Calcium in PDB 8t2r: Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State

Enzymatic activity of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State

All present enzymatic activity of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State:
2.7.7.49;

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State (pdb code 8t2r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State, PDB code: 8t2r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 8t2r

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Calcium binding site 1 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:89.5
occ:1.00
 O3' A:U8 2.4 63.0 1.0
OP2 B:C581 2.4 54.1 1.0
CA B:CA702 2.7 66.2 1.0
OP1 B:U579 2.8 44.0 1.0
P B:C581 3.3 44.4 1.0
OP1 B:C581 3.3 44.6 1.0
C3' A:U8 3.8 61.0 1.0
OP1 B:G563 3.8 60.2 1.0
P B:U579 4.1 50.9 1.0
OP1 B:G640 4.2 106.5 1.0
O3' B:A580 4.3 38.2 1.0
C5' B:U639 4.5 96.6 1.0
O2' A:U8 4.6 72.6 1.0
C4' B:U639 4.6 99.1 1.0
O5' B:C581 4.6 40.7 1.0
OP2 B:U579 4.6 42.3 1.0
C2' A:U8 4.6 66.4 1.0
C4' A:U8 4.7 61.6 1.0
C4' B:A580 4.7 40.7 1.0
O3' B:G578 4.7 37.3 1.0
C3' B:A580 4.7 26.6 1.0
P B:G563 4.8 53.6 1.0
OP2 B:G563 4.8 41.6 1.0
O3' B:U639 4.9 97.4 1.0
C5' B:A580 5.0 45.5 1.0

Calcium binding site 2 out of 13 in 8t2r

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Calcium binding site 2 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:66.2
occ:1.00
 OP1 B:G640 2.3 106.5 1.0
OP1 B:C581 2.3 44.6 1.0
CA B:CA701 2.7 89.5 1.0
OP1 B:C562 2.7 58.6 1.0
P B:C581 3.4 44.4 1.0
OP2 B:C581 3.7 54.1 1.0
P B:G640 3.8 110.6 1.0
OP1 B:G563 4.0 60.2 1.0
OP2 B:G563 4.1 41.6 1.0
O3' B:A580 4.1 38.2 1.0
P B:C562 4.2 58.1 1.0
O3' B:U639 4.3 97.4 1.0
P B:G563 4.5 53.6 1.0
O5' B:G640 4.6 113.6 1.0
O3' A:U8 4.7 63.0 1.0
O5' B:C581 4.7 40.7 1.0
OP2 B:G640 4.8 107.7 1.0
C5' B:U639 4.8 96.6 1.0
OP2 B:C562 4.8 46.4 1.0
O5' B:C562 4.9 48.6 1.0

Calcium binding site 3 out of 13 in 8t2r

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Calcium binding site 3 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:107.2
occ:1.00
 O2' B:C561 3.8 66.4 1.0
O5' B:G640 3.9 113.6 1.0
OP2 B:A641 3.9 130.6 1.0
C5' B:G640 4.1 112.1 1.0
O3' B:C561 4.1 56.6 1.0
OP2 B:G640 4.5 107.7 1.0
P B:G640 4.6 110.6 1.0
OP1 B:G640 4.8 106.5 1.0
C3' B:C561 4.8 54.7 1.0
C4' B:C561 4.8 55.7 1.0
C2' B:C561 4.9 53.4 1.0
OP1 B:C562 5.0 58.6 1.0

Calcium binding site 4 out of 13 in 8t2r

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Calcium binding site 4 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:59.3
occ:1.00
 OP2 B:A580 2.5 55.5 1.0
O4 B:U4 2.7 62.3 1.0
O6 B:G5 3.5 55.6 1.0
O3' B:U579 3.6 37.9 1.0
P B:A580 3.6 60.6 1.0
C4 B:U4 3.8 57.0 1.0
N1 B:G5 4.2 50.5 1.0
C6 B:G5 4.3 55.0 1.0
OP2 B:U3 4.3 71.2 1.0
C5' B:A580 4.4 45.5 1.0
O5' B:A580 4.6 46.3 1.0
C5 B:U4 4.6 59.0 1.0
O6 B:G110 4.7 55.0 1.0
O4 B:U3 4.7 73.1 1.0
OP1 B:A580 4.7 55.2 1.0
N3 B:U4 4.9 64.7 1.0
C5 B:U3 4.9 56.2 1.0
C3' B:U579 5.0 30.6 1.0

Calcium binding site 5 out of 13 in 8t2r

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Calcium binding site 5 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:69.4
occ:1.00
 OP2 B:A120 2.4 77.2 1.0
P B:A120 3.7 87.9 1.0
OP1 B:A119 3.8 76.2 1.0
O5' B:A120 4.0 70.8 1.0
N7 B:A120 4.2 68.6 1.0
OP2 B:A119 4.3 69.9 1.0
P B:A119 4.3 86.1 1.0
C8 B:A120 4.3 71.9 1.0
O5' B:A119 4.4 79.5 1.0
OP1 B:A120 4.7 79.3 1.0
N7 B:G121 4.8 66.6 1.0
O3' B:A119 4.8 73.3 1.0
C3' B:A119 5.0 69.3 1.0

