Atomistry » Calcium » PDB 7c52-7cgz » 7cdl
Atomistry »
  Calcium »
    PDB 7c52-7cgz »
      7cdl »

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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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

Go back to Calcium Binding Sites List in 7cdl
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: Thu Jul 18 23:36:20 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy