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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
Calcium binding site 2 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 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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
Calcium binding site 8 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 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

Go back to Calcium Binding Sites List in 8v1i
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

Go back to Calcium Binding Sites List in 8v1i
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy