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Calcium in PDB 4jbe: 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.

Protein crystallography data

The structure of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis., PDB code: 4jbe was solved by G.Minasov, E.V.Filippova, A.Halavaty, L.Shuvalova, O.Kiryukhina, M.Endres, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.73 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 265.510, 55.118, 64.246, 90.00, 91.18, 90.00
R / Rfree (%) 16.8 / 20.8

Other elements in 4jbe:

The structure of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. (pdb code 4jbe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis., PDB code: 4jbe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4jbe

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Calcium binding site 1 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:54.7
occ:1.00
 O A:HOH868 2.3 42.7 1.0
O A:HOH867 2.3 39.4 1.0
O A:HOH663 2.4 33.5 1.0
O A:SER209 2.4 31.3 1.0
OG A:SER212 2.6 27.9 1.0
O A:HOH837 2.7 38.2 1.0
C A:SER209 3.6 30.4 1.0
CB A:SER212 3.7 30.4 1.0
N A:SER212 4.2 28.9 1.0
N A:SER209 4.2 29.7 1.0
OG A:SER209 4.5 36.9 1.0
CA A:SER212 4.5 28.4 1.0
CA A:GLY210 4.5 29.7 1.0
CA A:SER209 4.5 31.5 1.0
N A:GLY210 4.5 28.9 1.0
C A:GLY210 4.6 29.8 1.0
N A:GLU211 4.7 31.0 1.0
O A:HOH622 4.7 35.1 1.0
N A:THR213 4.8 24.2 1.0
O A:HOH614 4.9 31.6 1.0
OE1 A:GLU126 4.9 55.4 1.0
OG1 A:THR213 5.0 23.3 1.0

Calcium binding site 2 out of 10 in 4jbe

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Calcium binding site 2 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:47.5
occ:1.00
 O A:HOH679 2.4 31.8 0.5
O A:HOH776 2.4 42.7 1.0
O A:ALA273 2.5 23.9 1.0
O A:HOH627 2.6 31.9 1.0
OE1 A:GLU277 2.6 28.2 1.0
OE2 A:GLU277 2.6 35.0 1.0
CD A:GLU277 3.0 31.3 1.0
C A:ALA273 3.4 24.0 1.0
N A:VAL274 4.2 21.9 1.0
CA A:VAL274 4.2 23.2 1.0
CA A:ALA273 4.3 24.1 1.0
CG A:GLU277 4.5 27.2 1.0
OE1 A:GLU276 4.6 42.3 1.0
O A:ASP272 4.8 22.0 1.0
C A:VAL274 4.9 22.8 1.0
CB A:GLU276 4.9 26.9 1.0

Calcium binding site 3 out of 10 in 4jbe

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Calcium binding site 3 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:60.6
occ:1.00
 O A:HOH925 2.1 51.5 1.0
O A:HOH924 2.2 50.1 1.0
OE1 A:GLU219 2.6 45.0 1.0
OE2 A:GLU219 2.7 43.1 1.0
CD A:GLU219 3.0 40.1 1.0
NE2 A:HIS223 4.1 45.1 1.0
O A:HOH709 4.3 39.1 1.0
OE1 A:GLN222 4.4 60.2 1.0
CG A:GLU219 4.5 36.3 1.0
NH2 A:ARG196 4.6 42.9 1.0
NE A:ARG196 4.8 44.0 1.0
CD2 A:HIS223 4.9 42.7 1.0

Calcium binding site 4 out of 10 in 4jbe

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Calcium binding site 4 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:53.0
occ:1.00
 O A:HOH851 2.3 41.1 0.5
O A:HOH900 2.4 24.4 0.5
O A:HOH939 2.4 31.4 0.5
O A:HOH830 2.5 42.7 1.0
O A:HOH827 2.5 41.4 1.0
O A:HOH899 2.5 29.1 0.5
O A:HOH961 2.8 41.4 0.5
OD1 A:ASP199 4.4 51.4 1.0
CB A:PRO198 4.4 36.3 1.0
CD B:LYS388 4.5 52.5 1.0
O A:PRO198 4.5 35.6 1.0
O A:GLY224 4.7 36.3 1.0
CE B:LYS388 4.8 56.2 1.0
O A:HOH678 4.8 31.9 1.0
C A:PRO198 4.9 36.9 1.0
CG B:LYS388 5.0 45.2 1.0

Calcium binding site 5 out of 10 in 4jbe

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Calcium binding site 5 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:53.8
occ:0.50
 O A:HOH744 2.3 53.3 1.0
O A:HOH713 2.3 52.9 1.0
O A:HOH946 2.4 71.1 1.0
O A:GLY25 2.4 34.5 1.0
C A:GLY25 3.5 33.6 1.0
CA A:GLY25 3.9 35.0 1.0
N A:ALA26 4.6 32.0 1.0
O A:HOH820 4.8 44.4 1.0
CA A:ALA26 5.0 31.7 1.0

