Calcium in PDB 7cdl: Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)

Enzymatic activity of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)

All present enzymatic activity of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath):
1.1.2.7;

Protein crystallography data

The structure of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath), PDB code: 7cdl was solved by P.Chuankhayan, S.I.Chan, P.K.R.Nareddy, I.K.Tsai, Y.F.Tsai, K.H.-C.Chen, S.S.-F.Yu, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 128.11, 211.107, 222.554, 90, 90, 90
R / Rfree (%) 15.2 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) (pdb code 7cdl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath), PDB code: 7cdl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7cdl

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Calcium binding site 1 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:44.6
occ:1.00
 O5 C:PQQ702 2.3 28.8 1.0
O7A C:PQQ702 2.5 38.2 1.0
OE2 C:GLU205 2.5 21.3 1.0
N6 C:PQQ702 2.6 35.0 1.0
OE1 C:GLU205 2.7 35.5 1.0
OD1 C:ASN289 2.8 17.6 1.0
CD C:GLU205 2.9 29.9 1.0
OD1 C:ASP331 2.9 21.6 1.0
O C:HOH831 3.0 56.8 1.0
C5 C:PQQ702 3.3 33.7 1.0
C7X C:PQQ702 3.4 40.8 1.0
C6A C:PQQ702 3.4 37.8 1.0
CG C:ASN289 3.5 18.3 1.0
C7 C:PQQ702 3.5 40.2 1.0
ND2 C:ASN289 3.7 18.4 1.0
CG C:ASP331 3.7 21.5 1.0
OD2 C:ASP331 3.8 22.4 1.0
O C:HOH834 4.1 25.0 1.0
CB C:ALA333 4.2 16.9 1.0
CG C:GLU205 4.4 25.8 1.0
NH2 C:ARG358 4.4 13.4 1.0
C4 C:PQQ702 4.6 41.0 1.0
NE1 C:TRP293 4.6 17.9 1.0
CB C:ALA204 4.6 18.4 1.0
O7B C:PQQ702 4.7 22.1 1.0
CZ2 C:TRP293 4.7 17.9 1.0
CZ2 C:TRP271 4.7 21.8 1.0
CB C:ASN289 4.8 14.6 1.0
NE1 C:TRP271 4.8 20.0 1.0
C9A C:PQQ702 4.8 35.9 1.0
C8 C:PQQ702 4.9 39.2 1.0
O C:HOH976 5.0 23.6 1.0

Calcium binding site 2 out of 8 in 7cdl

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Calcium binding site 2 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:47.2
occ:1.00
 O5 D:PQQ702 2.4 36.9 1.0
O7A D:PQQ702 2.5 44.4 1.0
OE2 D:GLU205 2.6 25.6 1.0
OD1 D:ASN289 2.6 16.8 1.0
N6 D:PQQ702 2.7 40.1 1.0
OE1 D:GLU205 2.7 38.3 1.0
OD1 D:ASP331 2.9 21.8 1.0
CD D:GLU205 3.0 31.6 1.0
C5 D:PQQ702 3.3 40.8 1.0
CG D:ASN289 3.4 17.6 1.0
C6A D:PQQ702 3.4 43.4 1.0
O D:HOH803 3.4 62.6 1.0
C7X D:PQQ702 3.5 43.0 1.0
C7 D:PQQ702 3.6 43.0 1.0
ND2 D:ASN289 3.7 19.3 1.0
CG D:ASP331 3.7 23.6 1.0
OD2 D:ASP331 3.8 22.3 1.0
O D:HOH844 4.0 26.3 1.0
CB D:ALA333 4.0 16.8 1.0
NH2 D:ARG358 4.4 16.5 1.0
CG D:GLU205 4.4 28.6 1.0
CZ2 D:TRP271 4.5 26.5 1.0
NE1 D:TRP271 4.5 21.7 1.0
CB D:ALA204 4.6 19.5 1.0
C4 D:PQQ702 4.6 47.4 1.0
CB D:ASN289 4.7 16.0 1.0
NE1 D:TRP293 4.7 17.6 1.0
O7B D:PQQ702 4.7 26.5 1.0
CZ2 D:TRP293 4.7 19.1 1.0
C9A D:PQQ702 4.8 41.2 1.0
CE2 D:TRP271 4.9 21.0 1.0
C8 D:PQQ702 4.9 38.9 1.0

