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Manganese in PDB 1xmf: Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath)

Enzymatic activity of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath)

All present enzymatic activity of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath):
1.14.13.25;

Protein crystallography data

The structure of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath), PDB code: 1xmf was solved by M.H.Sazinsky, M.Merkx, E.Cadieux, S.Tang, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.76 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.820, 171.679, 220.275, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 26.3

Other elements in 1xmf:

The structure of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath) (pdb code 1xmf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath), PDB code: 1xmf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1xmf

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Manganese binding site 1 out of 4 in the Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn5001

b:32.5
occ:1.00
 O A:HOH5125 2.1 26.1 1.0
OE2 A:GLU144 2.1 30.4 1.0
ND1 A:HIS147 2.1 32.8 1.0
OE1 A:GLU114 2.3 31.8 1.0
OE2 A:GLU243 2.3 34.5 1.0
O A:HOH5122 2.4 35.2 1.0
CE1 A:HIS147 2.9 34.0 1.0
CD A:GLU114 3.1 33.1 1.0
CD A:GLU144 3.2 32.0 1.0
CD A:GLU243 3.2 35.9 1.0
OE2 A:GLU114 3.3 34.5 1.0
CG A:HIS147 3.3 34.0 1.0
MN A:MN5002 3.5 39.6 1.0
OE1 A:GLU144 3.5 33.9 1.0
CB A:HIS147 3.8 29.4 1.0
CG A:GLU243 4.0 37.1 1.0
OE1 A:GLU243 4.0 37.2 1.0
NE2 A:HIS147 4.1 31.8 1.0
CD2 A:HIS147 4.3 33.0 1.0
CE1 A:HIS246 4.5 56.1 1.0
CG A:GLU144 4.5 32.0 1.0
CG A:GLU114 4.6 33.5 1.0
CG2 A:ILE239 4.6 29.2 1.0
CA A:GLU144 4.6 29.1 1.0
ND1 A:HIS246 4.7 56.0 1.0
OE2 A:GLU209 4.8 78.3 1.0
CB A:GLU144 4.9 28.8 1.0

Manganese binding site 2 out of 4 in 1xmf

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Manganese binding site 2 out of 4 in the Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn5002

b:39.6
occ:1.00
 OE2 A:GLU209 2.0 78.3 1.0
OE1 A:GLU144 2.0 33.9 1.0
ND1 A:HIS246 2.2 56.0 1.0
OE1 A:GLU243 2.4 37.2 1.0
OE2 A:GLU243 2.4 34.5 1.0
O A:HOH5122 2.7 35.2 1.0
CD A:GLU243 2.8 35.9 1.0
CE1 A:HIS246 3.0 56.1 1.0
CD A:GLU144 3.1 32.0 1.0
CD A:GLU209 3.2 78.6 1.0
CG A:HIS246 3.3 56.2 1.0
OE2 A:GLU144 3.4 30.4 1.0
MN A:MN5001 3.5 32.5 1.0
NE2 A:GLN140 3.6 47.6 1.0
CB A:HIS246 3.8 58.1 1.0
OE1 A:GLU209 3.9 77.3 1.0
CD A:GLN140 4.1 48.9 1.0
NE2 A:HIS246 4.2 55.6 1.0
CG A:GLN140 4.3 45.9 1.0
CG A:GLU243 4.3 37.1 1.0
CG A:GLU209 4.3 78.4 1.0
CD2 A:HIS246 4.4 55.6 1.0
CG A:GLU144 4.4 32.0 1.0
O A:HOH5125 4.6 26.1 1.0
OE1 A:GLN140 4.9 49.8 1.0
ND1 A:HIS147 4.9 32.8 1.0
CE1 A:HIS147 4.9 34.0 1.0
CD1 A:LEU204 5.0 69.6 1.0

Manganese binding site 3 out of 4 in 1xmf

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Manganese binding site 3 out of 4 in the Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn5003

b:35.9
occ:1.00
 O B:HOH5215 2.1 35.9 1.0
ND1 B:HIS147 2.1 25.3 1.0
OE1 B:GLU114 2.2 33.0 1.0
OE2 B:GLU243 2.2 40.7 1.0
OE2 B:GLU144 2.3 27.6 1.0
O B:HOH5102 2.5 45.1 1.0
CE1 B:HIS147 2.8 24.9 1.0
CD B:GLU114 3.1 31.2 1.0
MN B:MN5004 3.2 48.3 1.0
CD B:GLU243 3.3 43.2 1.0
OE2 B:GLU114 3.3 33.9 1.0
CG B:HIS147 3.3 24.2 1.0
CD B:GLU144 3.3 30.3 1.0
OE1 B:GLU144 3.7 33.7 1.0
CB B:HIS147 3.9 25.5 1.0
NE2 B:HIS147 4.1 24.7 1.0
CG B:GLU243 4.1 42.9 1.0
OE1 B:GLU243 4.1 45.2 1.0
CE1 B:HIS246 4.3 70.9 1.0
CD2 B:HIS147 4.3 23.5 1.0
ND1 B:HIS246 4.4 70.5 1.0
CG B:GLU114 4.5 31.6 1.0
CA B:GLU144 4.6 31.6 1.0
OE1 B:GLU209 4.6 65.8 1.0
CG2 B:ILE239 4.7 31.4 1.0
CG B:GLU144 4.7 30.9 1.0
CB B:GLU144 4.9 28.9 1.0
CB B:GLU114 4.9 32.0 1.0

Manganese binding site 4 out of 4 in 1xmf

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Manganese binding site 4 out of 4 in the Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn5004

b:48.3
occ:1.00
 OE1 B:GLU209 1.9 65.8 1.0
ND1 B:HIS246 2.0 70.5 1.0
OE2 B:GLU243 2.2 40.7 1.0
OE1 B:GLU144 2.4 33.7 1.0
O B:HOH5215 2.4 35.9 1.0
OE1 B:GLU243 2.5 45.2 1.0
CD B:GLU243 2.7 43.2 1.0
CE1 B:HIS246 2.8 70.9 1.0
CD B:GLU209 3.0 65.0 1.0
MN B:MN5003 3.2 35.9 1.0
CD B:GLU144 3.2 30.3 1.0
CG B:HIS246 3.2 70.6 1.0
OE2 B:GLU144 3.3 27.6 1.0
CB B:HIS246 3.7 69.0 1.0
OE2 B:GLU209 3.8 65.5 1.0
CG B:GLU209 3.9 64.7 1.0
NE2 B:GLN140 4.0 52.3 1.0
NE2 B:HIS246 4.0 71.2 1.0
CG B:GLU243 4.2 42.9 1.0
CD2 B:HIS246 4.2 71.1 1.0
CD B:GLN140 4.4 51.3 1.0
O B:HOH5102 4.4 45.1 1.0
CG B:GLN140 4.5 47.6 1.0
CG B:GLU144 4.6 30.9 1.0
CE1 B:HIS147 4.6 24.9 1.0
ND1 B:HIS147 4.7 25.3 1.0

Reference:

M.H.Sazinsky, M.Merkx, E.Cadieux, S.Tang, S.J.Lippard. Preparation and X-Ray Structures of Metal-Free, Dicobalt and Dimanganese Forms of Soluble Methane Monooxygenase Hydroxylase From Methylococcus Capsulatus (Bath) Biochemistry V. 43 16263 2004.
ISSN: ISSN 0006-2960
PubMed: 15610020
DOI: 10.1021/BI048140Z
Page generated: Sat Oct 5 13:07:29 2024

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