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Calcium in PDB 7ce9: Pqq-Soaked Apo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath)

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

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

Protein crystallography data

The structure of Pqq-Soaked Apo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath), PDB code: 7ce9 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 128.563, 211.756, 223.736, 90, 90, 90
R / Rfree (%) 16.1 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Pqq-Soaked Apo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath) (pdb code 7ce9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pqq-Soaked Apo-Methanol Dehydrogenase (Mdh) From Methylococcus Capsulatus (Bath), PDB code: 7ce9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7ce9

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

b:57.4
occ:1.00
 O5 A:PQQ702 2.6 23.4 1.0
OD1 A:ASN289 2.6 23.2 1.0
OE1 A:GLU205 2.8 34.0 1.0
N6 A:PQQ702 2.9 24.8 1.0
OE2 A:GLU205 2.9 27.3 1.0
O7B A:PQQ702 2.9 25.6 1.0
OD1 A:ASP331 2.9 29.0 1.0
CD A:GLU205 3.1 31.9 1.0
CG A:ASN289 3.3 24.0 1.0
O A:HOH838 3.4 66.6 1.0
C5 A:PQQ702 3.5 25.2 1.0
ND2 A:ASN289 3.5 22.6 1.0
C6A A:PQQ702 3.7 25.7 1.0
OD2 A:ASP331 3.7 30.8 1.0
C7X A:PQQ702 3.7 26.3 1.0
CG A:ASP331 3.7 27.6 1.0
C7 A:PQQ702 3.7 24.4 1.0
CB A:ALA333 3.9 23.3 1.0
O A:HOH852 3.9 27.2 1.0
NH2 A:ARG358 4.3 18.7 1.0
CB A:ASN289 4.6 22.5 1.0
CG A:GLU205 4.6 28.7 1.0
CB A:ALA204 4.7 21.1 1.0
NE1 A:TRP293 4.8 21.2 1.0
C4 A:PQQ702 4.8 23.7 1.0
CZ2 A:TRP271 4.8 18.1 1.0
O7A A:PQQ702 4.8 23.5 1.0
NE1 A:TRP271 4.8 20.1 1.0

Calcium binding site 2 out of 8 in 7ce9

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

b:61.3
occ:1.00
 OD1 B:ASN289 2.6 16.5 1.0
O5 B:PQQ702 2.6 18.3 1.0
OE2 B:GLU205 2.8 30.6 1.0
O7A B:PQQ702 2.8 19.1 1.0
OE1 B:GLU205 2.8 36.3 1.0
OD1 B:ASP331 2.8 25.9 1.0
N6 B:PQQ702 2.9 20.3 1.0
CD B:GLU205 3.2 29.9 1.0
CG B:ASN289 3.3 15.6 1.0
C5 B:PQQ702 3.5 19.1 1.0
O B:HOH984 3.6 52.9 1.0
CG B:ASP331 3.6 21.7 1.0
OD2 B:ASP331 3.6 25.1 1.0
ND2 B:ASN289 3.6 16.8 1.0
C6A B:PQQ702 3.7 20.8 1.0
C7X B:PQQ702 3.7 20.0 1.0
C7 B:PQQ702 3.8 19.9 1.0
O B:HOH864 3.8 20.9 1.0
CB B:ALA333 4.0 13.2 1.0
NH2 B:ARG358 4.3 16.1 1.0
CB B:ASN289 4.5 15.6 1.0
NE1 B:TRP293 4.5 21.0 1.0
CG B:GLU205 4.6 25.2 1.0
CB B:ALA204 4.7 17.8 1.0
C4 B:PQQ702 4.8 18.4 1.0
CZ2 B:TRP293 4.9 19.2 1.0
CZ2 B:TRP271 4.9 17.3 1.0
O7B B:PQQ702 4.9 18.4 1.0
NE1 B:TRP271 5.0 18.1 1.0

Calcium binding site 3 out of 8 in 7ce9

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

b:54.7
occ:1.00
 O5 C:PQQ702 2.4 20.5 1.0
OE1 C:GLU205 2.7 34.5 1.0
OE2 C:GLU205 2.8 30.4 1.0
OD1 C:ASN289 2.8 18.9 1.0
N6 C:PQQ702 2.8 22.2 1.0
OD1 C:ASP331 3.0 18.4 1.0
O7A C:PQQ702 3.0 27.9 1.0
CD C:GLU205 3.0 30.3 1.0
O C:HOH843 3.1 37.3 1.0
C5 C:PQQ702 3.4 24.6 1.0
CG C:ASN289 3.5 19.4 1.0
C6A C:PQQ702 3.6 22.5 1.0
C7 C:PQQ702 3.7 24.1 1.0
ND2 C:ASN289 3.7 19.9 1.0
CG C:ASP331 3.7 18.6 1.0
OD2 C:ASP331 3.7 19.6 1.0
C7X C:PQQ702 3.7 24.8 1.0
O C:HOH817 4.1 19.7 1.0
CB C:ALA333 4.2 15.4 1.0
NH2 C:ARG358 4.4 15.3 1.0
CG C:GLU205 4.5 25.8 1.0
NE1 C:TRP293 4.6 20.5 1.0
CB C:ASN289 4.7 18.7 1.0
C4 C:PQQ702 4.7 24.9 1.0
CB C:ALA204 4.8 17.4 1.0
CZ2 C:TRP271 4.9 15.9 1.0
CZ2 C:TRP293 4.9 19.6 1.0
NE1 C:TRP271 4.9 15.6 1.0
O7B C:PQQ702 4.9 25.2 1.0
C9A C:PQQ702 5.0 20.9 1.0
O C:HOH1003 5.0 18.8 1.0
C8 C:PQQ702 5.0 22.8 1.0