Calcium binding site 6 out of 13 in 8t2r

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Calcium binding site 6 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:52.7
occ:1.00
 OP1 B:G110 2.4 52.3 1.0
OP1 B:G111 3.0 49.8 1.0
P B:G110 3.7 48.6 1.0
OP1 B:A112 3.9 53.5 1.0
O5' B:G110 4.0 40.5 1.0
C5' B:G110 4.2 44.0 1.0
C5' B:G111 4.3 51.1 1.0
N7 B:A108 4.3 68.4 1.0
P B:G111 4.4 61.3 1.0
C8 B:A108 4.6 63.6 1.0
O3' B:A109 4.6 29.2 1.0
N7 B:A270 4.7 53.9 1.0
C8 B:A270 4.7 41.3 1.0
OP2 B:G110 4.8 52.1 1.0
O5' B:G111 4.9 45.9 1.0
C3' B:G111 5.0 45.4 1.0
C4' B:G111 5.0 53.2 1.0

Calcium binding site 7 out of 13 in 8t2r

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Calcium binding site 7 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca707

b:87.9
occ:1.00
 OP2 B:A323 2.4 82.1 1.0
O6 B:G324 3.6 72.2 1.0
P B:A323 3.9 89.4 1.0
OP2 B:A322 4.2 83.9 1.0
C6 B:G324 4.2 66.1 1.0
N7 B:A323 4.5 72.0 1.0
O5' B:A323 4.5 73.4 1.0
C3' B:A322 4.6 77.3 1.0
O5' B:A322 4.6 81.3 1.0
C8 B:A323 4.6 79.7 1.0
C5 B:G324 4.7 60.2 1.0
N7 B:G324 4.7 65.2 1.0
O3' B:A322 4.7 77.7 1.0
OP1 B:A323 4.8 78.4 1.0
P B:A322 4.9 86.9 1.0

Calcium binding site 8 out of 13 in 8t2r

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Calcium binding site 8 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca708

b:64.6
occ:1.00
 OP2 B:A157 2.4 78.3 1.0
N7 B:G158 3.5 55.3 1.0
O4 B:U229 3.6 62.3 1.0
P B:A157 3.7 80.5 1.0
O6 B:G159 3.9 56.9 1.0
O6 B:G158 4.0 67.0 1.0
OP1 B:A157 4.2 72.2 1.0
C5 B:G158 4.2 54.7 1.0
C8 B:G158 4.4 63.7 1.0
O5' B:A157 4.4 65.3 1.0
C6 B:G158 4.4 61.8 1.0
N7 B:G159 4.4 58.1 1.0
C4 B:U229 4.7 49.0 1.0
C6 B:G159 4.8 49.7 1.0
O3' B:A156 4.9 82.0 1.0
O6 B:G228 4.9 59.2 1.0
C5 B:G159 5.0 45.4 1.0

Calcium binding site 9 out of 13 in 8t2r

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Calcium binding site 9 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca709

b:67.3
occ:1.00
 OP1 B:G247 3.1 46.0 1.0
OP1 B:C122 3.4 58.0 1.0
OP2 B:G248 3.4 53.2 1.0
OP1 B:A177 4.3 38.6 1.0
P B:G247 4.5 55.0 1.0
C5' B:G247 4.7 49.5 1.0
P B:G248 4.7 49.0 1.0
O5' B:G247 4.7 50.6 1.0
P B:C122 4.8 53.3 1.0
O3' B:G247 4.9 44.8 1.0

Calcium binding site 10 out of 13 in 8t2r

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Calcium binding site 10 out of 13 in the Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of A Group II Intron Ribonucleoprotein in the Pre-Ligation (Pre-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca710

b:21.2
occ:1.00
 OP2 B:G139 2.4 53.9 1.0
P B:G139 3.7 61.7 1.0
OP2 B:U233 3.9 54.6 1.0
N3 B:A141 4.0 52.6 1.0
O5' B:G139 4.1 58.0 1.0
C2 B:A141 4.3 58.3 1.0
C8 B:G139 4.6 50.1 1.0
OP1 B:G139 4.7 56.0 1.0
N7 B:G139 4.7 51.1 1.0
O5' B:C138 4.7 43.2 1.0
OP2 B:G140 4.8 68.8 1.0
O3' B:C138 4.8 43.3 1.0
OP2 B:C138 4.8 48.8 1.0
OP1 B:C138 4.8 49.8 1.0
C3' B:C138 5.0 43.8 1.0

Reference:

L.Xu, T.Liu, K.Chung, A.M.Pyle. Structural Insights Into Intron Catalysis and Dynamics During Splicing Nature 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06746-6
Page generated: Fri Jul 19 11:57:01 2024

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