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Cobalt in PDB 1m38: Structure of Inorganic Pyrophosphatase

Enzymatic activity of Structure of Inorganic Pyrophosphatase

All present enzymatic activity of Structure of Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Structure of Inorganic Pyrophosphatase, PDB code: 1m38 was solved by I.P.Kuranova, K.M.Polyakov, V.M.Levdikov, E.A.Smirnova, W.E.Hohne, V.S.Lamzin, R.Meijers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.59 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.690, 93.230, 69.840, 90.00, 99.74, 90.00
R / Rfree (%) 19.3 / 24.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Inorganic Pyrophosphatase (pdb code 1m38). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Structure of Inorganic Pyrophosphatase, PDB code: 1m38:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 1m38

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Cobalt binding site 1 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:19.5
occ:0.99
 OD2 A:ASP152 2.0 22.3 1.0
O A:HOH3668 2.1 8.9 0.5
O A:HOH3670 2.1 14.5 1.0
OD1 A:ASP115 2.1 18.1 1.0
OD2 A:ASP120 2.2 14.3 1.0
O3 A:PO43301 2.3 24.6 0.5
O A:HOH3667 2.3 10.4 0.5
O2 A:PO43301 2.7 25.1 0.5
CG A:ASP152 2.9 23.8 1.0
CG A:ASP120 3.0 14.2 1.0
CG A:ASP115 3.1 21.7 1.0
P A:PO43301 3.1 19.2 0.5
OD1 A:ASP120 3.1 19.8 1.0
OD1 A:ASP152 3.4 24.8 1.0
OD2 A:ASP115 3.5 18.8 1.0
O A:HOH3669 3.7 12.3 0.5
CO A:CO402 3.7 31.2 1.0
CO A:CO404 3.7 35.9 1.0
O A:HOH3386 3.8 25.2 0.9
O A:HOH3309 3.8 17.4 1.0
NZ A:LYS154 3.9 26.9 1.0
O1 A:PO43301 4.1 22.8 0.5
O4 A:PO43301 4.2 22.6 0.5
OD2 A:ASP117 4.2 25.1 1.0
CB A:ASP117 4.3 20.1 1.0
CB A:ASP152 4.3 17.5 1.0
CB A:ASP120 4.4 11.2 1.0
CB A:ASP115 4.4 20.4 1.0
O A:PRO118 4.4 17.9 1.0
O A:HOH3324 4.5 18.3 1.0
O A:HOH3364 4.6 23.1 0.9
O A:HOH3674 4.7 37.4 0.5
CA A:ASP152 4.7 21.2 1.0
CG A:ASP117 4.8 26.4 1.0
OH A:TYR93 4.8 16.6 1.0

Cobalt binding site 2 out of 7 in 1m38

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Cobalt binding site 2 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:31.2
occ:0.99
 OD1 A:ASP120 2.0 19.8 1.0
O A:HOH3669 2.0 12.3 0.5
O3 A:PO43301 2.0 24.6 0.5
O A:HOH3667 2.1 10.4 0.5
O A:HOH3671 2.1 18.6 1.0
O A:HOH3672 2.3 26.9 1.0
O1 A:PO43301 2.3 22.8 0.5
O A:HOH3324 2.4 18.3 1.0
P A:PO43301 2.8 19.2 0.5
CG A:ASP120 3.0 14.2 1.0
OD2 A:ASP120 3.5 14.3 1.0
O4 A:PO43301 3.7 22.6 0.5
CO A:CO401 3.7 19.5 1.0
O2 A:PO43301 3.8 25.1 0.5
O A:HOH3406 3.9 32.1 1.0
OH A:TYR93 4.0 16.6 1.0
O A:HOH3668 4.1 8.9 0.5
OD2 A:ASP117 4.2 25.1 1.0
OE2 A:GLU48 4.2 16.4 1.0
O A:PRO118 4.2 17.9 1.0
CB A:ASP120 4.2 11.2 1.0
O A:HOH3670 4.3 14.5 1.0
CE1 A:TYR93 4.4 15.8 1.0
CB A:ASP117 4.4 20.1 1.0
NZ A:LYS56 4.5 24.1 1.0
CG A:ASP117 4.6 26.4 1.0
CZ A:TYR93 4.7 16.4 1.0
OE1 A:GLU48 4.7 16.0 1.0
O A:HOH3377 4.7 25.9 1.0
O A:GLY94 4.7 14.3 1.0
O A:HOH3326 4.7 18.2 1.0
CA A:ASP120 4.8 12.0 1.0
CD A:GLU48 4.9 16.4 1.0

