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Calcium in PDB 2zy6: Crystal Structure of A Truncated Trna, TPHE39A

Protein crystallography data

The structure of Crystal Structure of A Truncated Trna, TPHE39A, PDB code: 2zy6 was solved by I.Tanaka, M.Yao, Y.Tanaka, Y.Kitago, S.Ymagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.42 / 1.75
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.366, 62.366, 115.200, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 24

Other elements in 2zy6:

The structure of Crystal Structure of A Truncated Trna, TPHE39A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Truncated Trna, TPHE39A (pdb code 2zy6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of A Truncated Trna, TPHE39A, PDB code: 2zy6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2zy6

Go back to Calcium Binding Sites List in 2zy6
Calcium binding site 1 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:14.9
occ:1.00
 OP2 A:U13 2.3 13.8 1.0
O A:HOH179 2.3 16.3 1.0
O A:HOH162 2.3 14.5 1.0
O A:HOH194 2.4 19.6 1.0
O A:HOH172 2.4 19.7 1.0
O A:HOH44 2.4 19.7 1.0
P A:U13 3.6 14.5 1.0
O5' A:U13 3.8 14.3 1.0
OP2 A:C15 4.3 14.6 1.0
O A:HOH193 4.3 20.1 1.0
O A:HOH140 4.4 20.6 1.0
OP1 A:G12 4.4 14.0 1.0
C3' A:G12 4.5 14.2 1.0
OP1 A:C15 4.6 14.7 1.0
O3' A:G12 4.6 15.3 1.0
O A:HOH169 4.6 17.1 1.0
OP1 A:U13 4.7 14.8 1.0
C5' A:G12 4.7 14.9 1.0
O2' A:U11 4.9 17.7 1.0
C2' A:U13 4.9 13.6 1.0
C4' A:G12 4.9 14.6 1.0
O3' A:U11 4.9 15.6 1.0
P A:C15 5.0 14.4 1.0

Calcium binding site 2 out of 7 in 2zy6

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Calcium binding site 2 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:15.6
occ:1.00
 OP2 A:G12 2.2 14.3 1.0
O A:HOH40 2.3 24.3 1.0
O A:HOH170 2.4 16.1 1.0
O A:HOH181 2.4 12.8 1.0
O A:HOH166 2.5 17.0 1.0
O6 A:G19 2.6 15.9 1.0
C6 A:G19 3.4 16.5 1.0
P A:G12 3.6 14.5 1.0
N7 A:G19 3.9 16.6 1.0
C5 A:G19 3.9 16.3 1.0
O2' A:G10 4.1 18.0 1.0
OP1 A:G12 4.2 14.0 1.0
O6 A:G20 4.2 15.7 1.0
O A:HOH164 4.4 18.3 1.0
O5' A:G12 4.4 14.8 1.0
O A:HOH138 4.4 35.4 1.0
N1 A:G19 4.5 15.5 1.0
O A:HOH188 4.5 22.6 1.0
N7 A:G20 4.6 15.3 1.0
O A:HOH65 4.6 23.4 1.0
O3' A:U11 4.6 15.6 1.0
C4' A:U11 4.6 18.1 1.0
O4 A:U13 4.7 14.5 1.0
C2' A:G10 4.7 18.9 1.0
O6 A:G18 4.8 16.1 1.0
O A:HOH46 4.8 32.7 1.0
C5' A:U11 4.8 19.2 1.0
C3' A:U11 4.9 16.4 1.0
C8 A:G12 4.9 13.8 1.0
O A:HOH85 5.0 39.0 1.0
N7 A:G18 5.0 16.4 1.0

Calcium binding site 3 out of 7 in 2zy6

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Calcium binding site 3 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca104

b:19.4
occ:0.50
 O A:HOH56 2.4 23.2 1.0
O A:HOH200 2.4 18.0 1.0
O A:HOH52 2.5 18.9 0.5
O A:HOH187 2.5 18.9 1.0
O2 A:U11 4.4 17.4 1.0
OP2 A:U16 4.4 13.5 1.0
O A:HOH82 4.5 40.2 1.0
O A:HOH193 4.5 20.1 1.0
OP1 A:C15 4.6 14.7 1.0
OP1 A:U16 4.6 14.7 1.0
O A:HOH44 4.9 19.7 1.0
P A:U16 4.9 14.9 1.0
O A:HOH139 4.9 34.6 1.0

