Calcium in PDB 5da8: Crystal Structure of Chaperonin Groel From

Protein crystallography data

The structure of Crystal Structure of Chaperonin Groel From, PDB code: 5da8 was solved by C.Chang, N.Marshall, B.Feldmann, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 138.996, 159.781, 228.823, 75.46, 90.51, 91.22
R / Rfree (%) 23 / 26.3

Other elements in 5da8:

The structure of Crystal Structure of Chaperonin Groel From also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Chaperonin Groel From (pdb code 5da8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Chaperonin Groel From, PDB code: 5da8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 5da8

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Calcium binding site 1 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:72.0
occ:1.00
 O A:LYS43 2.6 67.6 1.0
C A:LYS43 3.5 64.5 1.0
O A:LYS42 3.6 55.5 1.0
CA A:LYS43 3.7 64.3 1.0
C A:LYS42 4.5 50.4 1.0
OD2 A:ASP41 4.5 40.9 1.0
N A:PHE44 4.6 55.6 1.0
N A:LYS43 4.6 57.0 1.0
CB A:LYS43 4.8 67.4 1.0

Calcium binding site 2 out of 18 in 5da8

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Calcium binding site 2 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:77.7
occ:1.00
 O B:LYS43 2.6 57.1 1.0
C B:LYS43 3.7 58.4 1.0
O B:LYS42 3.9 46.0 1.0
CA B:LYS43 4.4 67.8 1.0
ND2 C:ASN68 4.6 35.2 1.0
N B:PHE44 4.6 50.7 1.0
CA B:PHE44 4.7 59.8 1.0
C B:LYS42 4.9 47.2 1.0

Calcium binding site 3 out of 18 in 5da8

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Calcium binding site 3 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca602

b:77.2
occ:1.00
 O F:LYS43 3.7 74.8 1.0
OD2 F:ASP41 4.1 36.9 1.0
O F:LYS42 4.1 44.8 1.0
C F:LYS43 4.5 65.4 1.0
ND2 G:ASN68 4.8 27.0 1.0
CA F:LYS43 4.8 67.5 1.0
OD1 F:ASP41 4.9 55.1 1.0
CG F:ASP41 4.9 47.6 1.0

Calcium binding site 4 out of 18 in 5da8

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Calcium binding site 4 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca602

b:76.2
occ:1.00
 O G:LYS43 3.8 65.9 1.0
OD2 G:ASP41 4.0 51.3 1.0
O G:LYS42 4.0 52.1 1.0
C G:LYS43 4.6 67.1 1.0
ND2 A:ASN68 4.6 24.0 1.0
CG G:ASP41 4.8 44.8 1.0
OD1 G:ASP41 4.8 52.9 1.0
CA G:LYS43 5.0 64.5 1.0

Calcium binding site 5 out of 18 in 5da8

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Calcium binding site 5 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca601

b:79.5
occ:1.00
 O I:LYS43 4.0 63.4 1.0
ND2 J:ASN68 4.5 23.3 1.0
O I:LYS42 4.6 42.4 1.0
OD2 I:ASP41 4.7 45.9 1.0
OD1 I:ASP41 4.9 44.7 1.0

Calcium binding site 6 out of 18 in 5da8

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Calcium binding site 6 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca602

b:72.2
occ:1.00
 O J:LYS43 3.6 71.0 1.0
O J:LYS42 3.7 46.3 1.0
OD2 J:ASP41 3.8 39.4 1.0
C J:LYS43 4.4 67.4 1.0
CG J:ASP41 4.6 36.9 1.0
OD1 J:ASP41 4.6 50.5 1.0
CA J:LYS43 4.7 68.1 1.0
C J:LYS42 4.8 58.1 1.0

Calcium binding site 7 out of 18 in 5da8

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Calcium binding site 7 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca602

b:82.8
occ:1.00
 O K:LYS43 2.6 62.1 1.0
C K:LYS43 3.5 62.1 1.0
O K:LYS42 3.7 52.4 1.0
CA K:LYS43 3.9 63.7 1.0
N K:PHE44 4.5 58.3 1.0
OD2 K:ASP41 4.6 46.7 1.0
C K:LYS42 4.6 51.6 1.0
N K:LYS43 4.8 51.5 1.0
ND2 L:ASN68 4.9 21.0 1.0
CA K:PHE44 4.9 70.4 1.0

Calcium binding site 8 out of 18 in 5da8

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Calcium binding site 8 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca603

b:78.9
occ:1.00
 O M:LYS43 2.7 68.0 1.0
C M:LYS43 3.6 67.3 1.0
O M:LYS42 3.8 51.8 1.0
CA M:LYS43 4.1 63.8 1.0
ND2 N:ASN68 4.5 25.9 1.0
N M:PHE44 4.6 67.0 1.0
OD2 M:ASP41 4.7 54.0 1.0
C M:LYS42 4.8 53.9 1.0
OE2 N:GLU61 4.8 52.7 1.0
CA M:PHE44 4.9 64.4 1.0
OD1 M:ASP41 4.9 57.9 1.0
N M:LYS43 5.0 57.6 1.0

Calcium binding site 9 out of 18 in 5da8

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Calcium binding site 9 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca601

b:73.8
occ:1.00
 O O:LYS43 2.7 71.3 1.0
C O:LYS43 3.7 60.8 1.0
O O:LYS42 3.9 48.2 1.0
CA O:LYS43 4.1 68.2 1.0
C O:LYS42 4.9 54.3 1.0
N O:PHE44 4.9 55.4 1.0
OD1 O:ASP41 5.0 46.0 1.0

Calcium binding site 10 out of 18 in 5da8

Go back to Calcium Binding Sites List in 5da8
Calcium binding site 10 out of 18 in the Crystal Structure of Chaperonin Groel From


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca602

b:71.3
occ:1.00
 OD2 P:ASP41 3.8 50.2 1.0
O P:LYS42 4.0 49.4 1.0
ND2 Q:ASN68 4.1 14.9 1.0
OD1 P:ASP41 4.2 54.4 1.0
CG P:ASP41 4.4 45.7 1.0
O P:LYS43 4.6 68.8 1.0

Reference:

C.Chang, N.Marshall, B.Feldmann, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Chaperonin Groel From To Be Published.
Page generated: Sat Dec 12 05:21:34 2020

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