Cobalt binding site 3 out of 7 in 1m38

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Cobalt binding site 3 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:34.8
occ:0.50
 O4 A:PO43301 2.0 22.6 0.5
OE2 A:GLU58 2.2 29.5 1.0
O A:HOH3464 2.3 35.2 1.0
CD A:GLU58 3.2 26.9 1.0
O A:HOH3565 3.5 33.5 1.0
OE1 A:GLU58 3.6 29.1 1.0
P A:PO43301 3.6 19.2 0.5
NZ A:LYS56 3.7 24.1 1.0
O A:HOH3674 3.8 37.4 0.5
OD2 A:ASP117 4.0 25.1 1.0
NH1 A:ARG78 4.2 33.7 1.0
O A:HOH3672 4.3 26.9 1.0
O1 A:PO43301 4.3 22.8 0.5
O3 A:PO43301 4.4 24.6 0.5
CG A:GLU58 4.4 26.6 1.0
O A:HOH3673 4.4 50.3 1.0
CE A:LYS56 4.4 27.8 1.0
O2 A:PO43301 4.5 25.1 0.5
O A:HOH3667 4.6 10.4 0.5
O A:HOH3668 4.7 8.9 0.5
OD1 A:ASP71 4.7 27.0 1.0
CD A:LYS56 4.8 27.5 1.0
O A:HOH3669 4.8 12.3 0.5
O A:HOH3386 4.9 25.2 0.9

Cobalt binding site 4 out of 7 in 1m38

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Cobalt binding site 4 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co404

b:35.9
occ:0.99
 O A:HOH3668 1.9 8.9 0.5
O A:HOH3386 2.1 25.2 0.9
OD2 A:ASP147 2.1 29.7 1.0
O2 A:PO43301 2.2 25.1 0.5
O A:HOH3364 2.2 23.1 0.9
OD1 A:ASP152 2.2 24.8 1.0
O A:HOH3565 2.2 33.5 1.0
CG A:ASP152 3.3 23.8 1.0
P A:PO43301 3.3 19.2 0.5
CG A:ASP147 3.3 27.6 1.0
CO A:CO401 3.7 19.5 1.0
CB A:ASP147 3.8 24.6 1.0
OD2 A:ASP152 3.8 22.3 1.0
O4 A:PO43301 3.8 22.6 0.5
OD1 A:ASP115 3.9 18.1 1.0
OH A:TYR192 4.0 21.4 1.0
O A:HOH3673 4.1 50.3 1.0
NZ A:LYS154 4.2 26.9 1.0
O3 A:PO43301 4.2 24.6 0.5
OD1 A:ASP147 4.3 25.0 1.0
O A:HOH3371 4.4 25.0 1.0
CB A:ASP152 4.4 17.5 1.0
O A:HOH3669 4.5 12.3 0.5
O1 A:PO43301 4.5 22.8 0.5
NZ A:LYS193 4.6 23.6 1.0
OD2 A:ASP120 4.6 14.3 1.0
O A:HOH3416 4.6 26.5 1.0
O A:HOH3667 4.7 10.4 0.5
OH A:TYR93 4.9 16.6 1.0
O A:HOH3674 4.9 37.4 0.5
CG A:ASP115 5.0 21.7 1.0

Cobalt binding site 5 out of 7 in 1m38

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Cobalt binding site 5 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:25.0
occ:0.50
 CO B:CO401 0.0 25.0 0.5
CO B:CO401 1.5 24.9 0.5
O B:HOH3789 1.6 26.9 1.0
OD1 B:ASP152 2.0 30.5 1.0
O B:HOH3788 2.2 27.1 1.0
OD1 B:ASP120 2.2 21.6 1.0
OD1 B:ASP115 2.3 43.9 1.0
CG B:ASP120 2.8 21.6 1.0
CG B:ASP152 3.2 27.5 1.0
O B:HOH3545 3.2 24.4 1.0
CG B:ASP115 3.3 42.0 1.0
OD2 B:ASP120 3.3 21.8 1.0
OD2 B:ASP115 3.7 40.2 1.0
OD2 B:ASP152 3.9 29.4 1.0
CB B:ASP120 4.0 20.3 1.0
O B:PRO118 4.0 28.8 1.0
NZ B:LYS154 4.2 24.4 1.0
N B:ASP120 4.2 21.3 1.0
OE1 B:GLU101 4.2 45.4 1.0
CB B:ASP152 4.2 28.5 1.0
CA B:ASP152 4.4 30.8 1.0
CB B:ASP115 4.4 43.6 1.0
O B:TRP153 4.4 27.4 1.0
CO B:CO402 4.5 41.7 1.0
CA B:ASP120 4.7 20.6 1.0
CB B:ASP117 4.8 28.3 1.0
C B:ASP152 4.8 30.4 1.0
O B:HOH3790 4.8 25.3 1.0
O B:HOH3542 4.9 23.9 1.0
CA B:ILE119 5.0 24.2 1.0