Calcium binding site 4 out of 7 in 2zy6

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Calcium binding site 4 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca105

b:20.2
occ:0.90
 O A:HOH50 2.2 27.2 1.0
O A:HOH195 2.3 27.7 1.0
O A:HOH75 2.3 29.6 1.0
O4 A:U11 2.6 17.2 1.0
O A:HOH76 2.7 28.0 1.0
C4 A:U11 3.6 16.8 1.0
O6 A:G28 4.0 26.1 1.0
C5 A:U11 4.1 16.5 1.0
O A:HOH159 4.3 47.5 1.0
N7 A:G28 4.5 25.4 1.0
N3 A:U11 4.8 16.4 1.0
C6 A:G28 4.8 25.5 1.0
O A:HOH92 4.9 21.8 1.0

Calcium binding site 5 out of 7 in 2zy6

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Calcium binding site 5 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca106

b:23.3
occ:1.00
 OP1 A:U8 2.3 29.1 1.0
O A:HOH110 2.3 33.9 1.0
O A:HOH111 2.4 29.7 1.0
O A:HOH109 2.6 35.9 1.0
P A:U8 3.7 28.7 1.0
O3' A:A7 4.2 27.5 1.0
O A:HOH131 4.2 35.9 1.0
C5' A:U8 4.4 28.8 1.0
O5' A:U8 4.5 27.1 1.0
OP2 A:U8 4.7 28.1 1.0

Calcium binding site 6 out of 7 in 2zy6

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Calcium binding site 6 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca107

b:27.8
occ:0.90
 O A:HOH205 2.3 33.2 1.0
O A:HOH197 2.4 25.8 1.0
O A:HOH114 2.4 35.6 1.0
O A:HOH203 2.5 26.7 1.0
O A:HOH204 2.7 33.1 1.0
OP1 A:A9 3.4 33.0 1.0
OP2 A:A9 3.9 31.6 1.0
OP2 A:G20 4.1 23.7 1.0
P A:A9 4.1 32.6 1.0
O A:HOH86 4.3 27.9 1.0
O2' A:G19 4.5 19.6 1.0
N7 A:G10 4.5 16.9 1.0
O6 A:G10 4.5 17.6 1.0
O A:HOH191 4.5 21.4 1.0
O A:HOH61 4.6 34.0 1.0
OP1 A:A22 4.6 24.4 1.0
O3' A:G19 4.6 22.7 1.0
N3 A:G19 4.8 15.5 1.0
O5' A:A9 4.9 31.1 1.0
N2 A:G19 4.9 15.8 1.0

Calcium binding site 7 out of 7 in 2zy6

Go back to Calcium Binding Sites List in 2zy6
Calcium binding site 7 out of 7 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca108

b:40.3
occ:0.70
 O A:HOH115 2.2 34.0 1.0
O A:HOH206 2.4 23.5 1.0
O6 A:G26 2.4 21.1 1.0
O A:HOH207 2.5 27.2 1.0
C6 A:G26 3.6 20.6 1.0
OP2 A:U8 3.8 28.1 1.0
O A:HOH68 4.0 30.4 1.0
OP2 A:C24 4.0 24.1 1.0
O A:HOH83 4.0 31.9 1.0
O A:HOH199 4.0 37.0 1.0
O A:HOH171 4.3 30.7 1.0
N4 A:C25 4.5 17.2 1.0
N1 A:G26 4.5 20.9 1.0
O A:HOH131 4.5 35.9 1.0
C5 A:G26 4.5 20.8 1.0
C5 A:C25 4.6 16.7 1.0
O A:HOH130 4.7 36.0 1.0
N7 A:G26 4.7 20.7 1.0
OP2 A:C25 4.8 22.1 1.0
C4 A:C25 5.0 17.4 1.0

Reference:

Y.Tanaka, S.Yamagata, Y.Kitago, Y.Yamada, S.Chimnaronk, M.Yao, I.Tanaka. Deduced Rna Binding Mechanism of Thii Based on Structural and Binding Analyses of A Minimal Rna Ligand Rna V. 15 1498 2009.
ISSN: ISSN 1355-8382
PubMed: 19509301
DOI: 10.1261/RNA.1614709
Page generated: Sat Dec 12 04:02:14 2020

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