105.459, 299.421, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.3

Other elements in 6vk5:

The structure of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex (pdb code 6vk5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex, PDB code: 6vk5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6vk5

Go back to Iron Binding Sites List in 6vk5
Iron binding site 1 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:24.3
occ:1.00
O A:HOH912 1.9 25.5 1.0
OE1 A:GLU114 2.0 24.1 1.0
O1 A:BEZ813 2.0 26.5 1.0
O A:HOH907 2.0 25.2 1.0
OE1 A:GLU144 2.0 22.8 1.0
ND1 A:HIS147 2.2 21.4 1.0
CD A:GLU114 2.9 24.1 1.0
CE1 A:HIS147 3.0 22.3 1.0
HE1 A:HIS147 3.0 26.8 1.0
C A:BEZ813 3.1 26.1 1.0
CD A:GLU144 3.1 24.4 1.0
OE2 A:GLU114 3.2 24.1 1.0
CG A:HIS147 3.4 20.7 1.0
OE2 A:GLU144 3.4 24.0 1.0
FE A:FE802 3.5 25.3 1.0
O2 A:BEZ813 3.5 26.2 1.0
HB2 A:HIS147 3.6 25.1 1.0
HA A:GLU144 3.6 25.8 1.0
OE1 A:GLU243 3.8 31.5 1.0
HB3 A:HIS147 3.8 25.1 1.0
CB A:HIS147 3.9 20.9 1.0
H6 A:BEZ813 3.9 30.6 1.0
HA A:GLU114 4.0 27.9 1.0
HE1 A:HIS246 4.0 29.6 1.0
C1 A:BEZ813 4.2 26.2 1.0
NE2 A:HIS147 4.2 21.8 1.0
HB3 A:GLU114 4.2 26.4 1.0
HG13 A:VAL239 4.3 26.4 1.0
CG A:GLU114 4.3 22.3 1.0
CD2 A:HIS147 4.4 22.3 1.0
CG A:GLU144 4.4 23.3 1.0
HB3 A:ALA117 4.4 27.9 1.0
C6 A:BEZ813 4.4 25.5 1.0
CA A:GLU144 4.5 21.5 1.0
HB3 A:GLU144 4.6 26.1 1.0
CB A:GLU114 4.6 22.0 1.0
CE1 A:HIS246 4.6 24.6 1.0
HB1 A:ALA117 4.7 27.9 1.0
CD A:GLU243 4.7 28.9 1.0
HG11 A:VAL239 4.7 26.4 1.0
OE2 A:GLU243 4.8 28.3 1.0
CA A:GLU114 4.8 23.3 1.0
CB A:GLU144 4.8 21.8 1.0
ND1 A:HIS246 4.8 24.5 1.0
HG3 A:GLU114 4.8 26.8 1.0
HB2 A:ALA117 4.9 27.9 1.0
HG2 A:GLU114 4.9 26.8 1.0
CB A:ALA117 4.9 23.2 1.0
CG1 A:VAL239 4.9 22.0 1.0
HG2 A:GLU144 4.9 27.9 1.0
HE2 A:HIS147 4.9 26.2 1.0
HG12 A:VAL239 4.9 26.4 1.0
HG3 A:GLU144 5.0 27.9 1.0