Cobalt binding site 6 out of 7 in 1m38

Go back to Cobalt Binding Sites List in 1m38
Cobalt binding site 6 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:24.9
occ:0.50
 CO B:CO401 0.0 24.9 0.5
CO B:CO401 1.5 25.0 0.5
OD1 B:ASP152 2.1 30.5 1.0
OD1 B:ASP120 2.3 21.6 1.0
O B:HOH3789 2.5 26.9 1.0
O B:HOH3545 2.6 24.4 1.0
OD1 B:ASP115 2.8 43.9 1.0
CG B:ASP152 2.9 27.5 1.0
OD2 B:ASP152 3.2 29.4 1.0
CG B:ASP120 3.3 21.6 1.0
CG B:ASP115 3.5 42.0 1.0
OD2 B:ASP120 3.6 21.8 1.0
O B:HOH3788 3.6 27.1 1.0
NZ B:LYS154 3.8 24.4 1.0
O B:HOH3542 4.1 23.9 1.0
OD2 B:ASP115 4.1 40.2 1.0
CB B:ASP115 4.2 43.6 1.0
CB B:ASP152 4.2 28.5 1.0
CO B:CO402 4.2 41.7 1.0
O1 B:PO43501 4.4 39.2 0.7
O B:HOH3781 4.5 32.1 0.5
CB B:ASP120 4.6 20.3 1.0
CB B:ASP117 4.8 28.3 1.0
CA B:ASP152 4.8 30.8 1.0
OD2 B:ASP117 4.8 32.8 1.0
OH B:TYR93 4.8 25.3 1.0

Cobalt binding site 7 out of 7 in 1m38

Go back to Cobalt Binding Sites List in 1m38
Cobalt binding site 7 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:41.7
occ:0.99
 O B:HOH3791 2.1 23.7 1.0
O B:HOH3792 2.1 23.8 0.5
O B:HOH3790 2.1 25.3 1.0
OD2 B:ASP120 2.2 21.8 1.0
O B:HOH3545 2.4 24.4 1.0
O B:HOH3542 2.4 23.9 1.0
O B:HOH3793 2.7 21.5 0.5
CG B:ASP120 3.3 21.6 1.0
O B:HOH3569 3.4 17.1 0.5
OD1 B:ASP120 3.7 21.6 1.0
OE1 B:GLU48 4.2 18.5 1.0
CO B:CO401 4.2 24.9 0.5
O B:PRO118 4.2 28.8 1.0
O B:HOH3789 4.3 26.9 1.0
OH B:TYR93 4.3 25.3 1.0
CB B:ASP120 4.4 20.3 1.0
CE1 B:TYR93 4.4 20.6 1.0
CO B:CO401 4.5 25.0 0.5
OE2 B:GLU48 4.5 21.4 1.0
O B:HOH3642 4.5 37.8 1.0
O B:HOH3688 4.5 37.6 1.0
OD2 B:ASP117 4.6 32.8 1.0
O B:HOH3620 4.6 37.2 1.0
O B:GLY94 4.7 16.9 1.0
CB B:ASP117 4.7 28.3 1.0
O B:HOH3502 4.7 26.2 1.0
CA B:ASP120 4.7 20.6 1.0
CZ B:TYR93 4.8 22.4 1.0
CG B:ASP117 4.8 32.4 1.0
CB B:ALA95 4.8 24.2 1.0
CD B:GLU48 4.8 19.6 1.0

Reference:

I.P.Kuranova, K.M.Polyakov, E.A.Smirnova, W.E.Hohne, V.S.Lamzin, R.Meijers. Three-Dimensional Structure of Saccharomyces Cerevisiae Inorganic Pyrophosphatase Complexed with Cobalt and Phosphate Ions Crystallography Reports V. 48 953 2003.
ISSN: ISSN 1063-7745
Page generated: Sun Jul 13 17:38:41 2025

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