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Calcium in PDB 7ce5: Methanol-Pqq Bound Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath)

Enzymatic activity of Methanol-Pqq Bound Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath)

All present enzymatic activity of Methanol-Pqq Bound Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath):
1.1.2.7;

Protein crystallography data

The structure of Methanol-Pqq Bound Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath), PDB code: 7ce5 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) 153.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 128.612, 211.828, 223.912, 90, 90, 90
R / Rfree (%) 14 / 17

Calcium Binding Sites:

The binding sites of Calcium atom in the Methanol-Pqq Bound Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) (pdb code 7ce5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Methanol-Pqq Bound Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath), PDB code: 7ce5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7ce5

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

b:41.3
occ:1.00
 O5 A:PQQ703 2.5 16.7 1.0
OD1 A:ASN289 2.6 16.7 1.0
OE2 A:GLU205 2.7 24.4 1.0
OE1 A:GLU205 2.8 29.9 1.0
O7A A:PQQ703 2.8 22.0 1.0
OD1 A:ASP331 2.9 22.7 1.0
N6 A:PQQ703 2.9 15.2 1.0
CD A:GLU205 3.0 24.4 1.0
CG A:ASN289 3.3 17.8 1.0
O A:MOH702 3.3 74.0 1.0
C5 A:PQQ703 3.4 17.7 1.0
C A:MOH702 3.6 67.5 1.0
ND2 A:ASN289 3.6 18.2 1.0
C6A A:PQQ703 3.6 16.7 1.0
C7X A:PQQ703 3.7 17.4 1.0
CG A:ASP331 3.8 19.9 1.0
C7 A:PQQ703 3.8 15.2 1.0
CB A:ALA333 3.9 14.9 1.0
OD2 A:ASP331 3.9 26.1 1.0
O A:HOH1091 4.0 17.2 1.0
NH2 A:ARG358 4.4 15.0 1.0
CG A:GLU205 4.5 19.8 1.0
CB A:ASN289 4.5 14.3 1.0
NE1 A:TRP293 4.6 16.9 1.0
CZ2 A:TRP271 4.7 14.1 1.0
CB A:ALA204 4.8 13.9 1.0
C4 A:PQQ703 4.8 16.0 1.0
NE1 A:TRP271 4.8 13.8 1.0
O7B A:PQQ703 4.9 15.2 1.0

Calcium binding site 2 out of 8 in 7ce5

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

b:42.3
occ:1.00
 OD1 B:ASN289 2.5 12.4 1.0
OE2 B:GLU205 2.5 22.4 1.0
O5 B:PQQ703 2.6 14.9 1.0
OD1 B:ASP331 2.8 22.7 1.0
O7B B:PQQ703 2.8 17.4 1.0
N6 B:PQQ703 2.9 12.7 1.0
OE1 B:GLU205 2.9 31.0 1.0
CD B:GLU205 3.1 25.3 1.0
CG B:ASN289 3.2 13.2 1.0
C5 B:PQQ703 3.5 15.0 1.0
ND2 B:ASN289 3.5 13.3 1.0
C B:MOH702 3.6 50.2 1.0
CG B:ASP331 3.6 24.1 1.0
O B:MOH702 3.7 56.7 1.0
C6A B:PQQ703 3.7 15.0 1.0
C7X B:PQQ703 3.7 16.1 1.0
C7 B:PQQ703 3.8 14.1 1.0
OD2 B:ASP331 3.8 26.5 1.0
CB B:ALA333 4.0 14.6 1.0
O B:HOH1107 4.1 16.8 1.0
NH2 B:ARG358 4.4 14.7 1.0
CB B:ASN289 4.5 12.2 1.0
CG B:GLU205 4.5 18.6 1.0
NE1 B:TRP293 4.5 17.1 1.0
CB B:ALA204 4.7 12.8 1.0
C4 B:PQQ703 4.8 15.1 1.0
CZ2 B:TRP271 4.9 13.0 1.0
NE1 B:TRP271 4.9 12.8 1.0
CZ2 B:TRP293 4.9 16.9 1.0
O7A B:PQQ703 4.9 14.5 1.0

