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Cobalt in PDB 4qlz: The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum

Protein crystallography data

The structure of The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum, PDB code: 4qlz was solved by Q.F.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.89 / 2.33
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 76.080, 76.080, 123.410, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 27

Cobalt Binding Sites:

The binding sites of Cobalt atom in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum (pdb code 4qlz). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum, PDB code: 4qlz:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 4qlz

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Cobalt binding site 1 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

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

b:0.1
occ:0.92
 O3 A:PO4405 1.8 82.2 0.8
O2 A:PO4405 2.2 43.2 0.8
OD2 A:ASP118 2.2 42.5 1.0
OD2 A:ASP113 2.4 60.9 1.0
P A:PO4405 2.4 46.5 0.8
OD1 A:ASP150 2.5 57.7 1.0
O A:HOH515 2.6 43.1 1.0
CG A:ASP118 3.1 49.9 1.0
CO A:CO402 3.2 69.2 0.7
O1 A:PO4405 3.3 38.5 0.8
OD1 A:ASP118 3.3 44.7 1.0
CG A:ASP113 3.3 60.7 1.0
CG A:ASP150 3.4 62.1 1.0
O A:HOH519 3.5 50.5 1.0
OD1 A:ASP113 3.6 53.6 1.0
OD2 A:ASP150 3.6 51.5 1.0
O4 A:PO4405 3.7 56.5 0.8
CO A:CO404 3.8 77.4 0.7
O A:HOH543 3.9 69.6 1.0
NZ A:LYS152 4.0 46.9 1.0
O A:HOH506 4.2 53.5 1.0
CB A:ASP115 4.2 68.5 1.0
O A:PRO116 4.3 50.1 1.0
OH A:TYR91 4.5 51.4 1.0
CB A:ASP118 4.5 43.9 1.0
CO A:CO403 4.7 0.8 0.9
CB A:ASP113 4.7 54.9 1.0
OD2 A:ASP115 4.7 94.7 1.0
CB A:ASP150 4.8 57.8 1.0
O A:HOH522 4.8 45.0 1.0
CG A:ASP115 4.9 85.8 1.0

Cobalt binding site 2 out of 8 in 4qlz

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Cobalt binding site 2 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

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

b:69.2
occ:0.65
 O1 A:PO4405 2.0 38.5 0.8
O3 A:PO4405 2.1 82.2 0.8
O A:HOH522 2.1 45.0 1.0
O A:HOH502 2.1 39.9 1.0
OD1 A:ASP118 2.2 44.7 1.0
P A:PO4405 2.5 46.5 0.8
CG A:ASP118 3.2 49.9 1.0
CO A:CO401 3.2 0.1 0.9
O4 A:PO4405 3.4 56.5 0.8
OD2 A:ASP118 3.5 42.5 1.0
O2 A:PO4405 3.7 43.2 0.8
OH A:TYR91 3.9 51.4 1.0
O A:HOH515 4.0 43.1 1.0
NZ A:LYS54 4.2 57.3 1.0
OE1 A:GLU46 4.3 66.0 1.0
O A:PRO116 4.4 50.1 1.0
CE2 A:TYR91 4.4 48.1 1.0
CO A:CO403 4.4 0.8 0.9
CB A:ASP118 4.5 43.9 1.0
CB A:ASP115 4.5 68.5 1.0
CZ A:TYR91 4.6 51.7 1.0
OE2 A:GLU46 4.8 71.4 1.0
O A:GLY92 4.8 48.7 1.0
CG A:ASP115 4.8 85.8 1.0
CD A:GLU46 5.0 68.6 1.0

Cobalt binding site 3 out of 8 in 4qlz

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Cobalt binding site 3 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

