Atomistry » Magnesium » PDB 4xtr-4y2q » 4y1n
Atomistry »
  Magnesium »
    PDB 4xtr-4y2q »
      4y1n »

Magnesium in PDB 4y1n: Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine

Protein crystallography data

The structure of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine, PDB code: 4y1n was solved by C.Zhao, K.R.Rajashankar, M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.44 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.738, 131.200, 84.640, 90.00, 91.71, 90.00
R / Rfree (%) 18.3 / 24.6

Other elements in 4y1n:

The structure of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine also contains other interesting chemical elements:

Potassium (K) 1 atom
Iridium (Ir) 28 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine (pdb code 4y1n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine, PDB code: 4y1n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 1 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg414

b:90.3
occ:1.00
 OP2 A:U66 2.1 0.4 1.0
OP1 A:A67 2.3 93.8 1.0
O3' A:U66 3.3 0.4 1.0
P A:A67 3.4 83.5 1.0
P A:U66 3.5 97.0 1.0
OP1 A:U66 4.3 91.5 1.0
O5' A:U66 4.3 95.7 1.0
C5' A:A67 4.4 81.9 1.0
O5' A:A67 4.4 85.6 1.0
OP2 A:A67 4.5 97.9 1.0
O3' A:U65 4.5 84.0 1.0
C3' A:U66 4.7 0.1 1.0

Magnesium binding site 2 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 2 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg415

b:55.8
occ:1.00
 OP2 A:A67 2.1 97.9 1.0
N7 A:G68 2.7 71.2 1.0
P A:A67 3.4 83.5 1.0
O6 A:G68 3.6 66.5 1.0
C5 A:G68 3.6 66.5 1.0
C8 A:G68 3.7 75.6 1.0
C6 A:G68 4.0 71.1 1.0
OP1 A:A67 4.1 93.8 1.0
OP1 A:U65 4.1 91.4 1.0
O3' A:U66 4.1 0.4 1.0
C3' A:U66 4.3 0.1 1.0
O5' A:U66 4.3 95.7 1.0
N1 A:A120 4.4 79.8 1.0
O5' A:A67 4.6 85.6 1.0
C4 A:G68 4.9 66.2 1.0
N9 A:G68 4.9 77.3 1.0

Magnesium binding site 3 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 3 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg416

b:0.8
occ:1.00
 OP2 A:A154 1.9 0.5 1.0
P A:A154 3.0 0.7 1.0
N7 A:G155 3.1 0.4 1.0
O3' A:G153 3.3 0.6 1.0
OP1 A:A154 3.7 0.8 1.0
O6 A:G155 3.8 0.5 1.0
C5 A:G155 4.0 0.9 1.0
C8 A:G155 4.1 0.1 1.0
C6 A:G155 4.3 0.6 1.0
O6 A:G156 4.3 0.4 1.0
O5' A:A154 4.3 0.6 1.0
O2' A:G153 4.5 0.5 1.0
O4 A:U221 4.5 0.2 1.0
C3' A:G153 4.5 0.4 1.0
N7 A:G156 4.6 0.9 1.0
OP2 A:G155 4.7 0.2 1.0
O6 A:G220 4.7 0.1 1.0

Magnesium binding site 4 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 4 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg416

b:0.5
occ:1.00
 OP1 B:U65 2.2 0.2 1.0
C5' B:U66 2.6 91.9 1.0
O5' B:U66 2.6 93.2 1.0
C5' B:U65 3.0 78.6 1.0
P B:U65 3.2 0.0 1.0
MG B:MG417 3.3 75.9 1.0
C3' B:U66 3.4 86.2 1.0
C4' B:U66 3.4 78.1 1.0
O5' B:U65 3.6 65.2 1.0
OP2 B:U65 3.6 0.6 1.0
N6 B:A120 3.7 60.0 1.0
N1 B:A120 3.7 83.3 1.0
OP2 B:A67 3.7 0.7 1.0
C6 B:U66 3.9 66.5 1.0
O3' B:U66 4.0 83.8 1.0
O4' B:U66 4.1 54.7 1.0
C6 B:A120 4.2 65.6 1.0
P B:U66 4.2 0.1 1.0
C4' B:U65 4.3 76.0 1.0
P B:A67 4.5 0.6 1.0
C5 B:U66 4.5 65.8 1.0
C2' B:U66 4.6 82.2 1.0
O6 B:G68 4.6 69.2 1.0
O3' B:G64 4.6 91.8 1.0
C1' B:U66 4.7 68.5 1.0
N1 B:U66 4.7 66.4 1.0
O3' B:U65 4.7 87.9 1.0
C3' B:U65 4.7 99.6 1.0
C2 B:A120 4.8 81.5 1.0
OP2 B:U66 4.8 0.0 1.0

