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Calcium in PDB 4tqo: The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath)

Protein crystallography data

The structure of The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath), PDB code: 4tqo was solved by M.A.Culpepper, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.15 / 2.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 128.490, 210.290, 231.420, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 20.8

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 4tqo

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Calcium binding site 1 out of 8 in the The Crystal Structure of Methanol Dehydrogenase 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 The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:38.0
occ:1.00
 OE2 B:GLU205 2.4 30.3 1.0
OE1 B:GLU205 2.5 35.8 1.0
OD1 B:ASN289 2.5 24.5 1.0
O5 B:PQQ702 2.6 38.3 1.0
CD B:GLU205 2.8 35.8 1.0
N6 B:PQQ702 2.8 37.7 1.0
OD1 B:ASP331 2.9 20.1 1.0
O7A B:PQQ702 3.1 37.1 1.0
CG B:ASN289 3.3 24.5 1.0
O B:HOH1034 3.4 32.5 1.0
C5 B:PQQ702 3.4 37.7 1.0
C6A B:PQQ702 3.5 39.8 1.0
ND2 B:ASN289 3.6 22.3 1.0
C7 B:PQQ702 3.7 36.3 1.0
CG B:ASP331 3.7 26.9 1.0
C7X B:PQQ702 3.7 36.5 1.0
OD2 B:ASP331 3.7 31.1 1.0
CG B:GLU205 4.3 26.2 1.0
O B:HOH981 4.4 26.8 1.0
CB B:ALA333 4.4 18.7 1.0
NE1 B:TRP293 4.4 27.0 1.0
CB B:ASN289 4.6 20.6 1.0
NH2 B:ARG358 4.6 17.9 1.0
CB B:ALA204 4.6 22.5 1.0
CZ2 B:TRP293 4.7 27.4 1.0
C4 B:PQQ702 4.8 38.7 1.0
O7B B:PQQ702 4.8 33.6 1.0
C9A B:PQQ702 4.9 40.1 1.0
CE2 B:TRP293 4.9 25.1 1.0
N B:GLU205 5.0 25.6 1.0
C8 B:PQQ702 5.0 33.0 1.0

Calcium binding site 2 out of 8 in 4tqo

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Calcium binding site 2 out of 8 in the The Crystal Structure of Methanol Dehydrogenase 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 The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:40.5
occ:1.00
 O5 A:PQQ702 2.5 34.5 1.0
OE1 A:GLU205 2.7 29.8 1.0
N6 A:PQQ702 2.8 33.7 1.0
OE2 A:GLU205 2.8 22.9 1.0
OD1 A:ASN289 2.8 22.6 1.0
OD1 A:ASP331 2.8 27.9 1.0
O7A A:PQQ702 2.9 30.2 1.0
CD A:GLU205 3.0 31.5 1.0
C5 A:PQQ702 3.4 35.2 1.0
CG A:ASN289 3.4 21.8 1.0
C6A A:PQQ702 3.5 34.7 1.0
OD2 A:ASP331 3.6 29.4 1.0
CG A:ASP331 3.6 27.4 1.0
ND2 A:ASN289 3.6 23.6 1.0
C7 A:PQQ702 3.7 31.2 1.0
C7X A:PQQ702 3.7 33.3 1.0
CB A:ALA333 4.2 19.2 1.0
NH2 A:ARG358 4.5 24.6 1.0
CZ2 A:TRP293 4.5 24.2 1.0
NE1 A:TRP293 4.5 25.1 1.0
CG A:GLU205 4.5 27.0 1.0
CB A:ASN289 4.6 17.0 1.0
C4 A:PQQ702 4.7 34.1 1.0
O A:HOH832 4.8 19.4 1.0
CE2 A:TRP293 4.9 27.6 1.0
C9A A:PQQ702 4.9 34.6 1.0
NE1 A:TRP271 4.9 22.5 1.0
O7B A:PQQ702 4.9 33.6 1.0
CZ2 A:TRP271 5.0 28.2 1.0
C8 A:PQQ702 5.0 28.7 1.0
CB A:ALA204 5.0 20.8 1.0

Calcium binding site 3 out of 8 in 4tqo

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

b:46.4
occ:1.00
 O5 C:PQQ702 2.3 39.9 1.0
OE2 C:GLU205 2.6 31.6 1.0
OD1 C:ASN289 2.6 29.7 1.0
OE1 C:GLU205 2.6 42.1 1.0
N6 C:PQQ702 2.8 38.0 1.0
OD1 C:ASP331 2.8 31.8 1.0
CD C:GLU205 2.9 37.4 1.0
O7A C:PQQ702 3.1 37.4 1.0
C5 C:PQQ702 3.2 41.1 1.0
CG C:ASN289 3.4 30.2 1.0
C6A C:PQQ702 3.4 39.4 1.0
OD2 C:ASP331 3.5 37.7 1.0
CG C:ASP331 3.5 31.1 1.0
C7 C:PQQ702 3.7 37.7 1.0
ND2 C:ASN289 3.8 28.1 1.0
C7X C:PQQ702 3.9 35.6 1.0
CB C:ALA333 4.3 23.2 1.0
NH2 C:ARG358 4.4 29.0 1.0
CG C:GLU205 4.4 37.7 1.0
O C:HOH879 4.4 30.7 1.0
CB C:ASN289 4.5 26.7 1.0
C4 C:PQQ702 4.5 40.8 1.0
CZ2 C:TRP293 4.6 35.3 1.0
NE1 C:TRP293 4.6 31.2 1.0
C9A C:PQQ702 4.8 36.5 1.0
O4 C:PQQ702 5.0 43.5 1.0
CE2 C:TRP293 5.0 33.4 1.0
CB C:ASP331 5.0 36.3 1.0

