Calcium in PDB 8v1i: Crystal Structure of Human Mascrna

Protein crystallography data

The structure of Crystal Structure of Human Mascrna, PDB code: 8v1i was solved by I.Skeparnias, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.99 / 2.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 137.063, 137.063, 135.805, 90, 90, 120
R / Rfree (%) 21.5 / 22.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Mascrna (pdb code 8v1i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Human Mascrna, PDB code: 8v1i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 8v1i

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Calcium binding site 1 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca104

b:119.6
occ:1.00
 O6 B:G53 4.1 94.6 1.0
O6 B:G52 4.2 91.7 1.0
N7 B:G52 4.4 92.2 1.0
N4 B:C51 4.5 85.0 1.0
N4 B:C5 4.7 91.9 1.0
C6 B:G52 5.0 92.2 1.0
C4 B:C51 5.0 84.2 1.0

Calcium binding site 2 out of 10 in 8v1i

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Calcium binding site 2 out of 10 in the Crystal Structure of Human Mascrna


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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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca105

b:56.4
occ:1.00
 O4 B:U25 2.5 56.2 1.0
O B:HOH206 2.6 57.2 1.0
O B:HOH214 2.6 57.1 1.0
O2 B:U26 2.7 56.1 1.0
O B:HOH203 2.9 55.4 1.0
C4 B:U25 3.5 56.4 1.0
C2 B:U26 3.6 55.9 1.0
C5 B:U25 3.9 56.7 1.0
N3 B:U26 3.9 55.6 1.0
N4 B:C28 4.2 56.5 1.0
O2' B:U26 4.7 57.2 1.0
N3 B:U25 4.7 56.1 1.0
N1 B:U26 4.8 56.1 1.0

Calcium binding site 3 out of 10 in 8v1i

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Calcium binding site 3 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca106

b:70.1
occ:1.00
 OP2 B:G32 2.4 64.8 1.0
O B:HOH215 2.6 66.3 1.0
O B:HOH207 2.6 62.6 1.0
O B:HOH209 2.7 67.5 1.0
O B:HOH210 2.8 63.3 1.0
O B:HOH208 3.0 60.4 1.0
P B:G32 3.7 64.8 1.0
O5' B:G32 3.9 63.6 1.0
N7 B:A44 4.2 68.4 1.0
C8 B:A44 4.3 66.0 1.0
OP2 B:A33 4.4 67.7 1.0
OP1 B:G32 4.6 68.3 1.0
C8 B:G32 4.6 60.8 1.0
N7 B:G32 4.6 60.8 1.0
O3' B:G31 4.9 59.8 1.0

Calcium binding site 4 out of 10 in 8v1i

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Calcium binding site 4 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca107

b:126.5
occ:1.00
 O2A B:GTP1 2.4 123.3 1.0
PA B:GTP1 3.9 123.3 1.0
O1B B:GTP1 4.1 130.9 1.0
O5' B:GTP1 4.5 110.9 1.0
O3A B:GTP1 4.6 121.6 1.0
O1A B:GTP1 4.9 117.8 1.0

Calcium binding site 5 out of 10 in 8v1i

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Calcium binding site 5 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:105.7
occ:1.00
 O2' A:U26 4.0 53.9 1.0
OP2 A:C28 4.3 56.5 1.0
C2' A:U26 4.3 54.1 1.0
OP2 A:U26 4.5 56.6 1.0
C5 A:C28 4.6 54.6 1.0
C6 A:U26 5.0 55.1 1.0

Calcium binding site 6 out of 10 in 8v1i

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Calcium binding site 6 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca104

b:99.6
occ:1.00
 O6 A:G38 4.0 75.3 1.0
N7 A:G38 4.3 78.0 1.0
O6 A:G37 4.4 79.5 1.0
N7 A:G37 4.5 88.1 1.0
O2' A:A43 4.6 68.2 1.0
C6 A:G38 4.9 73.9 1.0

Calcium binding site 7 out of 10 in 8v1i

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Calcium binding site 7 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca105

b:97.5
occ:1.00
 OP1 A:A42 2.5 65.6 1.0
O3' A:C41 3.6 67.2 1.0
P A:A42 3.7 65.5 1.0
C5' A:A42 4.4 64.6 1.0
O5' A:A42 4.5 67.0 1.0
OP2 A:A42 4.8 67.3 1.0
C3' A:C41 4.9 66.7 1.0

Calcium binding site 8 out of 10 in 8v1i

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Calcium binding site 8 out of 10 in the Crystal Structure of Human Mascrna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca106

b:62.5
occ:1.00
 OP1 A:G23 2.3 61.2 1.0
O A:HOH204 2.4 60.5 1.0
O A:HOH210 2.5 58.8 1.0
P A:G23 3.6 61.3 1.0
O5' A:G23 3.9 62.9 1.0
C8 A:G23 4.1 60.2 1.0
N7 A:G23 4.2 60.3 1.0
O3' A:U22 4.3 60.1 1.0
C2' A:U22 4.4 61.2 1.0
C3' A:U22 4.5 60.7 1.0
OP2 A:G23 4.8 60.8 1.0
O2' A:U22 4.8 60.1 1.0

Calcium binding site 9 out of 10 in 8v1i

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Calcium binding site 9 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca107

b:67.1
occ:1.00
 O A:HOH207 2.2 62.3 1.0
OP2 A:G32 2.2 59.1 1.0
O A:HOH209 2.5 57.9 1.0
O A:HOH203 2.5 62.1 1.0
O A:HOH206 2.6 67.5 1.0
O A:HOH208 2.9 57.5 1.0
P A:G32 3.6 62.0 1.0
O5' A:G32 3.9 59.7 1.0
N7 A:A44 4.3 74.4 1.0
OP2 A:A33 4.4 63.3 1.0
OP1 A:G32 4.5 61.6 1.0
C8 A:G32 4.5 58.4 1.0
C8 A:A44 4.5 73.2 1.0
N7 A:G32 4.5 57.8 1.0
O3' A:G31 4.7 62.7 1.0

Calcium binding site 10 out of 10 in 8v1i

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Calcium binding site 10 out of 10 in the Crystal Structure of Human Mascrna


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 Human Mascrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca108

b:102.0
occ:1.00
 OP1 A:C28 2.8 53.3 1.0
P A:C28 4.1 58.8 1.0
OP1 A:C18 4.3 78.5 1.0
O3' A:U27 4.4 56.1 1.0
OP2 A:U19 4.4 82.0 1.0
OP2 A:C29 4.7 56.1 1.0
C5' A:C28 4.8 53.2 1.0
O5' A:C28 4.8 58.2 1.0
OP1 A:C29 5.0 54.9 1.0

Reference:

I.Skeparnias, C.Bou-Nader, D.G.Anastasakis, L.Fan, Y.X.Wang, M.Hafner, J.Zhang. Structural Basis of MALAT1 Rna Maturation and Mascrna Biogenesis Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01340-4
Page generated: Fri Jul 19 12:25:24 2024

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