Iron binding site 2 out of 4 in 6vk5

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Iron binding site 2 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:25.3
occ:1.00
O A:HOH912 2.0 25.5 1.0
OE2 A:GLU209 2.1 26.4 1.0
OE2 A:GLU144 2.1 24.0 1.0
O2 A:BEZ813 2.2 26.2 1.0
OE2 A:GLU243 2.2 28.3 1.0
ND1 A:HIS246 2.3 24.5 1.0
HG2 A:GLU209 2.9 32.0 1.0
CD A:GLU209 3.1 27.6 1.0
CD A:GLU243 3.1 28.9 1.0
CE1 A:HIS246 3.1 24.6 1.0
C A:BEZ813 3.2 26.1 1.0
CD A:GLU144 3.2 24.4 1.0
HE1 A:HIS246 3.2 29.6 1.0
OE1 A:GLU243 3.3 31.5 1.0
O1 A:BEZ813 3.4 26.5 1.0
CG A:HIS246 3.4 26.4 1.0
FE A:FE801 3.5 24.3 1.0
CG A:GLU209 3.5 26.6 1.0
OE1 A:GLU144 3.5 22.8 1.0
HB3 A:HIS246 3.6 32.7 1.0
HB2 A:HIS246 3.7 32.7 1.0
CB A:HIS246 3.8 27.2 1.0
HE21 A:GLN140 4.1 36.4 1.0
HG3 A:GLU209 4.1 32.0 1.0
OE1 A:GLU209 4.2 28.0 1.0
HE1 A:HIS147 4.2 26.8 1.0
HG3 A:GLN140 4.2 28.8 1.0
HD11 A:LEU204 4.3 31.9 1.0
HA A:GLU243 4.3 32.4 1.0
HB1 A:ALA117 4.3 27.9 1.0
NE2 A:HIS246 4.3 25.1 1.0
H2 A:BEZ813 4.3 30.8 1.0
O A:HOH907 4.4 25.2 1.0
C1 A:BEZ813 4.4 26.2 1.0
NE2 A:GLN140 4.4 30.3 1.0
CD2 A:HIS246 4.4 25.8 1.0
CG A:GLU144 4.5 23.3 1.0
HB3 A:GLU209 4.5 32.4 1.0
CG A:GLU243 4.5 28.6 1.0
HG2 A:GLU144 4.6 27.9 1.0
HG3 A:GLU243 4.7 34.3 1.0
HG3 A:GLU144 4.7 27.9 1.0
CB A:GLU209 4.7 27.0 1.0
HE22 A:GLN140 4.8 36.4 1.0
C2 A:BEZ813 4.8 25.7 1.0
CE1 A:HIS147 4.8 22.3 1.0
HG21 A:THR213 4.8 32.6 1.0
HD21 A:LEU204 4.9 30.2 1.0
CG A:GLN140 4.9 24.0 1.0
CD A:GLN140 4.9 27.6 1.0
ND1 A:HIS147 5.0 21.4 1.0

Iron binding site 3 out of 4 in 6vk5

Go back to Iron Binding Sites List in 6vk5
Iron binding site 3 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe801

b:23.4
occ:1.00
OE1 E:GLU114 1.9 22.9 1.0
O E:HOH912 2.0 24.3 1.0
OE1 E:GLU144 2.0 24.2 1.0
O E:HOH907 2.0 24.4 1.0
O2 E:BEZ810 2.1 25.3 1.0
ND1 E:HIS147 2.2 22.5 1.0
CD E:GLU114 3.0 23.1 1.0
CE1 E:HIS147 3.0 23.0 1.0
HE1 E:HIS147 3.0 27.6 1.0
CD E:GLU144 3.1 24.0 1.0
C E:BEZ810 3.1 26.2 1.0
OE2 E:GLU114 3.3 23.8 1.0
CG E:HIS147 3.4 23.9 1.0
OE2 E:GLU144 3.4 24.2 1.0
FE E:FE802 3.5 25.0 1.0
O1 E:BEZ810 3.6 24.6 1.0
HB2 E:HIS147 3.6 25.6 1.0
HA E:GLU144 3.6 25.9 1.0
HB3 E:HIS147 3.8 25.6 1.0
CB E:HIS147 3.8 21.3 1.0
OE1 E:GLU243 3.9 31.7 1.0
H2 E:BEZ810 3.9 30.5 1.0
HA E:GLU114 4.0 28.8 1.0
HE1 E:HIS246 4.0 29.8 1.0
NE2 E:HIS147 4.2 21.9 1.0
HB3 E:GLU114 4.2 27.7 1.0
C1 E:BEZ810 4.2 23.7 1.0
CG E:GLU114 4.3 22.9 1.0
HG13 E:VAL239 4.3 26.8 1.0
CD2 E:HIS147 4.4 21.2 1.0
HB3 E:ALA117 4.4 28.5 1.0
CG E:GLU144 4.4 21.8 1.0
C2 E:BEZ810 4.5 25.4 1.0
CA E:GLU144 4.5 21.6 1.0
CB E:GLU114 4.6 23.1 1.0
HB3 E:GLU144 4.6 27.1 1.0
CE1 E:HIS246 4.7 24.8 1.0
HB1 E:ALA117 4.7 28.5 1.0
CD E:GLU243 4.7 29.3 1.0
OE2 E:GLU243 4.7 27.9 1.0
CA E:GLU114 4.7 24.0 1.0
CB E:GLU144 4.8 22.6 1.0
HG3 E:GLU114 4.8 27.4 1.0
ND1 E:HIS246 4.8 24.3 1.0
HG2 E:GLU114 4.8 27.4 1.0
HG11 E:VAL239 4.9 26.8 1.0
CB E:ALA117 4.9 23.8 1.0
HB2 E:ALA117 4.9 28.5 1.0
CG1 E:VAL239 4.9 22.3 1.0
HE2 E:HIS147 4.9 26.2 1.0
HG2 E:GLU144 4.9 26.2 1.0
HG12 E:VAL239 5.0 26.8 1.0
HG3 E:GLU144 5.0 26.2 1.0

