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Calcium in PDB 3bju: Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase

Enzymatic activity of Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase

All present enzymatic activity of Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase:
6.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase, PDB code: 3bju was solved by M.Guo, X.L.Yang, P.Schimmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.31
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 152.013, 152.013, 108.838, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 25.2

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase (pdb code 3bju). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase, PDB code: 3bju:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 3bju

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Calcium binding site 1 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:22.8
occ:1.00
 OE2 A:GLU487 2.2 16.9 1.0
O1B A:ATP603 2.3 21.6 1.0
O1A A:ATP603 2.3 15.2 1.0
OE2 A:GLU494 2.4 19.9 1.0
O A:HOH794 2.4 22.5 1.0
O A:HOH786 2.5 18.8 1.0
OE1 A:GLU494 2.7 17.6 1.0
CD A:GLU494 2.9 19.2 1.0
CD A:GLU487 3.4 19.9 1.0
PA A:ATP603 3.5 17.1 1.0
CA A:CA608 3.5 22.7 1.0
PB A:ATP603 3.6 20.4 1.0
O3A A:ATP603 3.7 20.4 1.0
NH2 A:ARG485 3.9 18.5 1.0
ND2 A:ASN497 4.1 19.4 1.0
OE1 A:GLU487 4.2 22.7 1.0
CG A:ASN497 4.2 20.5 1.0
CG A:GLU487 4.3 19.6 1.0
O2A A:ATP603 4.3 18.9 1.0
CB A:ASN497 4.3 19.0 1.0
CG A:GLU494 4.4 17.8 1.0
O3B A:ATP603 4.5 21.9 1.0
O3' A:ATP603 4.7 18.7 1.0
OD1 A:ASN497 4.7 20.4 1.0
O2B A:ATP603 4.8 21.8 1.0
O5' A:ATP603 4.8 19.2 1.0
C3' A:ATP603 5.0 17.3 1.0

Calcium binding site 2 out of 12 in 3bju

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Calcium binding site 2 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:30.7
occ:1.00
 O1G A:ATP603 2.2 25.6 1.0
O2B A:ATP603 2.3 21.8 1.0
O A:HOH653 2.6 18.1 1.0
O A:HOH714 2.7 29.8 1.0
PG A:ATP603 3.4 23.9 1.0
PB A:ATP603 3.4 20.4 1.0
O3B A:ATP603 3.6 21.9 1.0
NE2 A:HIS331 3.9 20.5 1.0
O3G A:ATP603 4.0 25.7 1.0
CD2 A:HIS331 4.3 19.2 1.0
NH1 A:ARG323 4.3 18.5 1.0
OE2 A:GLU325 4.4 22.8 1.0
OE1 A:GLU325 4.5 30.0 1.0
O3A A:ATP603 4.5 20.4 1.0
O1B A:ATP603 4.5 21.6 1.0
O A:HOH824 4.6 27.7 1.0
O2G A:ATP603 4.7 24.1 1.0
O A:HOH825 4.8 24.8 1.0
N7 A:ATP603 4.8 15.8 1.0
CD A:GLU325 4.9 24.2 1.0

Calcium binding site 3 out of 12 in 3bju

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Calcium binding site 3 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca608

b:22.7
occ:1.00
 OE1 A:GLU494 2.2 17.6 1.0
O A:HOH786 2.3 18.8 1.0
O A:HOH674 2.3 20.2 1.0
O3G A:ATP603 2.4 25.7 1.0
O A:HOH824 2.5 27.7 1.0
O1B A:ATP603 2.6 21.6 1.0
CD A:GLU494 3.4 19.2 1.0
PG A:ATP603 3.5 23.9 1.0
CA A:CA606 3.5 22.8 1.0
O3B A:ATP603 3.6 21.9 1.0
PB A:ATP603 3.6 20.4 1.0
OE2 A:GLU494 4.2 19.9 1.0
O2G A:ATP603 4.3 24.1 1.0
CB A:GLU494 4.3 18.3 1.0
O A:HOH776 4.4 25.9 1.0
CG A:GLU494 4.4 17.8 1.0
OE2 A:GLU453 4.5 30.3 1.0
O2B A:ATP603 4.5 21.8 1.0
OE2 A:GLU487 4.5 16.9 1.0
OD2 A:ASP445 4.5 28.1 1.0
O1G A:ATP603 4.6 25.6 1.0
CZ A:PHE489 4.6 18.8 1.0
OD1 A:ASP445 4.6 26.9 1.0
O A:HOH701 4.7 26.6 1.0
OE1 A:GLU453 4.8 28.4 1.0
O3A A:ATP603 4.8 20.4 1.0

