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Magnesium in PDB 4oav: Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate.

Protein crystallography data

The structure of Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate., PDB code: 4oav was solved by Y.Han, J.Donovan, S.Rath, G.Whitney, A.Chitrakar, A.Korennykh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.62 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.610, 160.700, 230.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate. (pdb code 4oav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate., PDB code: 4oav:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4oav

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Magnesium binding site 1 out of 4 in the Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:49.7
occ:1.00
 O2B B:ACP801 2.1 48.0 1.0
OD2 B:ASP503 2.1 43.5 1.0
OD1 B:ASN490 2.1 44.4 1.0
O B:HOH907 2.1 43.1 1.0
O1A B:ACP801 2.1 45.1 1.0
O B:HOH918 2.2 42.7 1.0
CG B:ASN490 3.1 44.0 1.0
CG B:ASP503 3.1 42.9 1.0
PB B:ACP801 3.3 49.8 1.0
PA B:ACP801 3.4 45.2 1.0
ND2 B:ASN490 3.4 40.1 1.0
CB B:ASP503 3.6 38.8 1.0
O3A B:ACP801 3.7 48.8 1.0
O1B B:ACP801 3.8 41.5 1.0
MG B:MG803 3.9 48.1 1.0
OD2 B:ASP485 4.0 55.3 1.0
O B:HOH989 4.1 47.7 1.0
OD1 B:ASP503 4.1 44.3 1.0
OE1 B:GLN487 4.1 67.6 1.0
O B:HOH1240 4.2 61.2 1.0
O2A B:ACP801 4.3 46.0 1.0
O3' B:ACP801 4.3 47.1 1.0
O5' B:ACP801 4.4 50.5 1.0
C5' B:ACP801 4.4 43.4 1.0
CB B:ASN490 4.4 40.6 1.0
O B:HOH926 4.5 41.6 1.0
O B:HOH1143 4.8 40.2 1.0
C3B B:ACP801 4.8 46.8 1.0
CA B:ASN490 4.8 43.2 1.0
C3' B:ACP801 4.9 43.4 1.0
N B:ASN490 5.0 42.1 1.0
O B:GLN489 5.0 50.8 1.0

Magnesium binding site 2 out of 4 in 4oav

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Magnesium binding site 2 out of 4 in the Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:48.1
occ:1.00
 O B:HOH1143 1.9 40.2 1.0
O B:HOH926 2.0 41.6 1.0
O1B B:ACP801 2.0 41.5 1.0
OD1 B:ASP503 2.0 44.3 1.0
OD1 B:ASP505 2.2 49.7 1.0
OD2 B:ASP503 2.3 43.5 1.0
CG B:ASP503 2.5 42.9 1.0
CG B:ASP505 3.2 49.2 1.0
PB B:ACP801 3.3 49.8 1.0
O2B B:ACP801 3.3 48.0 1.0
OD2 B:ASP505 3.6 50.1 1.0
OD2 B:ASP485 3.7 55.3 1.0
MG B:MG802 3.9 49.7 1.0
NZ B:LYS392 4.0 43.4 1.0
CB B:ASP503 4.0 38.8 1.0
O1G B:ACP801 4.0 56.2 1.0
O B:HOH907 4.2 43.1 1.0
NH1 B:ARG400 4.3 57.3 1.0
O3A B:ACP801 4.3 48.8 1.0
N B:ASP505 4.4 40.0 1.0
CB B:ASP505 4.4 47.3 1.0
O B:HOH945 4.5 55.2 1.0
C3B B:ACP801 4.5 46.8 1.0
O1A B:ACP801 4.5 45.1 1.0
C B:ASP503 4.7 43.6 1.0
O B:HOH920 4.7 41.4 1.0
CA B:ASP505 4.7 46.4 1.0
CA B:ASP503 4.7 44.0 1.0
O B:ASP503 4.7 41.2 1.0
CG B:LYS506 4.7 57.2 1.0
CG B:ASP485 4.7 53.1 1.0
N B:LYS506 4.8 48.6 1.0
CD B:LYS506 4.8 61.4 1.0
C B:ASP505 4.9 47.2 1.0
PG B:ACP801 4.9 61.8 1.0
PA B:ACP801 4.9 45.2 1.0
ND2 B:ASN490 5.0 40.1 1.0

