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Calcium in PDB 2zni: Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense

Enzymatic activity of Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense

All present enzymatic activity of Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense:
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense, PDB code: 2zni was solved by K.Nozawa, Y.Araiso, D.Soll, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.64 / 3.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.627, 103.627, 214.044, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 29.6

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense (pdb code 2zni). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense, PDB code: 2zni:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 2zni

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Calcium binding site 1 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca77

b:0.9
occ:1.00
 O6 C:G4 2.9 0.2 1.0
C6 C:G4 3.8 0.8 1.0
O6 C:G5 3.8 0.7 1.0
N7 C:G4 4.2 0.4 1.0
C5 C:G4 4.3 0.8 1.0
N7 C:G5 4.4 0.3 1.0
N4 C:C69 4.6 0.8 1.0
C6 C:G5 4.7 0.8 1.0
N1 C:G4 4.9 1.0 1.0
O4 C:U68 4.9 0.6 1.0
C5 C:G5 5.0 0.9 1.0

Calcium binding site 2 out of 13 in 2zni

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Calcium binding site 2 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca78

b:0.3
occ:1.00
 O4 C:U65 3.0 0.8 1.0
O6 C:G64 3.9 0.2 1.0
N7 C:G64 4.0 0.9 1.0
C4 C:U65 4.0 0.5 1.0
N4 C:C63 4.6 0.9 1.0
C6 C:G64 4.7 0.3 1.0
C5 C:G64 4.7 0.8 1.0
C5 C:U65 4.8 0.6 1.0
O6 C:G49 4.9 0.0 1.0
N3 C:U65 4.9 0.8 1.0
N6 C:A66 5.0 0.9 1.0

Calcium binding site 3 out of 13 in 2zni

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Calcium binding site 3 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca79

b:93.5
occ:1.00
 O6 C:G14 2.8 0.0 1.0
N7 C:G14 3.1 1.0 1.0
C6 C:G14 3.5 0.2 1.0
C5 C:G14 3.6 0.3 1.0
OP1 C:G6 3.9 0.3 1.0
C8 C:G14 4.3 0.1 1.0
OP1 C:C61 4.4 0.2 1.0
OP2 C:C13 4.5 0.8 1.0
C5 C:C13 4.8 0.2 1.0
N1 C:G14 4.8 0.1 1.0
N4 C:C13 4.9 0.9 1.0
C4 C:G14 5.0 0.9 1.0

Calcium binding site 4 out of 13 in 2zni

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Calcium binding site 4 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca80

b:0.0
occ:1.00
 O6 C:G53 3.9 0.4 1.0
O6 C:G52 3.9 1.0 1.0
N7 C:G52 4.1 0.5 1.0
N7 C:G53 4.5 0.2 1.0
C6 C:G52 4.6 0.9 1.0
C5 C:G52 4.7 0.2 1.0
C6 C:G53 4.8 0.9 1.0
OP2 C:C59 4.8 0.9 1.0

Calcium binding site 5 out of 13 in 2zni

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Calcium binding site 5 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca81

b:85.0
occ:1.00
 OP1 C:G9 2.9 0.5 1.0
O2' C:A46 3.9 0.4 1.0
P C:G9 4.0 0.0 1.0
OP2 C:G9 4.2 0.1 1.0
N7 C:A11 4.2 0.2 1.0
C5' C:U7 4.3 0.4 1.0
OP2 C:A11 4.6 0.5 1.0
C8 C:A11 4.9 0.6 1.0
C4' C:U7 4.9 0.1 1.0
C3' C:U7 5.0 0.7 1.0

Calcium binding site 6 out of 13 in 2zni

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Calcium binding site 6 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca82

b:0.5
occ:1.00
 O4 C:U43 3.7 0.1 1.0
OP2 C:C24 4.5 0.8 1.0
C4 C:U43 4.8 0.1 1.0

Calcium binding site 7 out of 13 in 2zni

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Calcium binding site 7 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca77

b:83.3
occ:1.00
 O6 D:G4 3.0 0.4 1.0
C6 D:G4 4.1 0.7 1.0
O6 D:G5 4.3 0.4 1.0
N7 D:G4 4.4 0.2 1.0
C5 D:G4 4.6 0.1 1.0
O4 D:U68 4.6 0.3 1.0
N4 D:C69 4.8 0.6 1.0
O6 D:G3 4.8 0.9 1.0

Calcium binding site 8 out of 13 in 2zni

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Calcium binding site 8 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca78

b:97.5
occ:1.00
 O4 D:U65 3.3 0.5 1.0
N7 D:G64 4.2 0.9 1.0
C4 D:U65 4.6 0.0 1.0
O6 D:G64 4.6 0.3 1.0

Calcium binding site 9 out of 13 in 2zni

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Calcium binding site 9 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca79

b:90.5
occ:1.00
 N7 D:G14 2.9 0.2 1.0
O6 D:G14 3.2 0.6 1.0
C5 D:G14 3.5 0.6 1.0
C6 D:G14 3.6 0.2 1.0
C8 D:G14 3.9 0.0 1.0
OP1 D:G6 4.3 0.1 1.0
OP2 D:C13 4.4 93.2 1.0
OP1 D:C61 4.6 0.1 1.0
OP2 D:G14 4.6 0.1 1.0
C4 D:G14 4.7 0.8 1.0
N1 D:G14 4.9 0.7 1.0
N9 D:G14 4.9 0.7 1.0

Calcium binding site 10 out of 13 in 2zni

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Calcium binding site 10 out of 13 in the Crystal Structure of Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense


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 Pyrrolysyl-Trna Synthetase-Trna(Pyl) Complex From Desulfitobacterium Hafniense within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca80

b:0.1
occ:1.00
 O6 D:G52 3.9 0.8 1.0
N7 D:G52 4.3 0.8 1.0
O6 D:G53 4.4 0.1 1.0
OP2 D:C59 4.7 0.6 1.0
C6 D:G52 4.7 1.0 1.0
C5 D:G52 4.8 0.2 1.0

Reference:

K.Nozawa, P.O'donoghue, S.Gundllapalli, Y.Araiso, R.Ishitani, T.Umehara, D.Soll, O.Nureki. Pyrrolysyl-Trna Synthetase-Trna(Pyl) Structure Reveals the Molecular Basis of Orthogonality Nature V. 457 1163 2009.
ISSN: ISSN 0028-0836
PubMed: 19118381
DOI: 10.1038/NATURE07611
Page generated: Tue Jul 8 10:05:35 2025

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