Calcium binding site 3 out of 8 in 7ce5

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

b:42.9
occ:1.00
 O5 C:PQQ702 2.5 16.1 1.0
OE2 C:GLU205 2.6 19.3 1.0
OD1 C:ASN289 2.6 13.3 1.0
OD1 C:ASP331 2.8 19.8 1.0
OE1 C:GLU205 2.8 23.4 1.0
N6 C:PQQ702 2.8 14.1 1.0
O7B C:PQQ702 2.8 22.6 1.0
CD C:GLU205 3.0 20.0 1.0
CG C:ASN289 3.3 14.5 1.0
C C:MOH703 3.4 44.0 1.0
C5 C:PQQ702 3.4 16.2 1.0
ND2 C:ASN289 3.5 16.7 1.0
O C:MOH703 3.6 54.0 1.0
C6A C:PQQ702 3.7 14.5 1.0
CG C:ASP331 3.7 18.9 1.0
C7X C:PQQ702 3.7 17.8 1.0
C7 C:PQQ702 3.8 15.8 1.0
OD2 C:ASP331 3.8 22.8 1.0
CB C:ALA333 3.9 12.9 1.0
O C:HOH1028 4.0 15.0 1.0
NH2 C:ARG358 4.4 12.8 1.0
CG C:GLU205 4.5 17.1 1.0
CB C:ASN289 4.5 12.8 1.0
NE1 C:TRP293 4.6 16.4 1.0
CB C:ALA204 4.8 15.8 1.0
CZ2 C:TRP271 4.8 13.3 1.0
C4 C:PQQ702 4.8 15.7 1.0
NE1 C:TRP271 4.8 13.2 1.0
O7A C:PQQ702 4.9 13.9 1.0
CZ2 C:TRP293 4.9 17.0 1.0

Calcium binding site 4 out of 8 in 7ce5

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

b:43.4
occ:1.00
 OD1 D:ASN289 2.5 13.8 1.0
O5 D:PQQ703 2.6 15.0 1.0
OE2 D:GLU205 2.7 22.7 1.0
O7A D:PQQ703 2.7 19.9 1.0
N6 D:PQQ703 2.8 14.2 1.0
OE1 D:GLU205 2.8 29.0 1.0
OD1 D:ASP331 3.0 19.2 1.0
CD D:GLU205 3.0 21.9 1.0
CG D:ASN289 3.2 14.9 1.0
C5 D:PQQ703 3.5 17.8 1.0
ND2 D:ASN289 3.5 15.4 1.0
C D:MOH702 3.5 59.0 1.0
C7X D:PQQ703 3.6 15.8 1.0
C6A D:PQQ703 3.6 15.6 1.0
CG D:ASP331 3.7 20.0 1.0
C7 D:PQQ703 3.7 14.9 1.0
O D:MOH702 3.8 56.7 1.0
OD2 D:ASP331 3.8 22.5 1.0
CB D:ALA333 3.9 13.9 1.0
O D:HOH1086 3.9 16.7 1.0
CB D:ASN289 4.5 14.7 1.0
CG D:GLU205 4.5 18.5 1.0
NH2 D:ARG358 4.6 13.6 1.0
CB D:ALA204 4.6 14.9 1.0
NE1 D:TRP293 4.7 15.7 1.0
CZ2 D:TRP271 4.8 14.2 1.0
O7B D:PQQ703 4.8 14.4 1.0
NE1 D:TRP271 4.8 16.5 1.0
C4 D:PQQ703 4.8 15.6 1.0
CZ2 D:TRP293 4.9 17.2 1.0

Calcium binding site 5 out of 8 in 7ce5

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

b:44.1
occ:1.00
 OD1 G:ASN289 2.5 13.3 1.0
O5 G:PQQ703 2.5 14.9 1.0
OE2 G:GLU205 2.7 20.1 1.0
OE1 G:GLU205 2.8 25.6 1.0
N6 G:PQQ703 2.8 16.6 1.0
O7B G:PQQ703 2.8 18.2 1.0
OD1 G:ASP331 3.0 19.8 1.0
CD G:GLU205 3.0 20.9 1.0
CG G:ASN289 3.3 14.4 1.0
C5 G:PQQ703 3.4 17.0 1.0
C G:MOH702 3.5 43.3 1.0
ND2 G:ASN289 3.6 15.6 1.0
C6A G:PQQ703 3.6 15.9 1.0
O G:MOH702 3.6 54.5 1.0
C7X G:PQQ703 3.7 17.3 1.0
C7 G:PQQ703 3.7 15.7 1.0
CG G:ASP331 3.8 19.1 1.0
OD2 G:ASP331 3.9 20.1 1.0
CB G:ALA333 4.0 14.9 1.0
O G:HOH963 4.1 16.7 1.0
NH2 G:ARG358 4.5 12.8 1.0
CG G:GLU205 4.5 17.5 1.0
CB G:ASN289 4.5 12.1 1.0
CB G:ALA204 4.6 12.4 1.0
CZ2 G:TRP271 4.7 13.4 1.0
NE1 G:TRP293 4.7 15.4 1.0
NE1 G:TRP271 4.7 12.5 1.0
C4 G:PQQ703 4.8 17.2 1.0
O7A G:PQQ703 4.8 14.4 1.0
O G:HOH933 5.0 15.2 1.0
C9A G:PQQ703 5.0 14.8 1.0

