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Cobalt in PDB 1xmh: Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath)

Enzymatic activity of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath)

All present enzymatic activity of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath):
1.14.13.25;

Protein crystallography data

The structure of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath), PDB code: 1xmh 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) 29.55 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.444, 171.842, 220.936, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.5

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 4 in 1xmh

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Cobalt binding site 1 out of 4 in the Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co5170

b:42.3
occ:1.00
 ND1 A:HIS246 2.0 46.1 1.0
OE2 A:GLU209 2.2 48.5 1.0
OE1 A:GLU243 2.2 50.9 1.0
OE1 A:GLU144 2.3 26.8 1.0
OE2 A:GLU243 2.4 49.0 1.0
O A:HOH5322 2.5 37.5 1.0
CD A:GLU243 2.6 50.9 1.0
CE1 A:HIS246 2.8 45.1 1.0
CO A:CO5171 3.1 30.3 1.0
CG A:HIS246 3.1 45.6 1.0
CD A:GLU209 3.2 50.5 1.0
CD A:GLU144 3.2 27.6 1.0
OE2 A:GLU144 3.5 27.9 1.0
NE2 A:GLN140 3.6 31.6 1.0
CB A:HIS246 3.7 46.3 1.0
OE1 A:GLU209 3.9 52.8 1.0
NE2 A:HIS246 4.0 42.7 1.0
CG A:GLU243 4.1 48.8 1.0
CD2 A:HIS246 4.2 43.7 1.0
CG A:GLU209 4.2 49.9 1.0
CD A:GLN140 4.3 32.4 1.0
O A:HOH5323 4.4 34.5 1.0
CG A:GLN140 4.5 29.8 1.0
ND1 A:HIS147 4.6 22.1 1.0
CE1 A:HIS147 4.6 25.2 1.0
CG A:GLU144 4.6 24.3 1.0
OE1 A:GLU114 4.8 30.9 1.0
CB A:GLU243 4.9 47.4 1.0

Cobalt binding site 2 out of 4 in 1xmh

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Cobalt binding site 2 out of 4 in the Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co5171

b:30.3
occ:1.00
 ND1 A:HIS147 2.1 22.1 1.0
OE1 A:GLU114 2.1 30.9 1.0
OE2 A:GLU144 2.2 27.9 1.0
O A:HOH5322 2.3 37.5 1.0
OE1 A:GLU243 2.3 50.9 1.0
O A:HOH5323 2.5 34.5 1.0
CE1 A:HIS147 2.9 25.2 1.0
CD A:GLU114 3.0 30.1 1.0
CD A:GLU144 3.1 27.6 1.0
CO A:CO5170 3.1 42.3 1.0
OE2 A:GLU114 3.2 33.8 1.0
CG A:HIS147 3.2 22.7 1.0
OE1 A:GLU144 3.4 26.8 1.0
CD A:GLU243 3.5 50.9 1.0
CB A:HIS147 3.6 23.6 1.0
CE1 A:HIS246 4.0 45.1 1.0
NE2 A:HIS147 4.1 26.3 1.0
CD2 A:HIS147 4.2 24.5 1.0
ND1 A:HIS246 4.2 46.1 1.0
OE2 A:GLU243 4.3 49.0 1.0
CG A:GLU114 4.4 29.1 1.0
CG A:GLU243 4.5 48.8 1.0
CG A:GLU144 4.5 24.3 1.0
CA A:GLU144 4.6 23.5 1.0
CG2 A:ILE239 4.6 24.0 1.0
CB A:GLU114 4.8 24.9 1.0
OE2 A:GLU209 4.8 48.5 1.0
CA A:GLU114 4.9 26.4 1.0
CB A:GLU144 4.9 23.2 1.0
O A:ASP143 5.0 26.6 1.0

Cobalt binding site 3 out of 4 in 1xmh

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Cobalt binding site 3 out of 4 in the Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co5172

b:32.7
occ:1.00
 OE1 B:GLU114 2.0 34.5 1.0
OE2 B:GLU144 2.1 32.8 1.0
ND1 B:HIS147 2.2 27.2 1.0
OE2 B:GLU243 2.4 49.4 1.0
O B:HOH5308 2.5 44.6 1.0
O B:HOH5307 2.5 33.5 1.0
CD B:GLU114 2.9 34.3 1.0
CO B:CO5173 3.0 50.1 1.0
CE1 B:HIS147 3.0 27.1 1.0
CD B:GLU144 3.1 33.4 1.0
OE2 B:GLU114 3.1 39.8 1.0
CG B:HIS147 3.3 26.0 1.0
OE1 B:GLU144 3.3 34.4 1.0
CD B:GLU243 3.6 51.2 1.0
CB B:HIS147 3.7 26.2 1.0
CE1 B:HIS246 4.1 50.6 1.0
ND1 B:HIS246 4.2 49.6 1.0
NE2 B:HIS147 4.2 28.4 1.0
OE1 B:GLU243 4.3 51.6 1.0
CG B:GLU114 4.3 31.8 1.0
CD2 B:HIS147 4.3 26.9 1.0
CG B:GLU144 4.5 31.9 1.0
OE1 B:GLU209 4.5 57.3 1.0
CA B:GLU144 4.5 29.2 1.0
CG2 B:ILE239 4.7 27.5 1.0
CG B:GLU243 4.7 48.4 1.0
CB B:GLU114 4.7 30.3 1.0
CA B:GLU114 4.9 29.3 1.0
CB B:GLU144 4.9 29.3 1.0

Cobalt binding site 4 out of 4 in 1xmh

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Cobalt binding site 4 out of 4 in the Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Co(II) Reconstituted Methane Monooxygenase Hydroxylase From M. Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co5173

b:50.1
occ:1.00
 ND1 B:HIS246 2.1 49.6 1.0
OE1 B:GLU209 2.2 57.3 1.0
OE2 B:GLU243 2.3 49.4 1.0
OE1 B:GLU243 2.4 51.6 1.0
OE1 B:GLU144 2.4 34.4 1.0
CD B:GLU243 2.7 51.2 1.0
O B:HOH5308 2.7 44.6 1.0
CE1 B:HIS246 2.9 50.6 1.0
CO B:CO5172 3.0 32.7 1.0
CD B:GLU209 3.1 55.9 1.0
CG B:HIS246 3.2 50.3 1.0
CD B:GLU144 3.3 33.4 1.0
OE2 B:GLU144 3.5 32.8 1.0
CB B:HIS246 3.7 49.6 1.0
OE2 B:GLU209 3.7 55.7 1.0
NE2 B:GLN140 3.8 34.9 1.0
CG B:GLU209 3.9 53.5 1.0
O B:HOH5307 4.1 33.5 1.0
NE2 B:HIS246 4.1 50.9 1.0
CG B:GLU243 4.2 48.4 1.0
CD2 B:HIS246 4.3 50.2 1.0
CD B:GLN140 4.3 36.2 1.0
ND1 B:HIS147 4.5 27.2 1.0
CG B:GLN140 4.5 33.3 1.0
CE1 B:HIS147 4.6 27.1 1.0
CG B:GLU144 4.7 31.9 1.0
OE1 B:GLU114 4.7 34.5 1.0
CA B:GLU243 4.9 46.5 1.0
CB B:GLU243 4.9 47.8 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: Tue Jul 30 14:46:33 2024

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