Iron in PDB 6ydi: Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, Diferrous State

Enzymatic activity of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, Diferrous State

All present enzymatic activity of Xfel Structure of the Soluble Methane Monooxygenase Hydroxylase and Regulatory Subunit Complex, From Methylosinus Trichosporium OB3B, Diferrous State:
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, Diferrous State, PDB code: 6ydi 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) 33.71 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.946, 106.946, 303.989, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.7

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, Diferrous State (pdb code 6ydi). 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, Diferrous State, PDB code: 6ydi:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6ydi

Go back to Iron Binding Sites List in 6ydi
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, Diferrous State


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, Diferrous State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:38.3
occ:1.00
OE2 D:GLU144 2.1 38.8 1.0
O D:HOH708 2.1 44.0 1.0
OE1 D:GLU114 2.1 35.0 1.0
OE1 D:GLU243 2.2 42.8 1.0
ND1 D:HIS147 2.2 32.1 1.0
O D:HOH882 2.4 40.5 1.0
CD D:GLU114 3.1 39.8 1.0
CD D:GLU144 3.1 43.2 1.0
CE1 D:HIS147 3.1 31.8 1.0
CD D:GLU243 3.2 47.0 1.0
FE D:FE2602 3.3 41.7 1.0
CG D:HIS147 3.3 34.3 1.0
OE2 D:GLU114 3.4 37.0 1.0
OE1 D:GLU144 3.5 38.5 1.0
CB D:HIS147 3.6 29.3 1.0
OE2 D:GLU243 3.9 39.4 1.0
CG D:GLU243 4.1 39.3 1.0
O D:HOH912 4.3 47.5 1.0
NE2 D:HIS147 4.3 31.6 1.0
CE1 D:HIS246 4.4 36.9 1.0
CG D:GLU114 4.4 33.3 1.0
CD2 D:HIS147 4.4 31.4 1.0
CG D:GLU144 4.5 34.7 1.0
ND1 D:HIS246 4.5 42.0 1.0
CA D:GLU144 4.6 32.9 1.0
CG1 D:VAL239 4.6 34.0 1.0
CA D:GLU114 4.6 35.9 1.0
CB D:GLU114 4.7 37.4 1.0
CB D:GLU144 4.8 34.8 1.0

Iron binding site 2 out of 2 in 6ydi

Go back to Iron Binding Sites List in 6ydi
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, Diferrous State


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, Diferrous State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe602

b:41.7
occ:1.00
OE1 D:GLU144 2.1 38.5 1.0
OE2 D:GLU209 2.2 44.6 1.0
OE2 D:GLU243 2.2 39.4 1.0
ND1 D:HIS246 2.2 42.0 1.0
OE1 D:GLU243 2.4 42.8 1.0
O D:HOH882 2.5 40.5 1.0
CD D:GLU243 2.6 47.0 1.0
CE1 D:HIS246 3.0 36.9 1.0
CD D:GLU144 3.0 43.2 1.0
CD D:GLU209 3.0 40.7 1.0
FE D:FE2601 3.3 38.3 1.0
OE2 D:GLU144 3.3 38.8 1.0
CG D:HIS246 3.3 42.2 1.0
NE2 D:GLN140 3.6 39.5 1.0
CG D:GLU209 3.7 38.0 1.0
CB D:HIS246 3.8 41.7 1.0
OE1 D:GLU209 3.8 43.0 1.0
CG D:GLU243 4.1 39.3 1.0
NE2 D:HIS246 4.2 37.1 1.0
O D:HOH708 4.2 44.0 1.0
CD D:GLN140 4.4 40.1 1.0
CD2 D:HIS246 4.4 34.9 1.0
O D:HOH912 4.4 47.5 1.0
CG D:GLU144 4.4 34.7 1.0
CG D:GLN140 4.6 36.6 1.0
CA D:GLU243 4.7 39.3 1.0
CB D:GLU243 4.8 37.2 1.0
CB D:GLU209 4.8 39.3 1.0
ND1 D:HIS147 4.9 32.1 1.0
CB D:ALA117 5.0 37.1 1.0
OE1 D:GLU114 5.0 35.0 1.0
CE1 D:HIS147 5.0 31.8 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: Sun Dec 13 17:35:47 2020

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