Calcium in PDB 3qgm: P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus

Protein crystallography data

The structure of P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus, PDB code: 3qgm was solved by J.Osipiuk, H.Zheng, X.Xu, A.Savchenko, A.Edwards, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.252, 68.843, 70.154, 74.99, 87.33, 85.76
R / Rfree (%) 16.9 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus (pdb code 3qgm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus, PDB code: 3qgm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3qgm

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Calcium binding site 1 out of 4 in the P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:27.0
occ:1.00
 O A:HOH365 2.1 24.0 1.0
OD1 A:ASP209 2.3 26.3 1.0
O A:ASP13 2.3 25.9 1.0
O A:HOH274 2.3 23.9 1.0
OD2 A:ASP11 2.4 26.2 1.0
O A:HOH282 2.4 26.3 1.0
OD1 A:ASP11 2.6 26.5 1.0
CG A:ASP11 2.8 27.4 1.0
CG A:ASP209 3.2 29.6 1.0
C A:ASP13 3.5 26.3 1.0
OD2 A:ASP209 3.6 33.0 1.0
OD2 A:ASP214 4.1 26.6 1.0
NE2 A:GLN210 4.1 27.7 1.0
CA A:ASP13 4.2 28.0 1.0
CB A:ASP11 4.3 27.2 1.0
O A:HOH276 4.3 21.0 1.0
O A:HOH271 4.4 29.2 1.0
CB A:ASP13 4.4 29.1 1.0
N A:ASP13 4.4 26.2 1.0
CB A:ASP209 4.5 28.7 1.0
N A:GLY14 4.5 27.2 1.0
N A:ASP209 4.6 27.5 1.0
CG A:GLN210 4.7 30.0 1.0
O A:HOH293 4.8 43.3 1.0
CA A:GLY14 4.8 27.0 1.0
CD A:GLN210 4.8 31.5 1.0
CG A:ASP214 4.9 30.2 1.0
OD1 A:ASP214 5.0 26.0 1.0
CA A:ASP209 5.0 28.6 1.0

Calcium binding site 2 out of 4 in 3qgm

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Calcium binding site 2 out of 4 in the P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:23.7
occ:1.00
 OD1 B:ASP209 2.2 22.9 1.0
O B:ASP13 2.3 25.8 1.0
O B:HOH294 2.4 27.6 1.0
OD2 B:ASP11 2.4 26.6 1.0
O B:HOH271 2.4 21.5 1.0
O B:HOH274 2.4 24.7 1.0
OD1 B:ASP11 2.6 26.4 1.0
CG B:ASP11 2.9 24.0 1.0
CG B:ASP209 3.2 26.6 1.0
C B:ASP13 3.4 26.5 1.0
OD2 B:ASP209 3.6 27.4 1.0
NE2 B:GLN210 4.1 23.3 1.0
CA B:ASP13 4.2 26.6 0.6
OD2 B:ASP214 4.2 26.2 1.0
CA B:ASP13 4.2 26.4 0.4
CB B:ASP13 4.3 26.4 0.6
CB B:ASP13 4.3 26.2 0.4
N B:ASP13 4.4 25.8 1.0
CB B:ASP11 4.4 23.9 1.0
O B:HOH267 4.4 14.8 1.0
CB B:ASP209 4.4 26.4 1.0
O B:HOH286 4.4 34.0 1.0
N B:GLY14 4.5 26.6 1.0
N B:ASP209 4.6 25.5 1.0
O B:HOH376 4.7 39.2 1.0
CA B:GLY14 4.7 27.0 1.0
CG B:GLN210 4.7 25.8 1.0
O B:HOH335 4.7 39.0 1.0
CD B:GLN210 4.8 25.2 1.0
O B:HOH297 4.9 35.1 1.0
CA B:ASP209 5.0 25.8 1.0

Calcium binding site 3 out of 4 in 3qgm

Go back to Calcium Binding Sites List in 3qgm
Calcium binding site 3 out of 4 in the P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:23.3
occ:1.00
 O C:HOH370 2.3 25.5 1.0
OD1 C:ASP209 2.3 23.4 1.0
OD2 C:ASP11 2.3 23.8 1.0
O C:ASP13 2.3 21.5 1.0
O C:HOH317 2.4 23.2 1.0
O C:HOH274 2.4 23.3 1.0
OD1 C:ASP11 2.7 23.2 1.0
CG C:ASP11 2.9 21.0 1.0
CG C:ASP209 3.2 25.2 1.0
C C:ASP13 3.4 22.4 1.0
OD2 C:ASP209 3.6 28.8 1.0
NE2 C:GLN210 4.0 29.3 1.0
OD2 C:ASP214 4.1 25.6 1.0
CA C:ASP13 4.2 22.2 0.3
CA C:ASP13 4.2 23.1 0.7
O C:HOH266 4.3 15.7 1.0
CB C:ASP13 4.3 22.7 0.3
N C:ASP13 4.4 22.3 1.0
CB C:ASP11 4.4 22.1 1.0
CB C:ASP13 4.4 24.1 0.7
CB C:ASP209 4.4 23.9 1.0
N C:GLY14 4.4 21.7 1.0
O C:HOH283 4.5 24.8 1.0
O C:HOH300 4.5 39.7 1.0
N C:ASP209 4.5 23.9 1.0
CA C:GLY14 4.7 22.6 1.0
CG C:GLN210 4.8 27.9 1.0
CD C:GLN210 4.8 29.9 1.0
CA C:ASP209 4.9 24.8 1.0
CG C:ASP214 4.9 25.6 1.0
OD1 C:ASP214 5.0 26.8 1.0
O C:HOH267 5.0 32.9 1.0

Calcium binding site 4 out of 4 in 3qgm

Go back to Calcium Binding Sites List in 3qgm
Calcium binding site 4 out of 4 in the P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:24.3
occ:1.00
 OD1 D:ASP209 2.3 22.9 1.0
O D:ASP13 2.3 24.4 1.0
OD2 D:ASP11 2.4 22.4 1.0
O D:HOH310 2.4 22.4 1.0
O D:HOH337 2.5 33.7 1.0
O D:HOH270 2.6 23.0 1.0
OD1 D:ASP11 2.6 28.6 1.0
CG D:ASP11 2.8 25.3 1.0
CG D:ASP209 3.3 25.9 1.0
C D:ASP13 3.5 24.4 1.0
OD2 D:ASP209 3.7 26.3 1.0
OE1 D:GLN210 4.2 30.1 1.0
CA D:ASP13 4.2 25.7 1.0
OD2 D:ASP214 4.2 25.1 1.0
CB D:ASP11 4.3 23.0 1.0
O D:HOH293 4.3 27.9 1.0
CB D:ASP13 4.3 27.7 1.0
N D:ASP13 4.4 24.6 1.0
CB D:ASP209 4.5 23.9 1.0
N D:GLY14 4.5 24.1 1.0
O D:HOH331 4.5 31.2 1.0
N D:ASP209 4.6 21.9 1.0
CG D:GLN210 4.7 24.2 1.0
CA D:GLY14 4.7 23.4 1.0
CD D:GLN210 4.8 30.3 1.0
O D:HOH285 5.0 38.3 1.0
CA D:ASP209 5.0 23.1 1.0

Reference:

J.Osipiuk, H.Zheng, X.Xu, A.Savchenko, A.Edwards, A.Joachimiak. P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus. To Be Published.
Page generated: Sat Dec 12 04:26:50 2020

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