Calcium binding site 6 out of 10 in 4jbe

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Calcium binding site 6 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:56.4
occ:1.00
 O A:HOH954 2.3 51.4 1.0
O A:HOH721 2.4 34.4 1.0
O A:HOH953 2.4 47.6 1.0
O A:HOH952 2.5 41.2 1.0
O A:HOH780 2.9 52.0 1.0
O A:HOH889 4.0 21.1 0.5
O A:HOH806 4.0 37.6 1.0
O A:HOH889 4.4 26.9 0.5
OD1 A:ASP322 4.5 27.7 1.0
OD2 A:ASP322 4.7 28.1 1.0
OE2 A:GLU326 4.7 24.3 1.0
OE1 A:GLU326 4.8 25.1 1.0
O A:ARG320 4.9 22.5 0.5
CG A:ASP322 5.0 27.4 1.0

Calcium binding site 7 out of 10 in 4jbe

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Calcium binding site 7 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:42.4
occ:0.50
 O B:HOH726 2.4 45.9 1.0
OD2 B:ASP246 2.4 41.9 1.0
OD2 B:ASP244 2.5 40.8 1.0
OD1 B:ASP244 2.7 32.1 1.0
CG B:ASP244 3.0 37.6 1.0
CG B:ASP246 3.5 40.7 1.0
CB B:ASP246 4.0 39.2 1.0
N B:ASP246 4.4 36.3 1.0
CB B:ASP244 4.4 36.8 1.0
OD1 B:ASP246 4.6 40.1 1.0
O B:HOH794 4.8 52.6 1.0
CA B:ASP246 4.8 37.9 1.0
N B:ARG245 4.9 35.9 1.0
O B:HOH720 4.9 51.4 1.0

Calcium binding site 8 out of 10 in 4jbe

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Calcium binding site 8 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:56.7
occ:0.50
 O B:HOH768 2.1 59.3 1.0
O B:HOH769 2.4 74.3 1.0
O B:ALA273 2.6 45.7 1.0
OE2 B:GLU277 2.6 59.8 1.0
OE1 B:GLU277 2.7 53.5 1.0
O B:HOH743 2.8 45.5 1.0
CD B:GLU277 3.0 56.8 1.0
C B:ALA273 3.6 44.1 1.0
N B:VAL274 4.4 43.0 1.0
CA B:ALA273 4.4 44.4 1.0
CA B:VAL274 4.4 42.4 1.0
CG B:GLU277 4.5 52.8 1.0
OE2 B:GLU276 4.6 60.9 1.0
CB B:GLU276 4.7 51.0 1.0
O B:ASP272 4.8 42.8 1.0
C B:VAL274 4.9 42.4 1.0
N B:GLU276 5.0 46.2 1.0

Calcium binding site 9 out of 10 in 4jbe

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Calcium binding site 9 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:71.4
occ:1.00
 O B:HOH774 2.6 46.3 1.0
O B:HOH813 3.1 31.8 0.5
O B:HOH789 3.4 62.8 1.0
O A:HOH902 3.5 58.8 1.0
O B:GLY107 4.1 34.8 1.0
O A:HOH810 4.3 36.8 1.0
O B:GLY108 4.6 29.4 1.0
O A:HOH848 4.6 45.0 1.0
CA B:GLY108 4.6 31.7 1.0
OE2 B:GLU412 4.9 57.7 1.0
O A:HOH672 4.9 28.1 1.0
C B:GLY108 5.0 30.3 1.0

Calcium binding site 10 out of 10 in 4jbe

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Calcium binding site 10 out of 10 in the 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:42.2
occ:0.50
 O B:HOH812 2.2 50.1 0.5
OE1 B:GLU288 2.3 66.4 1.0
O B:HOH773 2.3 59.5 1.0
O B:HOH772 2.5 47.0 0.5
OE1 B:GLU284 2.6 53.9 1.0
CD B:GLU288 3.4 61.5 1.0
CD B:GLU284 3.7 49.3 1.0
OE2 B:GLU288 4.0 65.1 1.0
CG B:GLU284 4.1 50.9 1.0
O B:GLU284 4.3 47.6 1.0
NH1 B:ARG249 4.3 45.9 1.0
CB B:GLU288 4.5 53.5 1.0
CG B:GLU288 4.5 56.9 1.0
CA B:GLU288 4.6 53.6 1.0
OE2 B:GLU284 4.7 48.6 1.0
N B:GLU288 4.9 52.2 1.0

Reference:

G.Minasov, E.V.Filippova, A.Halavaty, L.Shuvalova, O.Kiryukhina, M.Endres, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics (Mcsg). 1.95 Angstrom Crystal Structure of Gamma-Glutamyl Phosphate Reductase From Saccharomonospora Viridis. To Be Published.
Page generated: Sun Jul 14 08:27:07 2024

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