Calcium binding site 3 out of 8 in 7cdl

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Calcium binding site 3 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:56.4
occ:1.00
 O5 A:PQQ702 2.3 44.4 1.0
N6 A:PQQ702 2.5 50.2 1.0
O7A A:PQQ702 2.5 54.1 1.0
OD1 A:ASN289 2.7 20.4 1.0
OE2 A:GLU205 2.7 29.1 1.0
OE1 A:GLU205 2.9 36.3 1.0
OD1 A:ASP331 3.0 25.4 1.0
CD A:GLU205 3.1 32.8 1.0
C5 A:PQQ702 3.2 48.0 1.0
C6A A:PQQ702 3.3 52.6 1.0
C7 A:PQQ702 3.4 46.0 1.0
C7X A:PQQ702 3.4 41.6 1.0
CG A:ASN289 3.5 23.5 1.0
O A:HOH837 3.7 59.0 1.0
ND2 A:ASN289 3.8 22.2 1.0
CG A:ASP331 3.8 27.7 1.0
OD2 A:ASP331 3.8 31.4 1.0
CB A:ALA333 3.9 21.4 1.0
O A:HOH877 3.9 27.3 1.0
NH2 A:ARG358 4.3 21.0 1.0
NE1 A:TRP271 4.4 25.1 1.0
CZ2 A:TRP271 4.5 24.9 1.0
C4 A:PQQ702 4.5 50.6 1.0
CG A:GLU205 4.6 27.8 1.0
O7B A:PQQ702 4.6 26.1 1.0
CB A:ASN289 4.7 20.5 1.0
C9A A:PQQ702 4.7 48.3 1.0
C8 A:PQQ702 4.8 50.3 1.0
NE1 A:TRP293 4.8 22.1 1.0
CB A:ALA204 4.8 23.9 1.0
CE2 A:TRP271 4.8 22.9 1.0
CZ2 A:TRP293 5.0 22.3 1.0
O4 A:PQQ702 5.0 52.1 1.0

Calcium binding site 4 out of 8 in 7cdl

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Calcium binding site 4 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:52.8
occ:1.00
 O5 B:PQQ702 2.3 35.7 1.0
OE2 B:GLU205 2.5 26.8 1.0
O7A B:PQQ702 2.5 42.5 1.0
OD1 B:ASN289 2.7 14.6 1.0
N6 B:PQQ702 2.7 44.1 1.0
OD1 B:ASP331 2.9 22.7 1.0
OE1 B:GLU205 3.0 38.4 1.0
CD B:GLU205 3.1 31.1 1.0
C5 B:PQQ702 3.3 45.0 1.0
CG B:ASN289 3.4 14.8 1.0
C6A B:PQQ702 3.5 47.7 1.0
C7X B:PQQ702 3.5 41.5 1.0
C7 B:PQQ702 3.6 44.1 1.0
ND2 B:ASN289 3.6 16.2 1.0
CG B:ASP331 3.6 20.5 1.0
O B:HOH979 3.6 53.7 1.0
OD2 B:ASP331 3.7 21.6 1.0
CB B:ALA333 4.1 14.8 1.0
O B:HOH821 4.1 27.2 1.0
NH2 B:ARG358 4.3 14.8 1.0
CG B:GLU205 4.5 25.7 1.0
NE1 B:TRP293 4.5 17.7 1.0
C4 B:PQQ702 4.6 47.6 1.0
CB B:ASN289 4.6 13.7 1.0
CZ2 B:TRP271 4.7 27.8 1.0
CZ2 B:TRP293 4.7 20.0 1.0
CB B:ALA204 4.7 16.7 1.0
NE1 B:TRP271 4.7 25.4 1.0
O7B B:PQQ702 4.8 25.0 1.0
C9A B:PQQ702 4.9 44.3 1.0
C8 B:PQQ702 4.9 46.8 1.0
CE2 B:TRP293 5.0 16.2 1.0

