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Iron in PDB 6yy3: Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation

Enzymatic activity of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation

All present enzymatic activity of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation:
1.14.13.25;

Protein crystallography data

The structure of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation, PDB code: 6yy3 was solved by V.Srinivas, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.66 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.041, 106.041, 301.029, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.4

Iron Binding Sites:

The binding sites of Iron atom in the Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation (pdb code 6yy3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation, PDB code: 6yy3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6yy3

Go back to Iron Binding Sites List in 6yy3
Iron binding site 1 out of 2 in the Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:40.1
occ:1.00
OE2 D:GLU144 2.1 38.0 1.0
OE1 D:GLU114 2.1 42.1 1.0
O D:HOH726 2.1 46.5 1.0
ND1 D:HIS147 2.3 32.8 1.0
O D:HOH872 2.3 45.9 1.0
OE1 D:GLU243 2.4 41.0 1.0
CD D:GLU114 3.0 43.0 1.0
CE1 D:HIS147 3.2 29.4 1.0
CD D:GLU144 3.2 39.8 1.0
OE2 D:GLU114 3.2 39.7 1.0
FE D:FE2602 3.2 42.3 1.0
CG D:HIS147 3.3 34.3 1.0
CD D:GLU243 3.3 50.5 1.0
OE1 D:GLU144 3.5 40.0 1.0
CB D:HIS147 3.7 30.1 1.0
OE2 D:GLU243 4.0 39.9 1.0
CG D:GLU243 4.3 45.6 1.0
O D:HOH908 4.3 50.5 1.0
NE2 D:HIS147 4.3 37.0 1.0
CE1 D:HIS246 4.4 36.1 1.0
CG D:GLU114 4.4 32.9 1.0
CD2 D:HIS147 4.4 30.6 1.0
ND1 D:HIS246 4.5 40.4 1.0
CG D:GLU144 4.5 35.2 1.0
CG1 D:VAL239 4.6 33.9 1.0
CA D:GLU144 4.6 38.5 1.0
CA D:GLU114 4.6 34.5 1.0
CB D:GLU114 4.7 36.7 1.0
CB D:GLU144 4.9 39.9 1.0
O D:ASP143 5.0 33.3 1.0

Iron binding site 2 out of 2 in 6yy3

Go back to Iron Binding Sites List in 6yy3
Iron binding site 2 out of 2 in the Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, T=0 Diferrous State Prior to Oxygen Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe602

b:42.3
occ:1.00
OE1 D:GLU144 2.1 40.0 1.0
OE2 D:GLU209 2.2 41.9 1.0
ND1 D:HIS246 2.2 40.4 1.0
OE2 D:GLU243 2.3 39.9 1.0
OE1 D:GLU243 2.4 41.0 1.0
O D:HOH872 2.7 45.9 1.0
CD D:GLU243 2.7 50.5 1.0
CD D:GLU209 3.0 41.4 1.0
CD D:GLU144 3.0 39.8 1.0
CE1 D:HIS246 3.1 36.1 1.0
FE D:FE2601 3.2 40.1 1.0
CG D:HIS246 3.3 41.6 1.0
OE2 D:GLU144 3.3 38.0 1.0
CG D:GLU209 3.5 33.3 1.0
NE2 D:GLN140 3.6 43.6 1.0
CB D:HIS246 3.6 42.6 1.0
OE1 D:GLU209 3.8 43.9 1.0
O D:HOH726 4.1 46.5 1.0
CG D:GLU243 4.2 45.6 1.0
NE2 D:HIS246 4.2 43.5 1.0
CD D:GLN140 4.3 43.9 1.0
CD2 D:HIS246 4.3 39.8 1.0
CG D:GLU144 4.4 35.2 1.0
O D:HOH908 4.5 50.5 1.0
CG D:GLN140 4.5 37.7 1.0
CA D:GLU243 4.6 41.3 1.0
CB D:GLU209 4.7 42.3 1.0
ND1 D:HIS147 4.9 32.8 1.0
OE1 D:GLU114 5.0 42.1 1.0
CE1 D:HIS147 5.0 29.4 1.0
CB D:GLU243 5.0 39.8 1.0

Reference:

V.Srinivas, R.Banerjee, H.Lebrette, J.C.Jones, O.Aurelius, I.S.Kim, C.C.Pham, S.Gul, K.D.Sutherlin, A.Bhowmick, J.John, E.Bozkurt, T.Fransson, P.Aller, A.Butryn, I.Bogacz, P.Simon, S.Keable, A.Britz, K.Tono, K.S.Kim, S.Y.Park, S.J.Lee, J.Park, R.Alonso-Mori, F.D.Fuller, A.Batyuk, A.S.Brewster, U.Bergmann, N.K.Sauter, A.M.Orville, V.K.Yachandra, J.Yano, J.D.Lipscomb, J.Kern, M.Hogbom. High-Resolution Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with Its Regulatory Component at Ambient Temperature in Two Oxidation States. J. Am. Chem. Soc. V. 142 14249 2020.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.0C05613
Page generated: Wed Aug 7 16:51:54 2024

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