Calcium binding site 4 out of 8 in 7ce9

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

b:59.8
occ:1.00
 OD1 D:ASN289 2.6 17.1 1.0
O5 D:PQQ702 2.6 21.1 1.0
OE2 D:GLU205 2.7 28.6 1.0
OD1 D:ASP331 2.8 22.2 1.0
O7B D:PQQ702 2.8 22.5 1.0
N6 D:PQQ702 2.9 20.2 1.0
OE1 D:GLU205 2.9 37.6 1.0
CD D:GLU205 3.1 30.0 1.0
CG D:ASN289 3.3 17.2 1.0
O D:HOH826 3.4 62.0 1.0
C5 D:PQQ702 3.5 21.6 1.0
C6A D:PQQ702 3.6 19.9 1.0
ND2 D:ASN289 3.6 19.5 1.0
CG D:ASP331 3.7 22.7 1.0
C7X D:PQQ702 3.7 22.0 1.0
C7 D:PQQ702 3.7 21.0 1.0
OD2 D:ASP331 3.8 27.3 1.0
CB D:ALA333 3.9 13.2 1.0
O D:HOH884 4.0 21.6 1.0
NH2 D:ARG358 4.4 14.8 1.0
CB D:ASN289 4.5 18.0 1.0
CB D:ALA204 4.6 17.2 1.0
CG D:GLU205 4.6 25.3 1.0
CZ2 D:TRP271 4.7 16.7 1.0
C4 D:PQQ702 4.7 19.2 1.0
NE1 D:TRP293 4.8 21.7 1.0
NE1 D:TRP271 4.8 17.0 1.0
O7A D:PQQ702 4.8 19.5 1.0
CZ2 D:TRP293 4.9 18.8 1.0
C9A D:PQQ702 5.0 19.1 1.0

Calcium binding site 5 out of 8 in 7ce9

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

b:67.5
occ:1.00
 OD1 G:ASN289 2.4 20.6 1.0
OE2 G:GLU205 2.8 32.0 1.0
OD1 G:ASP331 2.8 24.7 1.0
O5 G:PQQ702 2.8 22.4 1.0
O7B G:PQQ702 2.9 26.6 1.0
OE1 G:GLU205 3.0 44.7 1.0
CG G:ASN289 3.1 22.9 1.0
N6 G:PQQ702 3.1 23.9 1.0
CD G:GLU205 3.2 35.7 1.0
ND2 G:ASN289 3.3 23.2 1.0
O G:HOH844 3.6 44.2 1.0
CG G:ASP331 3.6 28.3 1.0
OD2 G:ASP331 3.7 30.4 1.0
C5 G:PQQ702 3.8 22.1 1.0
C7X G:PQQ702 3.8 24.7 1.0
O G:HOH865 3.8 30.1 1.0
CB G:ALA333 3.9 20.6 1.0
C7 G:PQQ702 3.9 24.9 1.0
C6A G:PQQ702 3.9 24.6 1.0
CB G:ASN289 4.3 21.6 1.0
NE1 G:TRP293 4.5 23.1 1.0
NH2 G:ARG358 4.5 17.6 1.0
CB G:ALA204 4.6 23.3 1.0
CG G:GLU205 4.7 30.1 1.0
CZ2 G:TRP271 4.9 20.3 1.0
O7A G:PQQ702 4.9 23.3 1.0
NE1 G:TRP271 4.9 19.0 1.0
N G:ASN289 5.0 19.8 1.0

