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Iron in PDB 6vk8: Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with Small Organic Carboxylate at Active Center

Protein crystallography data

The structure of Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with Small Organic Carboxylate at Active Center, PDB code: 6vk8 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) 85.99 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.866, 105.349, 297.720, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.8

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 with Small Organic Carboxylate at Active Center (pdb code 6vk8). 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 with Small Organic Carboxylate at Active Center, PDB code: 6vk8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6vk8

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Iron binding site 1 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with Small Organic Carboxylate at Active Center


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 with Small Organic Carboxylate at Active Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:34.8
occ:1.00
 O1 A:SIN803 1.9 48.6 1.0
OE1 A:GLU114 2.0 33.9 1.0
O A:HOH919 2.0 36.4 1.0
OE1 A:GLU144 2.1 32.0 1.0
ND1 A:HIS147 2.2 27.3 1.0
O A:HOH909 2.2 34.9 1.0
C1 A:SIN803 3.0 48.4 1.0
CD A:GLU114 3.0 35.7 1.0
CE1 A:HIS147 3.0 28.9 1.0
CD A:GLU144 3.2 25.3 1.0
OE2 A:GLU114 3.3 36.9 1.0
CG A:HIS147 3.3 26.8 1.0
FE A:FE802 3.4 40.5 1.0
OE2 A:GLU144 3.6 38.6 1.0
CB A:HIS147 3.7 20.1 1.0
O2 A:SIN803 3.8 45.0 1.0
C2 A:SIN803 3.9 47.7 1.0
OE1 A:GLU243 3.9 62.7 1.0
NE2 A:HIS147 4.2 27.5 1.0
CG A:GLU114 4.3 28.3 1.0
CD2 A:HIS147 4.4 26.8 1.0
CA A:GLU144 4.5 26.1 1.0
CG A:GLU144 4.5 29.9 1.0
OE2 A:GLU243 4.6 54.4 1.0
CE1 A:HIS246 4.6 34.4 1.0
CB A:GLU114 4.6 32.4 1.0
CG1 A:VAL239 4.7 30.4 1.0
CD A:GLU243 4.7 57.2 1.0
CA A:GLU114 4.7 35.7 1.0
CB A:GLU144 4.7 24.5 1.0
ND1 A:HIS246 4.7 33.6 1.0

Iron binding site 2 out of 4 in 6vk8

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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 with Small Organic Carboxylate at Active Center


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 with Small Organic Carboxylate at Active Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:40.5
occ:1.00
 O A:HOH919 1.8 36.4 1.0
OE2 A:GLU243 2.2 54.4 1.0
ND1 A:HIS246 2.3 33.6 1.0
OE2 A:GLU144 2.3 38.6 1.0
OE2 A:GLU209 2.3 46.7 1.0
O2 A:SIN803 2.5 45.0 1.0
O1 A:SIN803 3.0 48.6 1.0
C1 A:SIN803 3.1 48.4 1.0
CE1 A:HIS246 3.1 34.4 1.0
CD A:GLU144 3.2 25.3 1.0
CD A:GLU209 3.2 43.8 1.0
CD A:GLU243 3.2 57.2 1.0
OE1 A:GLU144 3.3 32.0 1.0
CG A:HIS246 3.4 35.4 1.0
FE A:FE801 3.4 34.8 1.0
OE1 A:GLU243 3.5 62.7 1.0
CG A:GLU209 3.6 42.5 1.0
CB A:HIS246 3.8 33.6 1.0
NE2 A:GLN140 4.2 37.6 1.0
OE1 A:GLU209 4.2 54.0 1.0
NE2 A:HIS246 4.3 33.2 1.0
CD2 A:HIS246 4.4 32.2 1.0
O A:HOH909 4.5 34.9 1.0
CG A:GLU243 4.5 46.8 1.0
C2 A:SIN803 4.6 47.7 1.0
CG A:GLU144 4.6 29.9 1.0
CB A:GLU209 4.7 44.1 1.0
CD A:GLN140 4.8 41.3 1.0
CE1 A:HIS147 4.8 28.9 1.0
CG A:GLN140 4.8 30.3 1.0
ND1 A:HIS147 4.9 27.3 1.0