Calcium binding site 5 out of 8 in 7cdl

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Calcium binding site 5 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca701

b:50.9
occ:1.00
 O5 G:PQQ702 2.3 33.8 1.0
OE2 G:GLU205 2.5 24.0 1.0
OD1 G:ASN289 2.6 21.5 1.0
N6 G:PQQ702 2.7 47.4 1.0
O7A G:PQQ702 2.8 44.9 1.0
OE1 G:GLU205 2.8 36.5 1.0
OD1 G:ASP331 2.9 22.6 1.0
CD G:GLU205 3.0 26.6 1.0
C5 G:PQQ702 3.2 48.5 1.0
CG G:ASN289 3.4 19.0 1.0
C6A G:PQQ702 3.4 54.0 1.0
O G:HOH803 3.5 55.4 1.0
C7X G:PQQ702 3.5 41.5 1.0
C7 G:PQQ702 3.6 46.7 1.0
ND2 G:ASN289 3.6 19.9 1.0
CG G:ASP331 3.6 22.8 1.0
OD2 G:ASP331 3.6 27.4 1.0
CB G:ALA333 4.0 17.2 1.0
O G:HOH802 4.0 24.1 1.0
NH2 G:ARG358 4.4 16.1 1.0
CG G:GLU205 4.4 23.2 1.0
C4 G:PQQ702 4.6 49.5 1.0
NE1 G:TRP293 4.6 21.0 1.0
CB G:ASN289 4.6 16.2 1.0
CZ2 G:TRP271 4.6 26.0 1.0
NE1 G:TRP271 4.7 24.6 1.0
CZ2 G:TRP293 4.7 21.7 1.0
O7B G:PQQ702 4.8 24.4 1.0
C9A G:PQQ702 4.8 48.5 1.0
CB G:ALA204 4.9 20.0 1.0
C8 G:PQQ702 5.0 47.6 1.0

Calcium binding site 6 out of 8 in 7cdl

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Calcium binding site 6 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca701

b:63.4
occ:1.00
 O5 H:PQQ702 2.3 40.1 1.0
OE2 H:GLU205 2.4 29.2 1.0
OD1 H:ASN289 2.8 23.9 1.0
N6 H:PQQ702 2.8 64.1 1.0
OD1 H:ASP331 2.9 28.5 1.0
O7A H:PQQ702 2.9 56.4 1.0
CD H:GLU205 3.0 36.5 1.0
O H:HOH801 3.1 46.3 1.0
OE1 H:GLU205 3.1 37.6 1.0
C5 H:PQQ702 3.3 56.1 1.0
CG H:ASN289 3.4 24.4 1.0
CG H:ASP331 3.5 27.1 1.0
OD2 H:ASP331 3.6 29.2 1.0
C6A H:PQQ702 3.6 67.0 1.0
ND2 H:ASN289 3.6 22.8 1.0
C7X H:PQQ702 3.7 56.2 1.0
C7 H:PQQ702 3.7 62.6 1.0
O H:HOH802 4.2 29.1 1.0
CB H:ALA333 4.2 21.1 1.0
NH2 H:ARG358 4.4 22.9 1.0
NE1 H:TRP293 4.4 28.4 1.0
CG H:GLU205 4.4 29.4 1.0
CZ2 H:TRP293 4.5 30.5 1.0
C4 H:PQQ702 4.6 56.4 1.0
CB H:ASN289 4.7 20.6 1.0
CZ2 H:TRP271 4.8 31.7 1.0
CE2 H:TRP293 4.8 29.9 1.0
CB H:ALA204 4.8 25.6 1.0
NE1 H:TRP271 4.9 28.3 1.0
O7B H:PQQ702 5.0 33.7 1.0
C9A H:PQQ702 5.0 59.9 1.0