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

b:0.8
occ:0.88
 O4 A:PO4405 1.9 56.5 0.8
O A:HOH539 2.3 73.3 1.0
O A:HOH543 2.5 69.6 1.0
OD2 A:ASP115 2.9 94.7 1.0
P A:PO4405 3.1 46.5 0.8
OE1 A:GLU56 3.2 91.5 1.0
O3 A:PO4405 3.2 82.2 0.8
O A:HOH522 3.7 45.0 1.0
CG A:ASP115 3.8 85.8 1.0
CD A:GLU56 3.9 88.6 1.0
OE2 A:GLU56 3.9 97.3 1.0
O2 A:PO4405 4.0 43.2 0.8
O1 A:PO4405 4.2 38.5 0.8
OD1 A:ASP115 4.4 71.4 1.0
CO A:CO402 4.4 69.2 0.7
NZ A:LYS54 4.6 57.3 1.0
CO A:CO401 4.7 0.1 0.9
OD2 A:ASP113 4.7 60.9 1.0
CB A:ASP115 4.7 68.5 1.0
CE A:LYS54 4.7 68.0 1.0
O A:HOH519 4.8 50.5 1.0

Cobalt binding site 4 out of 8 in 4qlz

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Cobalt binding site 4 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

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

b:77.4
occ:0.69
 O2 A:PO4405 2.0 43.2 0.8
O A:HOH538 2.1 55.0 1.0
OD2 A:ASP145 2.1 55.8 1.0
OD2 A:ASP150 2.2 51.5 1.0
O A:HOH519 2.2 50.5 1.0
NZ A:LYS152 3.2 46.9 1.0
CG A:ASP150 3.2 62.1 1.0
CG A:ASP145 3.3 58.6 1.0
P A:PO4405 3.5 46.5 0.8
OD1 A:ASP150 3.7 57.7 1.0
CO A:CO401 3.8 0.1 0.9
OH A:TYR190 3.8 82.6 1.0
CB A:ASP145 3.9 57.9 1.0
O4 A:PO4405 4.0 56.5 0.8
O1 A:PO4405 4.1 38.5 0.8
OD2 A:ASP113 4.2 60.9 1.0
CE A:LYS152 4.2 56.6 1.0
OD1 A:ASP145 4.3 69.1 1.0
OD2 A:ASP118 4.4 42.5 1.0
O3 A:PO4405 4.4 82.2 0.8
CB A:ASP150 4.5 57.8 1.0
OH A:TYR91 4.6 51.4 1.0
O A:HOH528 4.9 60.0 1.0
CZ A:TYR190 5.0 80.2 1.0

Cobalt binding site 5 out of 8 in 4qlz

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Cobalt binding site 5 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

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

b:79.9
occ:0.66
 OD2 B:ASP118 1.9 46.0 1.0
O3 B:PO4405 2.1 57.3 0.8
OD1 B:ASP150 2.1 51.5 1.0
O B:HOH523 2.3 43.3 1.0
OD2 B:ASP113 2.3 57.0 1.0
O2 B:PO4405 2.5 40.9 0.8
P B:PO4405 2.7 40.5 0.8
CG B:ASP118 2.9 46.2 1.0
CG B:ASP150 3.2 49.4 1.0
OD1 B:ASP118 3.2 50.4 1.0
CG B:ASP113 3.3 60.8 1.0
O B:HOH521 3.5 57.2 1.0
OD2 B:ASP150 3.5 53.1 1.0
O1 B:PO4405 3.5 38.8 0.8
CO B:CO402 3.5 67.8 0.8
O B:HOH504 3.6 48.2 1.0
OD1 B:ASP113 3.6 56.3 1.0
NZ B:LYS152 3.8 48.0 1.0
CO B:CO404 3.8 79.3 0.6
O4 B:PO4405 4.0 52.7 0.8
CB B:ASP118 4.2 37.2 1.0
O B:PRO116 4.3 47.2 1.0
CB B:ASP150 4.5 52.8 1.0
OH B:TYR91 4.5 47.9 1.0
CB B:ASP113 4.6 56.9 1.0
CB B:ASP115 4.6 56.5 1.0
CA B:ASP150 4.8 49.0 1.0
N B:ASP118 4.9 44.2 1.0
CE B:LYS152 4.9 50.5 1.0