Iron binding site 3 out of 4 in 6vk8

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Iron binding site 3 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with Small Organic Carboxylate at Active Center


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 with Small Organic Carboxylate at Active Center within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe801

b:35.5
occ:1.00
 O E:HOH959 1.9 35.9 1.0
OE1 E:GLU114 1.9 39.9 1.0
O2 E:BEZ803 2.1 37.6 1.0
OE1 E:GLU144 2.1 34.6 1.0
O E:HOH919 2.2 43.7 1.0
ND1 E:HIS147 2.3 33.6 1.0
CD E:GLU114 2.9 35.5 1.0
CE1 E:HIS147 3.0 27.6 1.0
C E:BEZ803 3.1 41.6 1.0
OE2 E:GLU114 3.2 44.9 1.0
CD E:GLU144 3.2 35.0 1.0
CG E:HIS147 3.4 32.6 1.0
FE E:FE802 3.5 39.2 1.0
OE2 E:GLU144 3.6 34.6 1.0
O1 E:BEZ803 3.6 37.7 1.0
CB E:HIS147 3.8 27.2 1.0
OE1 E:GLU243 3.9 64.5 1.0
CG E:GLU114 4.2 31.1 1.0
NE2 E:HIS147 4.2 33.5 1.0
C1 E:BEZ803 4.3 47.7 1.0
CD2 E:HIS147 4.4 30.1 1.0
C6 E:BEZ803 4.5 51.7 1.0
OE2 E:GLU243 4.5 58.8 1.0
CG E:GLU144 4.5 36.0 1.0
CA E:GLU144 4.6 31.2 1.0
CB E:GLU114 4.6 26.0 1.0
CD E:GLU243 4.6 60.7 1.0
CE1 E:HIS246 4.6 35.1 1.0
CG1 E:VAL239 4.7 28.2 1.0
CA E:GLU114 4.7 29.8 1.0
ND1 E:HIS246 4.8 31.9 1.0
CB E:GLU144 4.8 34.0 1.0

Iron binding site 4 out of 4 in 6vk8

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Iron binding site 4 out of 4 in the Crystal Structure of Methylosinus Trichosporium OB3B Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with Small Organic Carboxylate at Active Center


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 with Small Organic Carboxylate at Active Center within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe802

b:39.2
occ:1.00
 O E:HOH959 1.9 35.9 1.0
O1 E:BEZ803 2.1 37.7 1.0
OE2 E:GLU209 2.2 48.8 1.0
OE2 E:GLU243 2.2 58.8 1.0
ND1 E:HIS246 2.2 31.9 1.0
OE2 E:GLU144 2.2 34.6 1.0
CE1 E:HIS246 3.0 35.1 1.0
C E:BEZ803 3.0 41.6 1.0
CD E:GLU209 3.1 43.2 1.0
CD E:GLU144 3.2 35.0 1.0
CD E:GLU243 3.2 60.7 1.0
O2 E:BEZ803 3.2 37.6 1.0
CG E:HIS246 3.3 34.6 1.0
OE1 E:GLU144 3.4 34.6 1.0
FE E:FE801 3.5 35.5 1.0
OE1 E:GLU243 3.6 64.5 1.0
CG E:GLU209 3.6 40.1 1.0
CB E:HIS246 3.8 31.1 1.0
OE1 E:GLU209 4.1 54.2 1.0
NE2 E:HIS246 4.2 35.2 1.0
NE2 E:GLN140 4.3 40.2 1.0
CD2 E:HIS246 4.4 34.5 1.0
C1 E:BEZ803 4.4 47.7 1.0
O E:HOH919 4.5 43.7 1.0
CG E:GLU243 4.5 55.1 1.0
CG E:GLU144 4.6 36.0 1.0
CB E:GLU209 4.7 35.9 1.0
CG E:GLN140 4.7 32.4 1.0
CD E:GLN140 4.8 39.6 1.0
CE1 E:HIS147 4.9 27.6 1.0
C2 E:BEZ803 4.9 50.3 1.0
ND1 E:HIS147 5.0 33.6 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: Wed Aug 6 15:07:04 2025

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