Iron binding site 4 out of 4 in 6vk5

Go back to Iron Binding Sites List in 6vk5
Iron binding site 4 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe802

b:25.0
occ:1.00
O E:HOH912 2.0 24.3 1.0
OE2 E:GLU144 2.2 24.2 1.0
OE2 E:GLU243 2.2 27.9 1.0
OE2 E:GLU209 2.2 26.3 1.0
O1 E:BEZ810 2.2 24.6 1.0
ND1 E:HIS246 2.3 24.3 1.0
HG2 E:GLU209 2.9 29.7 1.0
CE1 E:HIS246 3.1 24.8 1.0
CD E:GLU243 3.1 29.3 1.0
HE1 E:HIS246 3.1 29.8 1.0
CD E:GLU209 3.1 25.5 1.0
CD E:GLU144 3.2 24.0 1.0
C E:BEZ810 3.2 26.2 1.0
OE1 E:GLU243 3.3 31.7 1.0
CG E:HIS246 3.4 25.8 1.0
O2 E:BEZ810 3.4 25.3 1.0
OE1 E:GLU144 3.5 24.2 1.0
CG E:GLU209 3.5 24.7 1.0
FE E:FE801 3.5 23.4 1.0
HB3 E:HIS246 3.6 31.4 1.0
HB2 E:HIS246 3.7 31.4 1.0
CB E:HIS246 3.8 26.1 1.0
HG3 E:GLU209 4.1 29.7 1.0
OE1 E:GLU209 4.2 27.7 1.0
HE1 E:HIS147 4.2 27.6 1.0
HG3 E:GLN140 4.2 28.0 1.0
HA E:GLU243 4.2 33.0 1.0
NE2 E:HIS246 4.3 26.0 1.0
HE21 E:GLN140 4.3 34.9 1.0
HB1 E:ALA117 4.3 28.5 1.0
HD11 E:LEU204 4.3 31.2 1.0
HB3 E:GLU209 4.4 32.9 1.0
CD2 E:HIS246 4.4 26.1 1.0
H6 E:BEZ810 4.4 29.6 1.0
C1 E:BEZ810 4.5 23.7 1.0
CG E:GLU243 4.5 29.9 1.0
O E:HOH907 4.5 24.4 1.0
CG E:GLU144 4.5 21.8 1.0
NE2 E:GLN140 4.6 29.1 1.0
HG3 E:GLU243 4.6 35.9 1.0
HG2 E:GLU144 4.6 26.2 1.0
CB E:GLU209 4.6 27.4 1.0
HD21 E:LEU204 4.7 29.6 1.0
HG3 E:GLU144 4.7 26.2 1.0
HG21 E:THR213 4.8 31.7 1.0
CE1 E:HIS147 4.9 23.0 1.0
HE22 E:GLN140 4.9 34.9 1.0
C6 E:BEZ810 4.9 24.7 1.0
CG E:GLN140 4.9 23.4 1.0
CD E:GLN140 5.0 25.2 1.0
ND1 E:HIS147 5.0 22.5 1.0

Reference:

J.C.Jones, R.Banerjee, K.Shi, H.Aihara, J.D.Lipscomb. Structural Studies of Themethylosinus TRICHOSPORIUMOB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal A Transient Substrate Tunnel. Biochemistry V. 59 2946 2020.
ISSN: ISSN 0006-2960
PubMed: 32692178
DOI: 10.1021/ACS.BIOCHEM.0C00459
Page generated: Sun Dec 13 17:20:02 2020

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