Calcium binding site 6 out of 8 in 7ce5

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

b:45.6
occ:1.00
 OD1 H:ASN289 2.5 23.6 1.0
O5 H:PQQ703 2.6 18.9 1.0
OE2 H:GLU205 2.6 24.8 1.0
OE1 H:GLU205 2.7 31.1 1.0
O7A H:PQQ703 2.8 22.2 1.0
N6 H:PQQ703 2.8 18.3 1.0
OD1 H:ASP331 2.9 23.5 1.0
CD H:GLU205 3.0 28.5 1.0
CG H:ASN289 3.3 22.9 1.0
C5 H:PQQ703 3.4 21.1 1.0
ND2 H:ASN289 3.5 21.6 1.0
C H:MOH702 3.5 64.8 1.0
O H:MOH702 3.6 72.6 1.0
C6A H:PQQ703 3.6 20.5 1.0
C7X H:PQQ703 3.7 20.4 1.0
C7 H:PQQ703 3.7 19.6 1.0
CG H:ASP331 3.7 23.5 1.0
OD2 H:ASP331 3.8 33.7 1.0
O H:HOH1070 4.0 21.5 1.0
CB H:ALA333 4.0 17.4 1.0
CG H:GLU205 4.4 23.8 1.0
NH2 H:ARG358 4.5 17.7 1.0
CB H:ASN289 4.5 21.9 1.0
NE1 H:TRP293 4.6 21.7 1.0
CB H:ALA204 4.7 19.6 1.0
C4 H:PQQ703 4.8 18.8 1.0
CZ2 H:TRP271 4.8 17.7 1.0
O7B H:PQQ703 4.9 18.4 1.0
NE1 H:TRP271 4.9 17.4 1.0
O H:HOH946 4.9 20.6 1.0
CZ2 H:TRP293 5.0 22.7 1.0

Calcium binding site 7 out of 8 in 7ce5

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

b:40.4
occ:1.00
 OD1 M:ASN289 2.5 16.4 1.0
O5 M:PQQ703 2.6 15.9 1.0
OE2 M:GLU205 2.6 19.6 1.0
OE1 M:GLU205 2.8 29.6 1.0
O7B M:PQQ703 2.8 19.0 1.0
OD1 M:ASP331 2.9 20.6 1.0
N6 M:PQQ703 2.9 13.9 1.0
CD M:GLU205 3.0 21.9 1.0
CG M:ASN289 3.3 15.3 1.0
C5 M:PQQ703 3.5 15.4 1.0
C M:MOH702 3.5 42.7 1.0
ND2 M:ASN289 3.5 16.6 1.0
O M:MOH702 3.6 45.5 1.0
C7X M:PQQ703 3.7 17.6 1.0
C6A M:PQQ703 3.7 15.6 1.0
CG M:ASP331 3.7 19.9 1.0
C7 M:PQQ703 3.8 15.7 1.0
OD2 M:ASP331 3.9 24.3 1.0
O M:HOH1003 4.0 16.4 1.0
CB M:ALA333 4.0 13.9 1.0
NH2 M:ARG358 4.5 14.6 1.0
CG M:GLU205 4.5 18.2 1.0
CB M:ASN289 4.5 13.6 1.0
NE1 M:TRP293 4.6 16.0 1.0
CB M:ALA204 4.7 15.2 1.0
C4 M:PQQ703 4.8 14.3 1.0
CZ2 M:TRP271 4.8 13.1 1.0
NE1 M:TRP271 4.9 12.2 1.0
O7A M:PQQ703 4.9 15.2 1.0

Calcium binding site 8 out of 8 in 7ce5

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

b:51.3
occ:1.00
 OD1 N:ASN289 2.5 19.8 1.0
O5 N:PQQ703 2.6 19.1 1.0
OE2 N:GLU205 2.7 27.1 1.0
O7A N:PQQ703 2.8 21.0 1.0
N6 N:PQQ703 2.8 16.0 1.0
OE1 N:GLU205 2.9 39.2 1.0
OD1 N:ASP331 2.9 26.2 1.0
CD N:GLU205 3.1 30.0 1.0
CG N:ASN289 3.3 21.4 1.0
C5 N:PQQ703 3.5 19.3 1.0
O N:MOH702 3.5 49.0 1.0
ND2 N:ASN289 3.5 21.9 1.0
CG N:ASP331 3.6 25.9 1.0
C N:MOH702 3.6 49.2 1.0
OD2 N:ASP331 3.6 29.3 1.0
C6A N:PQQ703 3.6 16.6 1.0
C7X N:PQQ703 3.7 19.5 1.0
C7 N:PQQ703 3.7 16.0 1.0
O N:HOH985 4.0 21.8 1.0
CB N:ALA333 4.0 17.2 1.0
NH2 N:ARG358 4.4 15.9 1.0
CG N:GLU205 4.5 22.7 1.0
CB N:ASN289 4.5 19.5 1.0
NE1 N:TRP293 4.6 20.8 1.0
CB N:ALA204 4.8 17.0 1.0
CZ2 N:TRP271 4.8 16.2 1.0
C4 N:PQQ703 4.8 16.9 1.0
O7B N:PQQ703 4.8 17.2 1.0
NE1 N:TRP271 4.9 15.4 1.0
CZ2 N:TRP293 4.9 20.2 1.0
O N:HOH842 5.0 20.6 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: Thu Jul 18 23:37:53 2024

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