Magnesium binding site 5 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 5 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg417

b:75.9
occ:1.00
 OP2 B:A67 2.1 0.7 1.0
N7 B:G68 2.2 72.9 1.0
O6 B:G68 3.1 69.2 1.0
C5 B:G68 3.1 72.8 1.0
C8 B:G68 3.3 80.0 1.0
MG B:MG416 3.3 0.5 1.0
C6 B:G68 3.4 73.7 1.0
P B:A67 3.5 0.6 1.0
N1 B:A120 3.9 83.3 1.0
OP1 B:A67 4.1 0.4 1.0
O3' B:U66 4.3 83.8 1.0
C4 B:G68 4.3 69.8 1.0
N9 B:G68 4.4 82.5 1.0
C3' B:U66 4.4 86.2 1.0
C2 B:A120 4.5 81.5 1.0
O5' B:A67 4.5 96.5 1.0
OP1 B:U65 4.7 0.2 1.0
O5' B:U66 4.8 93.2 1.0
N1 B:G68 4.8 51.2 1.0
C6 B:A120 4.8 65.6 1.0
N6 B:A120 4.9 60.0 1.0

Magnesium binding site 6 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 6 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg418

b:0.6
occ:1.00
 OP1 B:A25 3.2 97.3 1.0
P B:A25 3.8 88.5 1.0
OP2 B:A25 3.9 99.5 1.0
O5' B:A25 3.9 0.3 1.0
O6 B:G28 4.6 0.7 1.0
OP2 B:A27 4.7 0.9 1.0
C5' B:A25 4.9 0.6 1.0

Magnesium binding site 7 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 7 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg419

b:0.1
occ:1.00
 O6 B:G114 3.4 83.6 1.0
OP2 B:U71 3.9 0.9 1.0
N7 B:G114 4.3 87.5 1.0
C6 B:G114 4.4 74.3 1.0
OP2 B:C70 4.8 93.0 1.0
C5 B:G114 4.8 72.1 1.0
OP1 B:C70 4.9 0.3 1.0

Magnesium binding site 8 out of 8 in 4y1n

Go back to Magnesium Binding Sites List in 4y1n
Magnesium binding site 8 out of 8 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg420

b:0.6
occ:1.00
 OP2 B:A154 2.3 1.0 1.0
N7 B:G155 3.0 0.2 1.0
P B:A154 3.5 0.7 1.0
O6 B:G155 3.5 0.2 1.0
C5 B:G155 3.7 0.0 1.0
OP1 B:A154 3.9 0.1 1.0
C6 B:G155 3.9 0.3 1.0
C8 B:G155 4.0 0.1 1.0
O6 B:G156 4.1 0.5 1.0
N7 B:G156 4.2 0.1 1.0
O2' B:G153 4.2 0.9 1.0
O5' B:A154 4.3 0.1 1.0
N6 B:A222 4.3 0.0 1.0
O4 B:U221 4.8 87.4 1.0
C6 B:G156 4.8 0.8 1.0
O3' B:G153 4.8 0.4 1.0
C5 B:G156 4.8 0.6 1.0
C4 B:G155 5.0 0.7 1.0

Reference:

C.Zhao, K.R.Rajashankar, M.Marcia, A.M.Pyle. Crystal Structure of Group II Intron Domain 1 Reveals A Template For Rna Assembly. Nat.Chem.Biol. V. 11 967 2015.
ISSN: ESSN 1552-4469
PubMed: 26502156
DOI: 10.1038/NCHEMBIO.1949
Page generated: Tue Aug 20 16:07:25 2024

Last articles

Cl in 3JX8
Cl in 3JVU
Cl in 3JVY
Cl in 3JW2
Cl in 3JVR
Cl in 3JVG
Cl in 3JVO
Cl in 3JQ1
Cl in 3JUH
Cl in 3JV9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy