Calcium in PDB 7cfx: Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath)

Enzymatic activity of Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath)

All present enzymatic activity of Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath):
1.1.2.7;

Protein crystallography data

The structure of Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath), PDB code: 7cfx 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 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.901, 211.028, 221.723, 90, 90, 90
R / Rfree (%) 18 / 24

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 7cfx

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Calcium binding site 1 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:118.8
occ:1.00
 O5 C:PQQ702 2.3 73.5 1.0
OD1 C:ASN289 2.5 25.8 1.0
N6 C:PQQ702 2.9 89.7 1.0
OE2 C:GLU205 2.9 43.1 1.0
OD1 C:ASP331 3.1 26.9 1.0
OE1 C:GLU205 3.2 45.2 1.0
O7B C:PQQ702 3.3 87.3 1.0
CG C:ASN289 3.3 27.7 1.0
C5 C:PQQ702 3.3 83.9 1.0
CD C:GLU205 3.4 45.8 1.0
C6A C:PQQ702 3.6 84.3 1.0
O C:HOH814 3.7 60.6 1.0
OD2 C:ASP331 3.7 29.7 1.0
ND2 C:ASN289 3.7 30.4 1.0
O C:HOH849 3.7 44.8 1.0
CG C:ASP331 3.8 26.3 1.0
C7 C:PQQ702 3.8 81.4 1.0
CB C:ALA333 3.8 23.9 1.0
C7X C:PQQ702 3.8 75.6 1.0
NH2 C:ARG358 4.3 34.5 1.0
NE1 C:TRP271 4.4 26.4 1.0
CB C:ASN289 4.5 26.0 1.0
CZ2 C:TRP271 4.6 30.1 1.0
C4 C:PQQ702 4.6 80.2 1.0
CB C:ALA204 4.7 27.0 1.0
CG C:GLU205 4.8 39.0 1.0
NE1 C:TRP293 4.8 28.1 1.0
CE2 C:TRP271 4.8 28.1 1.0
O7A C:PQQ702 4.9 55.1 1.0

Calcium binding site 2 out of 8 in 7cfx

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Calcium binding site 2 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:122.8
occ:1.00
 OD1 D:ASN289 2.3 26.0 1.0
N6 D:PQQ702 2.8 101.4 1.0
O5 D:PQQ702 2.8 72.0 1.0
O7A D:PQQ702 2.9 54.6 1.0
OE2 D:GLU205 3.2 41.0 1.0
O D:HOH806 3.2 62.1 1.0
CG D:ASN289 3.4 28.3 1.0
OE1 D:GLU205 3.4 52.1 1.0
C5 D:PQQ702 3.5 92.6 1.0
C7 D:PQQ702 3.6 89.7 1.0
C6A D:PQQ702 3.6 94.5 1.0
CB D:ALA333 3.6 25.8 1.0
C7X D:PQQ702 3.6 80.4 1.0
CD D:GLU205 3.7 46.4 1.0
OD1 D:ASP331 3.7 33.0 1.0
NE1 D:TRP271 3.8 30.7 1.0
ND2 D:ASN289 3.9 28.8 1.0
CZ2 D:TRP271 4.0 31.0 1.0
CB D:ALA204 4.0 30.1 1.0
CE2 D:TRP271 4.2 29.8 1.0
CB D:ASN289 4.6 29.7 1.0
O D:HOH802 4.6 51.1 1.0
O7B D:PQQ702 4.6 77.0 1.0
CG D:ASP331 4.6 31.8 1.0
N D:ASN289 4.7 26.6 1.0
OD2 D:ASP331 4.7 31.3 1.0
C4 D:PQQ702 4.8 100.1 1.0
C8 D:PQQ702 4.8 80.5 1.0
CA D:ALA333 4.8 25.2 1.0
C9A D:PQQ702 4.9 87.8 1.0
NH2 D:ARG358 4.9 38.2 1.0
CD1 D:TRP271 5.0 30.8 1.0

Calcium binding site 3 out of 8 in 7cfx

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Calcium binding site 3 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:124.9
occ:1.00
 O5 A:PQQ702 2.5 88.0 1.0
OD1 A:ASN289 2.6 45.9 1.0
N6 A:PQQ702 2.8 118.5 1.0
OE1 A:GLU205 3.0 60.5 1.0
O7A A:PQQ702 3.1 97.3 1.0
O A:HOH816 3.1 35.5 1.0
OE2 A:GLU205 3.2 61.1 1.0
C5 A:PQQ702 3.4 104.0 1.0
OD1 A:ASP331 3.4 49.6 1.0
CG A:ASN289 3.4 45.0 1.0
CD A:GLU205 3.5 58.1 1.0
C6A A:PQQ702 3.5 112.4 1.0
C7 A:PQQ702 3.7 114.2 1.0
C7X A:PQQ702 3.7 107.2 1.0
ND2 A:ASN289 3.7 49.5 1.0
CB A:ALA333 3.8 38.7 1.0
CB A:ALA204 3.9 42.9 1.0
OD2 A:ASP331 4.1 42.8 1.0
NE1 A:TRP271 4.1 36.8 1.0
CG A:ASP331 4.2 43.7 1.0
CZ2 A:TRP271 4.3 39.7 1.0
NH2 A:ARG358 4.6 36.6 1.0
CE2 A:TRP271 4.6 37.0 1.0
C4 A:PQQ702 4.6 104.9 1.0
CB A:ASN289 4.7 46.9 1.0
O7B A:PQQ702 4.7 95.1 1.0
N A:ASN289 4.9 46.2 1.0
C9A A:PQQ702 4.9 113.5 1.0
O4 A:PQQ702 5.0 99.8 1.0
C8 A:PQQ702 5.0 110.1 1.0
CG A:GLU205 5.0 54.5 1.0

Calcium binding site 4 out of 8 in 7cfx

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Calcium binding site 4 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:128.2
occ:1.00
 O5 B:PQQ702 2.3 73.3 1.0
OD1 B:ASN289 2.6 22.7 1.0
OE2 B:GLU205 2.7 39.4 1.0
N6 B:PQQ702 2.9 114.3 1.0
OE1 B:GLU205 3.0 47.2 1.0
CD B:GLU205 3.1 45.9 1.0
C5 B:PQQ702 3.3 96.6 1.0
OD1 B:ASP331 3.3 23.2 1.0
CG B:ASN289 3.4 23.0 1.0
O7B B:PQQ702 3.4 97.7 1.0
O B:HOH841 3.5 46.6 1.0
C6A B:PQQ702 3.6 103.7 1.0
ND2 B:ASN289 3.8 23.9 1.0
C7 B:PQQ702 3.9 103.8 1.0
CB B:ALA333 3.9 22.0 1.0
O B:HOH802 4.0 58.7 1.0
C7X B:PQQ702 4.0 93.6 1.0
CG B:ASP331 4.0 24.4 1.0
OD2 B:ASP331 4.1 25.6 1.0
NH2 B:ARG358 4.2 29.7 1.0
CZ2 B:TRP271 4.4 28.0 1.0
C4 B:PQQ702 4.5 99.9 1.0
CB B:ALA204 4.5 29.2 1.0
CB B:ASN289 4.6 22.6 1.0
NE1 B:TRP271 4.6 26.4 1.0
CG B:GLU205 4.6 40.9 1.0
O4 B:PQQ702 4.8 100.3 1.0
CE2 B:TRP271 4.8 27.2 1.0
NE1 B:TRP293 4.8 29.8 1.0
C9A B:PQQ702 5.0 103.0 1.0
CZ2 B:TRP293 5.0 27.2 1.0