Cobalt binding site 6 out of 8 in 4qlz

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Cobalt binding site 6 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:67.8
occ:0.77
 O1 B:PO4405 2.1 38.8 0.8
OD1 B:ASP118 2.2 50.4 1.0
O3 B:PO4405 2.2 57.3 0.8
O B:HOH514 2.3 42.1 1.0
P B:PO4405 2.5 40.5 0.8
CG B:ASP118 3.2 46.2 1.0
O4 B:PO4405 3.4 52.7 0.8
CO B:CO401 3.5 79.9 0.7
OD2 B:ASP118 3.6 46.0 1.0
O2 B:PO4405 3.8 40.9 0.8
OH B:TYR91 4.0 47.9 1.0
OE1 B:GLU46 4.2 54.6 1.0
NZ B:LYS54 4.3 54.3 1.0
O B:HOH523 4.3 43.3 1.0
O B:PRO116 4.4 47.2 1.0
CE2 B:TYR91 4.4 54.9 1.0
CB B:ASP118 4.5 37.2 1.0
CZ B:TYR91 4.6 55.8 1.0
CB B:ASP115 4.7 56.5 1.0
OE2 B:GLU56 4.8 98.2 1.0
OE2 B:GLU46 4.9 69.1 1.0
CO B:CO403 4.9 0.6 0.7
CA B:ASP118 4.9 51.5 1.0
CD B:GLU46 5.0 66.1 1.0

Cobalt binding site 7 out of 8 in 4qlz

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Cobalt binding site 7 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co403

b:0.6
occ:0.72
 O4 B:PO4405 2.1 52.7 0.8
OE2 B:GLU56 2.6 98.2 1.0
P B:PO4405 3.4 40.5 0.8
CD B:GLU56 3.6 98.5 1.0
O3 B:PO4405 3.7 57.3 0.8
OE1 B:GLU56 3.8 0.2 1.0
O B:HOH521 4.0 57.2 1.0
OD2 B:ASP115 4.0 84.7 1.0
O2 B:PO4405 4.1 40.9 0.8
O1 B:PO4405 4.5 38.8 0.8
CG B:ASP115 4.6 75.6 1.0
OD2 B:ASP113 4.7 57.0 1.0
NZ B:LYS54 4.8 54.3 1.0
CG B:GLU56 4.9 93.5 1.0
CE B:LYS54 4.9 68.1 1.0
CO B:CO402 4.9 67.8 0.8
CO B:CO404 5.0 79.3 0.6

Cobalt binding site 8 out of 8 in 4qlz

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Cobalt binding site 8 out of 8 in the The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of The Structure of Inorganic Pyrophosphatase From Schistosoma Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co404

b:79.3
occ:0.59
 O2 B:PO4405 1.9 40.9 0.8
O B:HOH526 2.0 57.2 1.0
OD2 B:ASP145 2.1 60.5 1.0
O B:HOH521 2.3 57.2 1.0
OD2 B:ASP150 2.3 53.1 1.0
CG B:ASP150 3.3 49.4 1.0
P B:PO4405 3.3 40.5 0.8
CG B:ASP145 3.3 66.3 1.0
NZ B:LYS152 3.5 48.0 1.0
OD1 B:ASP150 3.7 51.5 1.0
O4 B:PO4405 3.8 52.7 0.8
CO B:CO401 3.8 79.9 0.7
OH B:TYR190 3.9 66.5 1.0
CB B:ASP145 4.0 76.4 1.0
OD2 B:ASP113 4.1 57.0 1.0
O1 B:PO4405 4.2 38.8 0.8
O3 B:PO4405 4.3 57.3 0.8
OD1 B:ASP145 4.3 72.7 1.0
OD2 B:ASP118 4.5 46.0 1.0
CB B:ASP150 4.5 52.8 1.0
CE B:LYS152 4.5 50.5 1.0
O B:HOH511 4.7 53.7 1.0
OH B:TYR91 4.9 47.9 1.0
CO B:CO403 5.0 0.6 0.7
NZ B:LYS191 5.0 75.3 1.0

Reference:

Q.F.Wu, Q.F.Wu. N/A N/A.
Page generated: Sun Dec 13 10:45:38 2020

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