Calcium binding site 4 out of 8 in 4tqo

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

b:44.2
occ:1.00
 OE2 D:GLU205 2.4 34.9 1.0
O5 D:PQQ702 2.6 35.2 1.0
OE1 D:GLU205 2.7 34.5 1.0
OD1 D:ASN289 2.7 26.2 1.0
N6 D:PQQ702 2.9 42.3 1.0
OD1 D:ASP331 2.9 24.1 1.0
CD D:GLU205 2.9 33.8 1.0
CG D:ASN289 3.2 26.0 1.0
ND2 D:ASN289 3.3 28.4 1.0
C5 D:PQQ702 3.4 39.6 1.0
O7A D:PQQ702 3.4 46.2 1.0
C6A D:PQQ702 3.6 41.0 1.0
CG D:ASP331 3.7 25.7 1.0
OD2 D:ASP331 3.7 30.2 1.0
C7 D:PQQ702 3.8 40.5 1.0
C7X D:PQQ702 3.9 39.5 1.0
CB D:ALA333 4.3 20.0 1.0
CG D:GLU205 4.4 36.1 1.0
CB D:ASN289 4.5 19.4 1.0
NE1 D:TRP293 4.5 26.6 1.0
CB D:ALA204 4.6 28.8 1.0
O D:HOH849 4.6 27.7 1.0
NH2 D:ARG358 4.6 28.2 1.0
CZ2 D:TRP293 4.7 26.1 1.0
C4 D:PQQ702 4.8 41.4 1.0
O7B D:PQQ702 4.9 31.1 1.0
C9A D:PQQ702 5.0 40.2 1.0
N D:GLU205 5.0 26.4 1.0

Calcium binding site 5 out of 8 in 4tqo

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Calcium binding site 5 out of 8 in the The Crystal Structure of Methanol Dehydrogenase 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 The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:39.5
occ:1.00
 O5 E:PQQ702 2.5 43.0 1.0
OE2 E:GLU205 2.6 33.1 1.0
OD1 E:ASN289 2.7 22.1 1.0
OE1 E:GLU205 2.7 35.9 1.0
N6 E:PQQ702 2.8 38.4 1.0
CD E:GLU205 3.0 34.6 1.0
OD1 E:ASP331 3.0 31.4 1.0
O7A E:PQQ702 3.0 34.0 1.0
C5 E:PQQ702 3.4 42.8 1.0
OD2 E:ASP331 3.5 31.0 1.0
CG E:ASN289 3.5 23.1 1.0
C6A E:PQQ702 3.6 40.5 1.0
CG E:ASP331 3.6 31.0 1.0
C7 E:PQQ702 3.8 38.4 1.0
C7X E:PQQ702 3.8 41.0 1.0
ND2 E:ASN289 3.9 24.7 1.0
CB E:ALA333 4.2 20.9 1.0
NH2 E:ARG358 4.3 24.3 1.0
CG E:GLU205 4.4 29.1 1.0
NE1 E:TRP293 4.7 25.2 1.0
CB E:ASN289 4.7 19.4 1.0
CZ2 E:TRP293 4.7 22.9 1.0
C4 E:PQQ702 4.7 43.9 1.0
CZ2 E:TRP271 4.8 34.8 1.0
C9A E:PQQ702 4.9 41.5 1.0
NE1 E:TRP271 5.0 26.8 1.0
CB E:ALA204 5.0 24.4 1.0

Calcium binding site 6 out of 8 in 4tqo

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Calcium binding site 6 out of 8 in the The Crystal Structure of Methanol Dehydrogenase 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 The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca701

