Magnesium in PDB 6h78: E1 Enzyme For Ubiquitin Like Protein Activation.

Protein crystallography data

The structure of E1 Enzyme For Ubiquitin Like Protein Activation., PDB code: 6h78 was solved by N.Soudah, P.Padala, F.Hassouna, B.Mashahreh, A.A.Lebedev, M.N.Isupov, E.Cohen-Kfir, R.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.98 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 143.860, 151.933, 153.543, 90.00, 93.07, 90.00
R / Rfree (%) 19 / 24.2

Other elements in 6h78:

The structure of E1 Enzyme For Ubiquitin Like Protein Activation. also contains other interesting chemical elements:

Zinc (Zn) 16 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the E1 Enzyme For Ubiquitin Like Protein Activation. (pdb code 6h78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the E1 Enzyme For Ubiquitin Like Protein Activation., PDB code: 6h78:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in 6h78

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Magnesium binding site 1 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:90.1
occ:1.00
 O1B A:ATP401 2.1 48.5 1.0
OD2 A:ASP183 2.1 73.7 1.0
O1G A:ATP401 2.1 79.4 1.0
O A:HOH502 2.1 97.1 1.0
O1A A:ATP401 2.1 69.1 1.0
PB A:ATP401 3.0 39.8 1.0
O3B A:ATP401 3.0 54.4 1.0
PG A:ATP401 3.2 52.7 1.0
PA A:ATP401 3.2 42.5 1.0
CG A:ASP183 3.2 54.5 1.0
O5' A:ATP401 3.4 50.5 1.0
O3A A:ATP401 3.5 63.5 1.0
O A:HOH569 3.5 59.1 1.0
O A:HOH572 3.8 26.3 1.0
CB A:ASP183 3.8 33.7 1.0
O A:HOH520 3.9 52.4 1.0
O3G A:ATP401 4.2 59.0 1.0
O2G A:ATP401 4.3 50.6 1.0
OD1 A:ASP183 4.3 50.4 1.0
O2B A:ATP401 4.4 67.3 1.0
O2A A:ATP401 4.6 47.1 1.0
O A:HOH526 4.6 74.5 1.0
NH2 A:ARG115 4.7 41.9 1.0
C5' A:ATP401 4.8 45.1 1.0
O A:HOH566 4.9 56.4 1.0

Magnesium binding site 2 out of 32 in 6h78

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Magnesium binding site 2 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:61.3
occ:1.00
 O A:HOH526 2.1 74.5 1.0
O A:HOH503 2.1 44.4 1.0
OD2 A:ASP106 2.1 0.6 1.0
O A:HOH501 2.1 53.8 1.0
O A:HOH567 2.1 87.9 1.0
O2B A:ATP401 2.1 67.3 1.0
CG A:ASP106 3.4 79.5 1.0
PB A:ATP401 3.5 39.8 1.0
NZ A:LYS127 3.8 42.5 1.0
O3G A:ATP401 3.8 59.0 1.0
O1B A:ATP401 4.0 48.5 1.0
OD1 A:ASP106 4.1 70.5 1.0
O3B A:ATP401 4.1 54.4 1.0
OD1 A:ASN112 4.3 36.2 1.0
CB A:ASP106 4.5 54.4 1.0
ND2 A:ASN112 4.5 46.8 1.0
O A:LYS107 4.5 33.2 1.0
O A:HOH578 4.6 43.3 1.0
PG A:ATP401 4.6 52.7 1.0
CE A:LYS127 4.7 55.2 1.0
O3A A:ATP401 4.8 63.5 1.0
O A:HOH520 4.8 52.4 1.0
CG A:ASN112 4.8 45.8 1.0

Magnesium binding site 3 out of 32 in 6h78

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Magnesium binding site 3 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:0.9
occ:1.00
 O1B B:ATP401 2.1 53.8 1.0
OD2 B:ASP183 2.1 70.2 1.0
O2G B:ATP401 2.1 64.7 1.0
O2A B:ATP401 2.1 55.2 1.0
PB B:ATP401 2.9 42.4 1.0
O3B B:ATP401 3.0 51.6 1.0
PA B:ATP401 3.2 43.0 1.0
CG B:ASP183 3.2 46.3 1.0
PG B:ATP401 3.2 49.1 1.0
O3A B:ATP401 3.4 59.8 1.0
O5' B:ATP401 3.4 43.8 1.0
CB B:ASP183 3.8 40.2 1.0
O B:HOH544 3.9 49.9 1.0
O B:HOH537 4.0 42.4 1.0
O3G B:ATP401 4.2 77.4 1.0
OD1 B:ASP183 4.2 36.0 1.0
O2B B:ATP401 4.3 78.7 1.0
O1G B:ATP401 4.3 47.1 1.0
O B:HOH527 4.5 49.5 1.0
O1A B:ATP401 4.6 41.7 1.0
O B:HOH519 4.7 40.8 1.0
O B:HOH524 4.8 46.8 1.0
C5' B:ATP401 4.8 34.5 1.0
NH2 B:ARG115 4.8 31.4 1.0
C3' B:ATP401 5.0 44.2 1.0

Magnesium binding site 4 out of 32 in 6h78

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Magnesium binding site 4 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:88.3
occ:1.00
 O B:HOH504 2.1 54.4 1.0
O2B B:ATP401 2.1 78.7 1.0
O A:HOH539 2.1 43.6 1.0
OD2 B:ASP106 2.1 0.9 1.0
CG B:ASP106 3.4 62.1 1.0
O3G B:ATP401 3.4 77.4 1.0
PB B:ATP401 3.5 42.4 1.0
O A:HOH577 3.8 63.8 1.0
O1B B:ATP401 3.9 53.8 1.0
NZ B:LYS127 4.0 48.6 1.0
OD1 B:ASP106 4.1 71.0 1.0
O3B B:ATP401 4.2 51.6 1.0
OD1 B:ASN112 4.2 55.6 1.0
ND2 B:ASN112 4.3 66.2 1.0
PG B:ATP401 4.5 49.1 1.0
CB B:ASP106 4.5 60.8 1.0
O B:LYS107 4.7 45.3 1.0
CG B:ASN112 4.7 68.3 1.0
O3A B:ATP401 4.8 59.8 1.0
OD1 A:ASP49 4.9 67.8 1.0

Magnesium binding site 5 out of 32 in 6h78

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Magnesium binding site 5 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:70.0
occ:1.00
 O3G C:ATP401 2.1 68.0 1.0
O1B C:ATP401 2.1 58.8 1.0
OD2 C:ASP183 2.1 0.3 1.0
O2A C:ATP401 2.1 56.9 1.0
PB C:ATP401 3.1 40.2 1.0
CG C:ASP183 3.2 69.3 1.0
O C:HOH534 3.3 40.0 1.0
O3B C:ATP401 3.3 43.0 1.0
PG C:ATP401 3.3 41.9 1.0
PA C:ATP401 3.4 42.2 1.0
O C:HOH511 3.6 70.1 1.0
O3A C:ATP401 3.6 55.7 1.0
CB C:ASP183 3.7 64.1 1.0
OD1 C:ASP183 4.2 72.1 1.0
O1G C:ATP401 4.3 58.3 1.0
O2G C:ATP401 4.4 45.8 1.0
O5' C:ATP401 4.4 54.9 1.0
O2B C:ATP401 4.5 47.1 1.0
O1A C:ATP401 4.5 58.8 1.0
C5' C:ATP401 4.6 37.9 1.0
O C:HOH523 4.9 42.4 1.0
NH2 C:ARG115 5.0 34.0 1.0

Magnesium binding site 6 out of 32 in 6h78

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Magnesium binding site 6 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:85.7
occ:1.00
 O C:HOH501 2.1 68.2 1.0
O C:HOH517 2.1 72.0 1.0
O2B C:ATP401 2.1 47.1 1.0
OD2 C:ASP106 2.1 0.6 1.0
CG C:ASP106 3.3 65.8 1.0
PB C:ATP401 3.4 40.2 1.0
O C:HOH523 3.5 42.4 1.0
O2G C:ATP401 3.6 45.8 1.0
NZ C:LYS127 3.6 36.5 1.0
O3B C:ATP401 3.8 43.0 1.0
OD1 C:ASP106 4.0 68.8 1.0
OD1 C:ASN112 4.1 49.6 1.0
O C:HOH511 4.1 70.1 1.0
O1B C:ATP401 4.2 58.8 1.0
ND2 C:ASN112 4.3 95.9 1.0
CB C:ASP106 4.4 54.8 1.0
PG C:ATP401 4.4 41.9 1.0
CE C:LYS127 4.6 36.8 1.0
O C:LYS107 4.6 43.6 1.0
O3A C:ATP401 4.6 55.7 1.0
CG C:ASN112 4.6 48.9 1.0

Magnesium binding site 7 out of 32 in 6h78

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Magnesium binding site 7 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:0.7
occ:1.00
 O1B D:ATP401 2.1 54.8 1.0
O1G D:ATP401 2.1 58.0 1.0
OD2 D:ASP183 2.1 75.8 1.0
O D:HOH503 2.1 81.5 1.0
O1A D:ATP401 2.1 53.6 1.0
PB D:ATP401 3.0 37.1 1.0
CG D:ASP183 3.1 64.5 1.0
O3B D:ATP401 3.2 47.0 1.0
PG D:ATP401 3.2 43.3 1.0
PA D:ATP401 3.3 38.7 1.0
O3A D:ATP401 3.5 47.9 1.0
O D:HOH543 3.6 55.4 1.0
CB D:ASP183 3.6 38.2 1.0
O D:HOH544 3.7 29.5 1.0
O D:HOH502 3.9 54.5 1.0
O D:HOH515 4.0 43.3 1.0
O3G D:ATP401 4.2 44.3 1.0
OD1 D:ASP183 4.2 58.4 1.0
O5' D:ATP401 4.2 67.0 1.0
C5' D:ATP401 4.3 36.9 1.0
O2G D:ATP401 4.3 51.4 1.0
O2B D:ATP401 4.4 73.3 1.0
O2A D:ATP401 4.5 72.0 1.0
O2 D:EDO405 4.6 54.5 1.0
O D:HOH510 4.8 31.2 1.0
NH2 D:ARG115 4.8 26.7 1.0