Calcium binding site 4 out of 12 in 3bju

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Calcium binding site 4 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:22.1
occ:1.00
 OE2 B:GLU494 2.0 23.1 1.0
O B:HOH812 2.1 18.6 1.0
O1A B:ATP603 2.2 21.4 1.0
O1B B:ATP603 2.3 24.7 1.0
O B:HOH866 2.4 21.7 1.0
OE2 B:GLU487 2.4 25.4 1.0
CD B:GLU494 2.7 24.7 1.0
OE1 B:GLU494 2.8 25.5 1.0
PA B:ATP603 3.4 21.6 1.0
CD B:GLU487 3.5 26.3 1.0
PB B:ATP603 3.6 21.3 1.0
O3A B:ATP603 3.7 21.9 1.0
CA B:CA608 3.7 26.7 1.0
ND2 B:ASN497 4.0 24.0 1.0
NH2 B:ARG485 4.1 21.6 1.0
CG B:GLU494 4.1 26.3 1.0
CG B:ASN497 4.2 24.9 1.0
OE1 B:GLU487 4.2 27.8 1.0
O2A B:ATP603 4.2 23.5 1.0
CB B:ASN497 4.3 23.9 1.0
CG B:GLU487 4.4 24.1 1.0
O B:HOH880 4.5 36.0 1.0
O3B B:ATP603 4.5 22.1 1.0
O5' B:ATP603 4.6 21.7 1.0
O2B B:ATP603 4.7 23.9 1.0
OD1 B:ASN497 4.7 27.3 1.0
O3' B:ATP603 4.8 24.7 1.0
O B:HOH759 4.8 36.5 1.0
C3' B:ATP603 4.9 23.3 1.0
C5' B:ATP603 4.9 22.4 1.0
OXT B:LYS601 4.9 30.1 1.0
O B:HOH875 4.9 25.6 1.0
O B:HOH840 4.9 32.1 1.0

Calcium binding site 5 out of 12 in 3bju

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Calcium binding site 5 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca607

b:30.3
occ:1.00
 O B:HOH914 2.3 34.0 1.0
O2B B:ATP603 2.3 23.9 1.0
O1G B:ATP603 2.4 23.2 1.0
O B:HOH827 2.7 31.9 1.0
O B:HOH903 2.8 46.1 1.0
PB B:ATP603 3.6 21.3 1.0
PG B:ATP603 3.6 23.1 1.0
O3B B:ATP603 3.8 22.1 1.0
O B:HOH875 4.1 25.6 1.0
O3G B:ATP603 4.1 24.7 1.0
NH1 B:ARG323 4.2 23.9 1.0
NE2 B:HIS331 4.2 21.2 1.0
OE2 B:GLU325 4.4 26.5 1.0
OE1 B:GLU325 4.6 23.1 1.0
O1B B:ATP603 4.6 24.7 1.0
CD2 B:HIS331 4.6 20.6 1.0
OE2 B:GLU525 4.6 31.6 1.0
O3A B:ATP603 4.7 21.9 1.0
O2G B:ATP603 4.9 24.2 1.0
CD B:GLU325 4.9 25.1 1.0
N7 B:ATP603 4.9 18.6 1.0