Calcium binding site 5 out of 8 in 7cfx

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Calcium binding site 5 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca701

b:149.9
occ:1.00
 OD1 G:ASN289 2.3 28.0 1.0
O5 G:PQQ702 2.7 114.5 1.0
O G:HOH813 2.7 51.4 1.0
N6 G:PQQ702 3.0 142.3 1.0
OE2 G:GLU205 3.2 48.8 1.0
O7B G:PQQ702 3.3 88.1 1.0
CG G:ASN289 3.3 30.4 1.0
CB G:ALA333 3.5 32.9 1.0
C5 G:PQQ702 3.5 124.1 1.0
OD1 G:ASP331 3.5 31.3 1.0
OE1 G:GLU205 3.6 60.3 1.0
NE1 G:TRP271 3.6 34.3 1.0
C6A G:PQQ702 3.7 135.3 1.0
CD G:GLU205 3.8 58.1 1.0
C7 G:PQQ702 3.8 123.0 1.0
C7X G:PQQ702 3.9 109.2 1.0
ND2 G:ASN289 3.9 30.4 1.0
CZ2 G:TRP271 4.0 36.9 1.0
CE2 G:TRP271 4.1 33.7 1.0
CB G:ALA204 4.3 37.9 1.0
NH2 G:ARG358 4.4 45.4 1.0
N G:ASN289 4.5 29.2 1.0
CG G:ASP331 4.5 34.9 1.0
CB G:ASN289 4.5 31.4 1.0
OD2 G:ASP331 4.7 36.2 1.0
C4 G:PQQ702 4.7 118.0 1.0
CD1 G:TRP271 4.8 33.1 1.0
OG1 G:THR269 4.8 31.8 1.0
CA G:ALA333 4.9 31.9 1.0
O7A G:PQQ702 4.9 99.7 1.0
C9A G:PQQ702 5.0 129.6 1.0

Calcium binding site 6 out of 8 in 7cfx

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Calcium binding site 6 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca701

b:119.8
occ:1.00
 O5 H:PQQ702 2.3 92.7 1.0
OD1 H:ASN289 2.5 26.2 1.0
OE2 H:GLU205 2.8 39.3 1.0
N6 H:PQQ702 3.0 126.0 1.0
OE1 H:GLU205 3.1 44.6 1.0
OD1 H:ASP331 3.2 36.0 1.0
CG H:ASN289 3.3 25.4 1.0
C5 H:PQQ702 3.3 109.1 1.0
O7B H:PQQ702 3.3 103.5 1.0
CD H:GLU205 3.3 39.1 1.0
C6A H:PQQ702 3.6 120.1 1.0
ND2 H:ASN289 3.7 24.9 1.0
O H:HOH807 3.7 39.8 1.0
CB H:ALA333 3.8 22.3 1.0
C7 H:PQQ702 3.9 111.7 1.0
CG H:ASP331 4.0 35.1 1.0
C7X H:PQQ702 4.1 100.4 1.0
OD2 H:ASP331 4.1 35.8 1.0
CZ2 H:TRP271 4.3 32.6 1.0
NE1 H:TRP271 4.4 30.7 1.0
CB H:ASN289 4.4 26.8 1.0
CB H:ALA204 4.5 30.1 1.0
C4 H:PQQ702 4.5 105.6 1.0
NH2 H:ARG358 4.5 28.2 1.0
CE2 H:TRP271 4.7 30.0 1.0
O4 H:PQQ702 4.8 109.1 1.0
CG H:GLU205 4.8 36.3 1.0
NE1 H:TRP293 4.9 28.8 1.0
C9A H:PQQ702 5.0 115.5 1.0