Magnesium binding site 3 out of 4 in 4oav

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Magnesium binding site 3 out of 4 in the Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:47.5
occ:1.00
 O D:HOH1492 1.9 42.4 1.0
O D:HOH1122 2.0 45.3 1.0
O1A D:ACP1001 2.0 47.1 1.0
OD2 D:ASP503 2.1 47.9 1.0
OD1 D:ASN490 2.1 40.0 1.0
O2B D:ACP1001 2.1 47.2 1.0
CG D:ASP503 3.0 44.7 1.0
CG D:ASN490 3.1 40.1 1.0
PB D:ACP1001 3.3 48.7 1.0
PA D:ACP1001 3.3 45.8 1.0
ND2 D:ASN490 3.4 39.2 1.0
CB D:ASP503 3.6 45.5 1.0
O1B D:ACP1001 3.6 45.3 1.0
O3A D:ACP1001 3.7 46.4 1.0
MG D:MG1003 4.0 48.8 1.0
OD2 D:ASP485 4.0 50.6 1.0
OD1 D:ASP503 4.0 44.2 1.0
NE2 D:GLN487 4.2 61.6 1.0
O2A D:ACP1001 4.2 46.1 1.0
O D:HOH1242 4.2 58.4 1.0
O D:HOH1468 4.3 54.4 1.0
O5' D:ACP1001 4.3 45.1 1.0
O D:HOH1493 4.4 41.2 1.0
O3' D:ACP1001 4.4 49.3 1.0
C5' D:ACP1001 4.4 43.7 1.0
CB D:ASN490 4.5 41.0 1.0
CA D:ASN490 4.8 45.4 1.0
O D:GLN489 4.8 46.2 1.0
C3B D:ACP1001 4.9 44.0 1.0
C3' D:ACP1001 4.9 47.2 1.0
O D:HOH1494 4.9 45.8 1.0

Magnesium binding site 4 out of 4 in 4oav

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Magnesium binding site 4 out of 4 in the Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complete Human Rnase L in Complex with 2-5A (5'-Ppp Heptamer), Amppcp and Rna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:48.8
occ:1.00
 OD1 D:ASP505 2.0 49.2 1.0
O1B D:ACP1001 2.0 45.3 1.0
O D:HOH1493 2.1 41.2 1.0
O D:HOH1494 2.1 45.8 1.0
OD1 D:ASP503 2.1 44.2 1.0
OD2 D:ASP503 2.4 47.9 1.0
CG D:ASP503 2.6 44.7 1.0
CG D:ASP505 3.0 47.1 1.0
PB D:ACP1001 3.4 48.7 1.0
OD2 D:ASP505 3.4 48.7 1.0
O2B D:ACP1001 3.5 47.2 1.0
OD2 D:ASP485 3.8 50.6 1.0
NZ D:LYS392 4.0 44.0 1.0
MG D:MG1002 4.0 47.5 1.0
CB D:ASP503 4.1 45.5 1.0
O D:HOH1492 4.2 42.4 1.0
O1G D:ACP1001 4.2 65.2 1.0
NH1 D:ARG400 4.3 59.2 1.0
CB D:ASP505 4.3 44.1 1.0
N D:ASP505 4.3 43.3 1.0
O3A D:ACP1001 4.4 46.4 1.0
O D:HOH1341 4.5 59.0 1.0
C3B D:ACP1001 4.5 44.0 1.0
O D:HOH1154 4.5 46.3 1.0
CG D:LYS506 4.5 65.0 1.0
O1A D:ACP1001 4.6 47.1 1.0
CA D:ASP505 4.6 44.3 1.0
N D:LYS506 4.7 49.2 1.0
C D:ASP503 4.7 42.7 1.0
CA D:ASP503 4.8 46.6 1.0
C D:ASP505 4.8 47.0 1.0
O D:ASP503 4.8 40.5 1.0
CD D:LYS506 4.8 67.9 1.0
CG D:ASP485 4.8 49.1 1.0
PG D:ACP1001 4.9 69.2 1.0
PA D:ACP1001 5.0 45.8 1.0

Reference:

Y.Han, J.Donovan, S.Rath, G.Whitney, A.Chitrakar, A.Korennykh. Structure of Human Rnase L Reveals the Basis For Regulated Rna Decay in the Ifn Response. Science V. 343 1244 2014.
ISSN: ISSN 0036-8075
PubMed: 24578532
DOI: 10.1126/SCIENCE.1249845
Page generated: Tue Aug 20 00:46:08 2024

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