Calcium binding site 6 out of 12 in 3bju

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Calcium binding site 6 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca608

b:26.7
occ:1.00
 OE1 B:GLU494 2.1 25.5 1.0
O3G B:ATP603 2.3 24.7 1.0
O B:HOH840 2.3 32.1 1.0
O B:HOH843 2.4 28.0 1.0
O1B B:ATP603 2.7 24.7 1.0
O B:HOH812 2.7 18.6 1.0
CD B:GLU494 3.3 24.7 1.0
PG B:ATP603 3.6 23.1 1.0
CA B:CA606 3.7 22.1 1.0
PB B:ATP603 3.7 21.3 1.0
O3B B:ATP603 3.8 22.1 1.0
OE2 B:GLU494 4.0 23.1 1.0
O B:HOH880 4.3 36.0 1.0
CB B:GLU494 4.3 28.0 1.0
CG B:GLU494 4.4 26.3 1.0
OD1 B:ASP445 4.4 29.4 1.0
O2G B:ATP603 4.4 24.2 1.0
O2B B:ATP603 4.5 23.9 1.0
O1G B:ATP603 4.6 23.2 1.0
OE2 B:GLU453 4.7 38.2 1.0
O B:HOH740 4.7 21.4 1.0
OE2 B:GLU487 4.8 25.4 1.0
OE1 B:GLU453 4.8 34.0 1.0
OD2 B:ASP445 4.8 31.7 1.0
CZ B:PHE489 4.9 27.7 1.0
OE1 B:GLU487 4.9 27.8 1.0
O3A B:ATP603 5.0 21.9 1.0

Calcium binding site 7 out of 12 in 3bju

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Calcium binding site 7 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca606

b:22.1
occ:1.00
 O1B C:ATP603 2.3 23.3 1.0
OE2 C:GLU487 2.3 20.1 1.0
O1A C:ATP603 2.3 19.3 1.0
OE2 C:GLU494 2.4 17.5 1.0
OE1 C:GLU494 2.6 20.0 1.0
CD C:GLU494 2.8 20.3 1.0
CD C:GLU487 3.4 19.8 1.0
PA C:ATP603 3.4 20.3 1.0
PB C:ATP603 3.6 20.0 1.0
CA C:CA608 3.6 23.8 1.0
O3A C:ATP603 3.8 21.3 1.0
ND2 C:ASN497 3.9 17.1 1.0
OE1 C:GLU487 4.0 21.3 1.0
NH2 C:ARG485 4.1 22.6 1.0
CG C:ASN497 4.2 20.3 1.0
O2A C:ATP603 4.2 23.4 1.0
CG C:GLU494 4.3 19.0 1.0
CG C:GLU487 4.4 17.9 1.0
CB C:ASN497 4.4 20.5 1.0
O3B C:ATP603 4.5 21.3 1.0
O C:HOH706 4.5 25.7 1.0
O2B C:ATP603 4.7 20.6 1.0
O5' C:ATP603 4.7 22.5 1.0
OD1 C:ASN497 4.8 19.4 1.0
O3' C:ATP603 4.8 17.7 1.0
O C:HOH671 4.9 16.9 1.0
C3' C:ATP603 4.9 19.3 1.0

Calcium binding site 8 out of 12 in 3bju

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Calcium binding site 8 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca607

b:26.6
occ:1.00
 O1G C:ATP603 2.1 22.1 1.0
O2B C:ATP603 2.2 20.6 1.0
O C:HOH704 2.5 29.5 1.0
O C:HOH856 2.8 32.3 1.0
PG C:ATP603 3.4 21.9 1.0
PB C:ATP603 3.5 20.0 1.0
O3B C:ATP603 3.7 21.3 1.0
NE2 C:HIS331 3.9 21.1 1.0
O3G C:ATP603 4.1 22.6 1.0
NH1 C:ARG323 4.2 14.6 1.0
CD2 C:HIS331 4.4 20.6 1.0
OE2 C:GLU325 4.5 31.0 1.0
O3A C:ATP603 4.6 21.3 1.0
OE1 C:GLU325 4.6 24.6 1.0
O1B C:ATP603 4.6 23.3 1.0
O2G C:ATP603 4.7 23.2 1.0
N7 C:ATP603 4.9 14.9 1.0
CD C:GLU325 5.0 27.5 1.0

