Magnesium in PDB 5xym: Large Subunit of Mycobacterium Smegmatis

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 146;

Binding sites:

The binding sites of Magnesium atom in the Large Subunit of Mycobacterium Smegmatis (pdb code 5xym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 146 binding sites of Magnesium where determined in the Large Subunit of Mycobacterium Smegmatis, PDB code: 5xym:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3201 b:44.8 occ:1.00 O6 A:G564 4.2 87.0 1.0 OP2 A:A538 4.2 77.1 1.0 O6 A:G565 4.3 81.3 1.0 OP2 A:A28 4.3 67.2 1.0 O5' A:A538 4.7 76.8 1.0 O6 A:G30 4.8 74.0 1.0 N4 A:C31 4.9 80.7 1.0 C2' A:A538 4.9 77.1 1.0 OP2 A:U29 4.9 69.3 1.0 C5 A:U29 4.9 70.0 1.0 O4 A:U29 5.0 69.6 1.0

Magnesium binding site 2 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3202 b:49.4 occ:1.00 OP1 A:U120 2.2 80.4 1.0 P A:U120 3.1 80.3 1.0 OP2 A:U120 3.1 80.3 1.0 O6 A:G122 4.1 77.9 1.0 OP1 A:G121 4.2 82.0 1.0 O5' A:U120 4.2 80.4 1.0 O3' A:A119 4.2 79.1 1.0 O6 A:G123 4.3 73.6 1.0 C5' A:U120 4.4 80.8 1.0 O2' A:A119 4.6 77.2 1.0 C3' A:U120 4.7 81.4 1.0 N7 A:G122 4.7 77.8 1.0 OP1 A:C116 5.0 73.7 1.0 C6 A:G122 5.0 77.6 1.0

Magnesium binding site 3 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3203 b:53.5 occ:1.00 OP2 A:G541 2.6 66.2 1.0 OP2 A:G543 3.4 70.1 1.0 P A:G541 3.9 65.9 1.0 N E:GLY87 3.9 79.6 1.0 CA E:GLY87 4.0 80.2 1.0 OP2 A:C542 4.2 67.9 1.0 O5' A:G541 4.3 65.9 1.0 OP1 A:G541 4.5 66.0 1.0 OP1 A:A540 4.6 70.6 1.0 CG2 E:VAL58 4.7 84.6 1.0 P A:G543 4.8 70.0 1.0

Magnesium binding site 4 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3204 b:55.3 occ:1.00 OP1 A:G544 2.1 72.5 1.0 O6 A:G541 2.3 63.4 1.0 P A:G544 3.4 72.0 1.0 C6 A:G541 3.4 63.3 1.0 OP2 A:G544 4.0 72.0 1.0 OP2 A:A540 4.0 71.1 1.0 N7 A:G541 4.0 64.0 1.0 C5 A:G541 4.1 63.5 1.0 N7 A:A540 4.3 65.7 1.0 O5' A:G544 4.3 73.1 1.0 C5' A:G544 4.3 74.2 1.0 O3' A:G543 4.5 71.5 1.0 OP1 A:A545 4.6 78.6 1.0 N1 A:G541 4.6 63.1 1.0 N6 A:A540 5.0 65.2 1.0

Magnesium binding site 5 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3205 b:41.7 occ:1.00 OP1 A:U620 4.6 73.2 1.0 N7 A:G2266 4.9 58.8 1.0 O2' A:A619 4.9 72.0 1.0 O4 A:U2267 5.0 61.6 1.0

Magnesium binding site 6 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3206 b:39.8 occ:1.00 OP1 A:U662 2.3 59.5 1.0 P A:U662 3.7 59.2 1.0 O3' A:U661 4.0 58.8 1.0 O4 A:U928 4.2 54.4 1.0 N7 A:G927 4.3 53.8 1.0 OP2 A:G926 4.4 55.7 1.0 C5' A:U662 4.5 60.1 1.0 OP2 A:G927 4.5 54.8 1.0 O5' A:U662 4.6 59.5 1.0 OP2 A:U662 4.8 59.5 1.0