Calcium binding site 6 out of 8 in 7ce9

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

b:60.0
occ:1.00
 O5 H:PQQ702 2.5 20.1 1.0
OD1 H:ASN289 2.6 17.8 1.0
N6 H:PQQ702 2.7 25.9 1.0
OE2 H:GLU205 2.7 22.9 1.0
OE1 H:GLU205 2.8 23.7 1.0
O7A H:PQQ702 2.8 25.0 1.0
OD1 H:ASP331 2.9 20.6 1.0
CD H:GLU205 3.1 23.6 1.0
O H:HOH805 3.2 37.9 1.0
C5 H:PQQ702 3.4 24.4 1.0
CG H:ASN289 3.4 16.3 1.0
C6A H:PQQ702 3.5 24.4 1.0
C7 H:PQQ702 3.6 27.5 1.0
C7X H:PQQ702 3.6 25.5 1.0
ND2 H:ASN289 3.7 16.7 1.0
CG H:ASP331 3.8 20.6 1.0
OD2 H:ASP331 4.0 25.4 1.0
CB H:ALA333 4.0 15.1 1.0
O H:HOH818 4.0 19.4 1.0
NH2 H:ARG358 4.4 13.9 1.0
CZ2 H:TRP271 4.6 17.7 1.0
CG H:GLU205 4.6 20.6 1.0
CB H:ASN289 4.6 15.6 1.0
CB H:ALA204 4.6 17.6 1.0
C4 H:PQQ702 4.7 24.1 1.0
NE1 H:TRP271 4.7 16.7 1.0
NE1 H:TRP293 4.8 23.1 1.0
O7B H:PQQ702 4.8 23.8 1.0
C9A H:PQQ702 4.8 23.3 1.0
O H:HOH882 4.9 15.1 1.0
C8 H:PQQ702 4.9 24.4 1.0
CE2 H:TRP271 5.0 16.8 1.0

Calcium binding site 7 out of 8 in 7ce9

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

b:58.6
occ:1.00
 O5 M:PQQ702 2.6 21.0 1.0
OD1 M:ASN289 2.6 21.1 1.0
OE2 M:GLU205 2.7 24.3 1.0
OE1 M:GLU205 2.8 31.4 1.0
O7A M:PQQ702 2.8 22.8 1.0
OD1 M:ASP331 2.8 24.9 1.0
N6 M:PQQ702 2.9 20.5 1.0
CD M:GLU205 3.0 27.2 1.0
CG M:ASN289 3.3 19.7 1.0
O M:HOH841 3.4 48.4 1.0
C5 M:PQQ702 3.5 24.7 1.0
CG M:ASP331 3.6 27.0 1.0
C7X M:PQQ702 3.7 23.3 1.0
C6A M:PQQ702 3.7 22.8 1.0
ND2 M:ASN289 3.7 18.1 1.0
OD2 M:ASP331 3.7 32.1 1.0
C7 M:PQQ702 3.7 22.6 1.0
O M:HOH805 4.0 25.5 1.0
CB M:ALA333 4.0 17.4 1.0
NH2 M:ARG358 4.4 17.9 1.0
CB M:ASN289 4.5 20.2 1.0
CG M:GLU205 4.5 25.4 1.0
NE1 M:TRP293 4.6 19.7 1.0
CB M:ALA204 4.7 19.9 1.0
C4 M:PQQ702 4.8 21.9 1.0
O7B M:PQQ702 4.8 20.7 1.0
CZ2 M:TRP293 4.9 19.7 1.0
NE1 M:TRP271 4.9 18.4 1.0
CZ2 M:TRP271 5.0 18.4 1.0

Calcium binding site 8 out of 8 in 7ce9

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

b:77.5
occ:1.00
 OD1 N:ASN289 2.6 26.4 1.0
OE2 N:GLU205 2.7 40.6 1.0
O5 N:PQQ702 2.7 27.6 1.0
OD1 N:ASP331 2.8 24.2 1.0
N6 N:PQQ702 2.9 25.4 1.0
O7B N:PQQ702 2.9 24.7 1.0
OE1 N:GLU205 3.0 44.9 1.0
CD N:GLU205 3.1 36.4 1.0
CG N:ASN289 3.3 27.6 1.0
O N:HOH817 3.4 45.1 1.0
C5 N:PQQ702 3.6 26.7 1.0
CG N:ASP331 3.6 28.4 1.0
ND2 N:ASN289 3.7 32.6 1.0
OD2 N:ASP331 3.7 34.5 1.0
C6A N:PQQ702 3.7 27.3 1.0
C7X N:PQQ702 3.7 28.2 1.0
C7 N:PQQ702 3.7 25.2 1.0
O N:HOH808 3.9 25.2 1.0
CB N:ALA333 4.0 21.2 1.0
NH2 N:ARG358 4.4 20.4 1.0
CB N:ASN289 4.4 26.6 1.0
CG N:GLU205 4.5 33.2 1.0
NE1 N:TRP293 4.6 27.1 1.0
CB N:ALA204 4.7 20.7 1.0
C4 N:PQQ702 4.8 25.4 1.0
CZ2 N:TRP271 4.8 23.0 1.0
O7A N:PQQ702 4.9 26.9 1.0
NE1 N:TRP271 4.9 23.2 1.0
O N:HOH802 4.9 28.8 1.0
CZ2 N:TRP293 5.0 27.9 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: Thu Jul 18 23:39:06 2024

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