Calcium binding site 9 out of 12 in 3bju

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Calcium binding site 9 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca608

b:23.8
occ:1.00
 O3G C:ATP603 2.3 22.6 1.0
OE1 C:GLU494 2.3 20.0 1.0
O C:HOH670 2.4 15.8 1.0
O C:HOH838 2.5 31.9 1.0
O1B C:ATP603 2.7 23.3 1.0
PG C:ATP603 3.5 21.9 1.0
CD C:GLU494 3.5 20.3 1.0
O3B C:ATP603 3.6 21.3 1.0
PB C:ATP603 3.6 20.0 1.0
CA C:CA606 3.6 22.1 1.0
O C:HOH797 4.1 23.3 1.0
OE2 C:GLU494 4.3 17.5 1.0
O2B C:ATP603 4.4 20.6 1.0
O2G C:ATP603 4.4 23.2 1.0
CB C:GLU494 4.4 19.8 1.0
CG C:GLU494 4.5 19.0 1.0
OD2 C:ASP445 4.5 25.6 1.0
O C:HOH678 4.5 19.2 1.0
O1G C:ATP603 4.5 22.1 1.0
OD1 C:ASP445 4.5 25.9 1.0
OE2 C:GLU453 4.6 25.8 1.0
OE2 C:GLU487 4.7 20.1 1.0
CZ C:PHE489 4.8 17.8 1.0
O C:HOH706 4.8 25.7 1.0
OE1 C:GLU453 4.8 27.2 1.0
OE1 C:GLU487 4.9 21.3 1.0
O3A C:ATP603 4.9 21.3 1.0
CG C:ASP445 5.0 23.6 1.0

Calcium binding site 10 out of 12 in 3bju

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Calcium binding site 10 out of 12 in the Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase


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 Tetrameric Form of Human Lysyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca606

b:25.1
occ:1.00
 OE2 D:GLU494 2.3 24.4 1.0
O1B D:ATP603 2.4 26.5 1.0
OE2 D:GLU487 2.5 29.2 1.0
O1A D:ATP603 2.5 22.1 1.0
OE1 D:GLU494 2.7 23.8 1.0
CD D:GLU494 2.8 26.1 1.0
PA D:ATP603 3.5 22.9 1.0
CD D:GLU487 3.5 27.1 1.0
PB D:ATP603 3.6 22.8 1.0
O3A D:ATP603 3.6 23.8 1.0
CA D:CA608 3.7 24.6 1.0
ND2 D:ASN497 4.0 24.1 1.0
OE1 D:GLU487 4.2 26.4 1.0
CG D:ASN497 4.2 24.7 1.0
O2A D:ATP603 4.2 25.8 1.0
CG D:GLU494 4.2 26.4 1.0
O D:HOH791 4.3 30.1 1.0
NH1 D:ARG485 4.4 26.3 1.0
CB D:ASN497 4.4 23.8 1.0
CG D:GLU487 4.5 25.0 1.0
O3B D:ATP603 4.5 21.8 1.0
O2B D:ATP603 4.6 23.5 1.0
O3' D:ATP603 4.7 24.4 1.0
OD1 D:ASN497 4.8 26.7 1.0
O5' D:ATP603 4.8 24.6 1.0
O D:HOH759 4.8 20.3 1.0
O D:HOH797 4.9 25.5 1.0
C3' D:ATP603 5.0 22.2 1.0
O3G D:ATP603 5.0 21.9 1.0

Reference:

M.Guo, M.Ignatov, K.Musier-Forsyth, P.Schimmel, X.L.Yang. Crystal Structure of Tetrameric Form of Human Lysyl-Trna Synthetase: Implications For Multisynthetase Complex Formation Proc.Natl.Acad.Sci.Usa V. 105 2331 2008.
ISSN: ISSN 0027-8424
PubMed: 18272479
DOI: 10.1073/PNAS.0712072105
Page generated: Sat Jul 13 08:20:25 2024

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