b:49.1
occ:1.00
 OE2 F:GLU205 2.4 34.1 1.0
OE1 F:GLU205 2.6 34.4 1.0
O5 F:PQQ702 2.6 36.8 1.0
OD1 F:ASN289 2.7 27.9 1.0
N6 F:PQQ702 2.7 38.9 1.0
CD F:GLU205 2.8 37.6 1.0
OD1 F:ASP331 3.0 29.9 1.0
O7A F:PQQ702 3.0 29.2 1.0
C5 F:PQQ702 3.4 38.8 1.0
O F:HOH919 3.5 33.3 1.0
C6A F:PQQ702 3.5 36.7 1.0
CG F:ASN289 3.5 27.8 1.0
C7 F:PQQ702 3.6 34.9 1.0
C7X F:PQQ702 3.7 34.0 1.0
OD2 F:ASP331 3.7 28.7 1.0
CG F:ASP331 3.7 26.8 1.0
ND2 F:ASN289 3.8 29.4 1.0
CG F:GLU205 4.2 35.9 1.0
CB F:ALA333 4.3 20.9 1.0
NH2 F:ARG358 4.5 26.9 1.0
NE1 F:TRP293 4.6 22.5 1.0
O F:HOH868 4.7 25.8 1.0
CB F:ASN289 4.7 26.2 1.0
CZ2 F:TRP293 4.8 22.3 1.0
C4 F:PQQ702 4.8 41.5 1.0
O7B F:PQQ702 4.8 39.3 1.0
CZ2 F:TRP271 4.8 31.4 1.0
CB F:ALA204 4.8 25.2 1.0
C9A F:PQQ702 4.9 40.4 1.0
C8 F:PQQ702 4.9 32.5 1.0
NE1 F:TRP271 4.9 29.6 1.0

Calcium binding site 7 out of 8 in 4tqo

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Calcium binding site 7 out of 8 in the The Crystal Structure of Methanol Dehydrogenase 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 The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca701

b:43.7
occ:1.00
 OE2 G:GLU205 2.5 32.7 1.0
O5 G:PQQ702 2.6 40.7 1.0
OD1 G:ASN289 2.6 29.8 1.0
N6 G:PQQ702 2.6 39.6 1.0
OE1 G:GLU205 2.7 40.2 1.0
O7A G:PQQ702 2.7 32.5 1.0
CD G:GLU205 2.9 38.3 1.0
OD1 G:ASP331 3.0 27.9 1.0
C5 G:PQQ702 3.4 43.5 1.0
C6A G:PQQ702 3.4 42.3 1.0
CG G:ASN289 3.4 26.8 1.0
C7 G:PQQ702 3.5 39.7 1.0
C7X G:PQQ702 3.5 35.6 1.0
ND2 G:ASN289 3.7 19.4 1.0
CG G:ASP331 3.9 31.0 1.0
OD2 G:ASP331 4.0 32.7 1.0
CG G:GLU205 4.4 37.0 1.0
CB G:ALA333 4.4 21.2 1.0
NH2 G:ARG358 4.6 22.9 1.0
CB G:ALA204 4.6 24.0 1.0
CZ2 G:TRP293 4.7 26.1 1.0
NE1 G:TRP293 4.7 28.2 1.0
O7B G:PQQ702 4.7 35.9 1.0
C4 G:PQQ702 4.8 38.7 1.0
CB G:ASN289 4.8 22.6 1.0
C9A G:PQQ702 4.8 37.2 1.0
C8 G:PQQ702 4.8 38.8 1.0
NE1 G:TRP271 4.9 27.3 1.0
N G:GLU205 4.9 26.9 1.0

Calcium binding site 8 out of 8 in 4tqo

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Calcium binding site 8 out of 8 in the The Crystal Structure of Methanol Dehydrogenase 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 The Crystal Structure of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca701

b:97.8
occ:1.00
 OE2 H:GLU205 2.3 38.8 1.0
O5 H:PQQ702 2.4 48.9 1.0
OD1 H:ASN289 2.5 31.3 1.0
N6 H:PQQ702 2.8 50.7 1.0
OD1 H:ASP331 2.8 27.9 1.0
O7B H:PQQ702 3.0 38.6 1.0
CD H:GLU205 3.1 43.0 1.0
OE1 H:GLU205 3.2 45.4 1.0
C5 H:PQQ702 3.2 48.8 1.0
CG H:ASN289 3.4 27.1 1.0
C6A H:PQQ702 3.5 48.8 1.0
CG H:ASP331 3.7 28.4 1.0
C7 H:PQQ702 3.7 42.1 1.0
OD2 H:ASP331 3.8 28.8 1.0
C7X H:PQQ702 3.8 40.7 1.0
CB H:ALA333 3.9 24.4 1.0
ND2 H:ASN289 3.9 29.9 1.0
NH2 H:ARG358 4.4 26.5 1.0
CG H:GLU205 4.5 34.8 1.0
CB H:ASN289 4.5 23.9 1.0
C4 H:PQQ702 4.6 46.8 1.0
CZ2 H:TRP271 4.6 35.5 1.0
NE1 H:TRP293 4.8 26.6 1.0
C9A H:PQQ702 4.8 44.0 1.0
CZ2 H:TRP293 4.9 28.2 1.0
NE1 H:TRP271 4.9 32.0 1.0
O H:HOH878 5.0 29.3 1.0

Reference:

M.A.Culpepper, A.C.Rosenzweig. Structure and Protein-Protein Interactions of Methanol Dehydrogenase From Methylococcus Capsulatus (Bath). Biochemistry V. 53 6211 2014.
ISSN: ISSN 0006-2960
PubMed: 25185034
DOI: 10.1021/BI500850J
Page generated: Wed Jul 9 02:08:23 2025

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