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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 19:49:00 2020

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