Calcium binding site 7 out of 8 in 7cdl

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Calcium binding site 7 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca701

b:68.5
occ:1.00
 O5 M:PQQ702 2.4 41.1 1.0
OE2 M:GLU205 2.4 32.4 1.0
OD1 M:ASN289 2.7 24.5 1.0
O7A M:PQQ702 2.7 49.5 1.0
OD1 M:ASP331 2.7 27.6 1.0
N6 M:PQQ702 2.9 62.0 1.0
OE1 M:GLU205 2.9 43.6 1.0
CD M:GLU205 2.9 40.3 1.0
O M:HOH804 3.3 57.7 1.0
CG M:ASN289 3.3 25.2 1.0
C5 M:PQQ702 3.4 50.2 1.0
ND2 M:ASN289 3.5 24.0 1.0
CG M:ASP331 3.6 28.9 1.0
C6A M:PQQ702 3.6 56.7 1.0
OD2 M:ASP331 3.6 34.7 1.0
C7X M:PQQ702 3.6 45.4 1.0
C7 M:PQQ702 3.7 55.7 1.0
CB M:ALA333 4.1 22.8 1.0
O M:HOH815 4.1 33.1 1.0
CG M:GLU205 4.4 33.0 1.0
NE1 M:TRP293 4.4 23.4 1.0
NH2 M:ARG358 4.4 21.6 1.0
CB M:ASN289 4.6 22.4 1.0
CB M:ALA204 4.6 26.3 1.0
C4 M:PQQ702 4.7 51.9 1.0
CZ2 M:TRP293 4.7 24.8 1.0
CZ2 M:TRP271 4.7 28.8 1.0
NE1 M:TRP271 4.8 27.3 1.0
O7B M:PQQ702 4.9 33.1 1.0
CE2 M:TRP293 4.9 24.0 1.0
C9A M:PQQ702 5.0 52.3 1.0

Calcium binding site 8 out of 8 in 7cdl

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Calcium binding site 8 out of 8 in the Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Holo-Methanol Dehydrogenase (Mdh) with CYS131-CYS132 Reduced From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca701

b:48.3
occ:1.00
 O5 N:PQQ702 2.4 38.5 1.0
OE2 N:GLU205 2.5 23.4 1.0
O7A N:PQQ702 2.6 41.4 1.0
OE1 N:GLU205 2.6 31.3 1.0
OD1 N:ASN289 2.7 17.8 1.0
N6 N:PQQ702 2.7 52.7 1.0
CD N:GLU205 2.9 24.7 1.0
OD1 N:ASP331 3.0 20.2 1.0
C5 N:PQQ702 3.2 51.3 1.0
CG N:ASN289 3.4 16.5 1.0
C6A N:PQQ702 3.4 52.9 1.0
O N:HOH827 3.5 56.5 1.0
C7X N:PQQ702 3.5 42.1 1.0
C7 N:PQQ702 3.6 49.1 1.0
ND2 N:ASN289 3.7 17.3 1.0
CG N:ASP331 3.8 21.6 1.0
OD2 N:ASP331 3.9 23.8 1.0
O N:HOH810 4.1 24.1 1.0
CB N:ALA333 4.1 15.2 1.0
CG N:GLU205 4.4 21.0 1.0
NH2 N:ARG358 4.5 15.9 1.0
CZ2 N:TRP271 4.5 28.3 1.0
C4 N:PQQ702 4.5 59.6 1.0
CB N:ALA204 4.6 19.5 1.0
CB N:ASN289 4.6 13.1 1.0
NE1 N:TRP293 4.6 19.8 1.0
NE1 N:TRP271 4.7 21.3 1.0
O7B N:PQQ702 4.7 28.6 1.0
CZ2 N:TRP293 4.8 17.9 1.0
C9A N:PQQ702 4.8 47.8 1.0
CE2 N:TRP271 4.9 22.1 1.0
C8 N:PQQ702 4.9 46.1 1.0
O N:HOH1084 5.0 21.8 1.0

Reference:

S.I.Chan, C.J.Chen, P.Chuankhayan, P.K.R.Nareddy, I.K.Tsai, Y.F.Tsai, K.H.-C.Chen, S.S.-F.Yu. Reduced C131-C132 Form-Methanol Dehydrogenase Structure (Mdh) From Methylococcus Capsulatus (Bath)-Reduced Form To Be Published.
Page generated: Sat Jul 10 11:15:42 2021

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