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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


Mono view


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

Go back to Calcium Binding Sites List in 8t2r
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

Go back to Calcium Binding Sites List in 8t2r
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: Thu Dec 28 01:50:31 2023

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