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Calcium 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:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 1xmf

Go back to Calcium Binding Sites List in 1xmf
Calcium 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 Calcium with other atoms in the Ca 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:Ca5006

b:47.2
occ:1.00
 O A:HOH5132 2.3 41.7 1.0
O A:HOH5151 2.3 42.7 1.0
O A:HOH5127 2.5 26.6 1.0
OXT A:ASN527 2.6 40.2 1.0
O E:HOH305 2.6 62.3 1.0
O A:HOH5129 2.7 34.8 1.0
C A:ASN527 3.6 40.7 1.0
CA A:ASN527 4.0 39.4 1.0
NH1 E:ARG162 4.1 52.3 1.0
O A:PHE526 4.6 39.6 1.0
O A:ASN527 4.7 41.1 1.0
OE1 A:GLU440 4.8 52.6 1.0
CB A:ASN527 5.0 37.8 1.0

Calcium binding site 2 out of 4 in 1xmf

Go back to Calcium Binding Sites List in 1xmf
Calcium 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 Calcium with other atoms in the Ca 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
C:Ca5005

b:38.0
occ:1.00
 OD1 C:ASP348 1.9 46.8 1.0
O C:HOH5169 2.1 41.8 1.0
O C:HOH5178 2.6 37.1 1.0
CG C:ASP348 3.1 45.4 1.0
O C:HOH5102 3.5 46.6 1.0
OD2 C:ASP348 3.8 44.1 1.0
OE1 C:GLU350 3.8 50.4 1.0
CB C:ASP348 4.2 44.4 1.0
O C:HOH5245 4.4 29.9 1.0
CB C:GLU350 4.5 43.3 1.0
CD C:GLU350 4.6 47.6 1.0

Calcium binding site 3 out of 4 in 1xmf

Go back to Calcium Binding Sites List in 1xmf
Calcium 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 Calcium with other atoms in the Ca 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
C:Ca5007

b:57.9
occ:1.00
 OD2 C:ASP378 2.4 56.0 1.0
O C:HOH5182 2.5 41.4 1.0
OD2 C:ASP376 2.8 54.6 1.0
OD1 C:ASP376 2.9 52.2 1.0
CG C:ASP376 3.1 51.1 1.0
CG C:ASP378 3.5 53.7 1.0
CB C:ASP378 4.0 49.6 1.0
O C:HOH5015 4.0 52.8 1.0
CB C:ASP376 4.4 48.6 1.0
O C:HOH5013 4.5 17.3 1.0
N C:ASP378 4.5 45.3 1.0
OD1 C:ASP378 4.6 57.8 1.0
CA C:ASP376 4.7 46.1 1.0
CA C:ASP378 4.9 46.2 1.0
N C:ARG377 4.9 44.3 1.0
C C:ASP376 5.0 44.8 1.0

Calcium binding site 4 out of 4 in 1xmf

Go back to Calcium Binding Sites List in 1xmf
Calcium 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 Calcium with other atoms in the Ca 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
C:Ca5008

b:56.1
occ:1.00
 OE1 C:GLU222 2.2 38.1 1.0
O C:HOH5145 2.3 32.2 1.0
O C:HOH5167 2.5 41.1 1.0
O C:HOH5159 2.8 39.9 1.0
CD C:GLU222 3.5 37.7 1.0
OD2 C:ASP334 4.0 42.1 1.0
OE2 C:GLU222 4.3 38.3 1.0
CG C:GLU222 4.4 35.6 1.0
CB C:GLU222 4.5 34.9 1.0
CD C:LYS225 4.5 44.8 1.0
CG C:ASP334 4.6 40.7 1.0
O C:HOH5218 4.6 27.5 1.0
O C:HOH5075 4.7 30.3 1.0
O C:GLU222 4.7 33.0 1.0
OD1 C:ASP334 4.8 43.9 1.0
CA C:GLU222 4.9 34.2 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: Fri Jul 12 07:43:16 2024

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