Calcium binding site 7 out of 8 in 7cfx

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Calcium binding site 7 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca701

b:118.5
occ:1.00
 O5 M:PQQ702 1.9 137.3 1.0
OD2 M:ASP331 2.6 35.3 1.0
OD1 M:ASP331 2.7 36.7 1.0
OE2 M:GLU205 2.8 51.1 1.0
CG M:ASP331 3.0 34.4 1.0
C5 M:PQQ702 3.2 137.3 1.0
CD M:GLU205 3.2 48.2 1.0
OE1 M:GLU205 3.3 47.0 1.0
N6 M:PQQ702 3.5 150.4 1.0
OD1 M:ASN289 3.5 33.1 1.0
NH2 M:ARG358 3.6 32.9 1.0
C6A M:PQQ702 3.9 140.4 1.0
CG M:ASN289 3.9 29.8 1.0
ND2 M:ASN289 4.0 30.6 1.0
CZ2 M:TRP293 4.0 33.2 1.0
CB M:ALA333 4.1 28.2 1.0
C4 M:PQQ702 4.2 131.1 1.0
O4 M:PQQ702 4.2 135.7 1.0
O7B M:PQQ702 4.3 95.0 1.0
NE1 M:TRP293 4.3 37.7 1.0
CG M:GLU205 4.4 45.8 1.0
CB M:ASP331 4.5 32.8 1.0
CE2 M:TRP293 4.5 34.9 1.0
C7 M:PQQ702 4.6 132.8 1.0
CZ M:ARG358 4.7 33.5 1.0
NH1 M:ARG358 4.9 35.1 1.0
CZ2 M:TRP271 4.9 41.2 1.0
O M:ASP331 4.9 31.2 1.0
CB M:ASN289 4.9 28.5 1.0
C7X M:PQQ702 5.0 119.2 1.0

Calcium binding site 8 out of 8 in 7cfx

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Calcium binding site 8 out of 8 in the Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) 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 Nad-Soaked Holo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca701

b:140.0
occ:1.00
 O5 N:PQQ702 2.1 112.9 1.0
OE2 N:GLU205 2.7 55.0 1.0
OD1 N:ASP331 2.7 38.5 1.0
OD1 N:ASN289 2.9 34.2 1.0
N6 N:PQQ702 3.2 149.0 1.0
C5 N:PQQ702 3.3 126.4 1.0
CG N:ASN289 3.4 33.2 1.0
CD N:GLU205 3.4 62.2 1.0
OD2 N:ASP331 3.4 41.3 1.0
OE1 N:GLU205 3.4 63.7 1.0
CG N:ASP331 3.4 37.3 1.0
ND2 N:ASN289 3.5 30.4 1.0
O7A N:PQQ702 3.7 98.8 1.0
C6A N:PQQ702 3.8 139.8 1.0
NH2 N:ARG358 4.0 44.4 1.0
CB N:ALA333 4.1 32.4 1.0
NE1 N:TRP293 4.3 40.7 1.0
O N:HOH802 4.3 49.9 1.0
C7 N:PQQ702 4.3 131.5 1.0
CZ2 N:TRP293 4.4 43.5 1.0
C7X N:PQQ702 4.4 118.6 1.0
C4 N:PQQ702 4.5 123.6 1.0
CB N:ASN289 4.6 33.3 1.0
O4 N:PQQ702 4.7 118.6 1.0
CE2 N:TRP293 4.7 38.5 1.0
CG N:GLU205 4.8 56.1 1.0
CZ2 N:TRP271 4.8 40.7 1.0
CB N:ASP331 4.9 35.4 1.0
CB N:ALA204 5.0 41.9 1.0

Reference:

S.I.Chan, P.Chuankhayan, P.K.Reddy Nareddy, I.K.Tsai, Y.F.Tsai, K.H.Chen, S.S.Yu, C.J.Chen. Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry From Spectroscopic and High-Resolution X-Ray Structural Studies of the Methanol Dehydrogenase From Methylococcus Capsulatus (Bath). J.Am.Chem.Soc. V. 143 3359 2021.
ISSN: ESSN 1520-5126
PubMed: 33629832
DOI: 10.1021/JACS.0C11414
Page generated: Sat Jul 10 11:18:43 2021

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