Magnesium binding site 7 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3207 b:38.9 occ:1.00 OP1 A:G949 3.7 63.3 1.0 OP1 A:U663 4.0 59.6 1.0 N7 A:G1065 4.0 58.1 1.0 OP2 A:G1064 4.2 58.5 1.0 C8 A:G1065 4.2 58.2 1.0 OP1 A:G1064 4.5 58.4 1.0 O L:THR37 4.7 75.2 1.0 CB L:LYS38 4.7 74.0 1.0 CD L:LYS38 4.7 74.0 1.0 N1 A:A2675 4.9 62.0 1.0 P A:G1064 4.9 58.4 1.0

Magnesium binding site 8 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3208 b:45.6 occ:1.00 OP2 A:A669 2.1 57.9 1.0 P A:A669 3.3 57.5 1.0 OP1 A:A669 3.7 57.4 1.0 C5 A:U671 4.2 56.5 1.0 O6 A:G672 4.3 52.8 1.0 O5' A:A669 4.4 58.6 1.0 O6 A:G658 4.4 64.9 1.0 O3' A:G668 4.4 58.1 1.0 C3' A:G668 4.5 58.3 1.0 O4 A:U671 4.5 56.0 1.0 OP2 A:U671 4.5 57.2 1.0 C4' A:G668 4.6 58.4 1.0 C5' A:A669 4.6 59.3 1.0 C5' A:G668 4.7 58.7 1.0 C4 A:U671 4.8 56.2 1.0 OP1 A:G668 4.8 59.4 1.0

Magnesium binding site 9 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3209 b:66.8 occ:1.00 OP1 A:U2243 2.7 60.9 1.0 OP1 A:A2285 3.4 69.2 1.0 OP2 A:A2286 3.7 77.1 1.0 P A:U2243 3.9 60.7 1.0 OP1 A:A2286 4.2 76.7 1.0 O5' A:U2243 4.4 60.5 1.0 OP2 A:U2243 4.5 60.5 1.0 P A:A2286 4.5 76.9 1.0 OP2 A:U2244 4.7 59.6 1.0 P A:A2285 4.8 69.3 1.0 C5' A:U2243 4.8 60.5 1.0 C5' A:A2285 4.9 71.6 1.0 O E:GLY72 5.0 95.8 1.0

Magnesium binding site 10 out of 146 in the Large Subunit of Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Large Subunit of Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3210 b:69.4 occ:1.00 O3' A:A673 2.7 56.2 1.0 OP1 A:G674 3.1 57.3 1.0 OP2 A:C675 3.2 57.4 1.0 P A:G674 3.4 57.1 1.0 O2' A:A673 3.4 55.4 1.0 O5' A:G674 3.7 56.7 1.0 C3' A:A673 3.8 55.4 1.0 C5 A:C675 3.9 55.0 1.0 C2' A:A673 4.1 55.2 1.0 C4' A:A673 4.4 55.1 1.0 C6 A:C675 4.6 55.2 1.0 P A:C675 4.6 57.3 1.0 OP2 A:G674 4.8 57.0 1.0 C5' A:G674 4.9 56.6 1.0 N4 A:C675 4.9 54.8 1.0 C4 A:C675 4.9 54.7 1.0 C3' A:G674 4.9 56.6 1.0

Z.Li, X.Ge, Y.Zhang, L.Zheng, S.Sanyal, N.Gao. Cryo-Em Structure of Mycobacterium Smegmatis Ribosome Reveals Two Unidentified Ribosomal Proteins Close to the Functional Centers. Protein Cell V. 9 384 2018.
ISSN: ESSN 1674-8018
PubMed: 28875450
DOI: 10.1007/S13238-017-0456-9