Magnesium binding site 8 out of 32 in 6h78

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Magnesium binding site 8 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:78.3
occ:1.00
 O D:HOH511 2.1 65.3 1.0
O D:HOH537 2.1 71.7 1.0
O2B D:ATP401 2.2 73.3 1.0
OD2 D:ASP106 2.2 97.0 1.0
O D:HOH502 3.2 54.5 1.0
CG D:ASP106 3.4 53.2 1.0
PB D:ATP401 3.5 37.1 1.0
O3G D:ATP401 3.6 44.3 1.0
O D:HOH509 3.9 48.4 1.0
NZ D:LYS127 3.9 49.9 1.0
OD1 D:ASP106 3.9 53.6 1.0
O1B D:ATP401 4.1 54.8 1.0
O3B D:ATP401 4.1 47.0 1.0
OD1 D:ASN112 4.2 76.0 1.0
PG D:ATP401 4.5 43.3 1.0
ND2 D:ASN112 4.5 60.0 1.0
CB D:ASP106 4.6 54.7 1.0
O D:LYS107 4.8 31.9 1.0
O3A D:ATP401 4.8 47.9 1.0
CG D:ASN112 4.8 53.8 1.0
O D:HOH515 4.8 43.3 1.0
CE D:LYS127 5.0 55.6 1.0

Magnesium binding site 9 out of 32 in 6h78

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Magnesium binding site 9 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:74.1
occ:1.00
 OD2 E:ASP183 2.1 60.0 1.0
O1A E:ATP401 2.1 81.4 1.0
O2B E:ATP401 2.1 59.8 1.0
O3G E:ATP401 2.1 53.2 1.0
PB E:ATP401 3.1 43.0 1.0
CG E:ASP183 3.2 59.4 1.0
PG E:ATP401 3.3 42.8 1.0
O3B E:ATP401 3.3 38.6 1.0
PA E:ATP401 3.3 44.1 1.0
O3A E:ATP401 3.6 52.8 1.0
O E:HOH547 3.7 36.4 1.0
O5' E:ATP401 3.7 43.1 1.0
CB E:ASP183 3.7 43.9 1.0
O1G E:ATP401 4.2 47.6 1.0
OD1 E:ASP183 4.3 38.2 1.0
O2G E:ATP401 4.3 37.5 1.0
O1B E:ATP401 4.5 87.6 1.0
O2A E:ATP401 4.6 47.6 1.0
O E:HOH512 4.7 37.7 1.0
NH2 E:ARG115 4.9 26.0 1.0

Magnesium binding site 10 out of 32 in 6h78

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Magnesium binding site 10 out of 32 in the E1 Enzyme For Ubiquitin Like Protein Activation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E1 Enzyme For Ubiquitin Like Protein Activation. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:0.9
occ:1.00
 O E:HOH501 2.1 76.5 1.0
O E:HOH540 2.1 79.3 1.0
OD2 E:ASP106 2.1 0.1 1.0
O1B E:ATP401 2.1 87.6 1.0
CG E:ASP106 3.1 93.4 1.0
OD1 E:ASP106 3.4 0.5 1.0
PB E:ATP401 3.6 43.0 1.0
O1G E:ATP401 4.1 47.6 1.0
NZ E:LYS127 4.1 52.0 1.0
OD1 E:ASN112 4.1 57.1 1.0
O3B E:ATP401 4.1 38.6 1.0
O2B E:ATP401 4.3 59.8 1.0
O E:LYS107 4.4 41.6 1.0
CB E:ASP106 4.4 64.9 1.0
ND2 E:ASN112 4.5 64.5 1.0
CE E:LYS127 4.7 42.7 1.0
CG E:ASN112 4.7 48.8 1.0
O3A E:ATP401 4.8 52.8 1.0
PG E:ATP401 4.8 42.8 1.0

Reference:

N.Soudah, P.Padala, F.Hassouna, M.Kumar, B.Mashahreh, A.A.Lebedev, M.N.Isupov, E.Cohen-Kfir, R.Wiener. An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-Like Protein Activation. J.Mol.Biol. V. 431 463 2019.
ISSN: ESSN 1089-8638
PubMed: 30412706
DOI: 10.1016/J.JMB.2018.10.007
Page generated: Mon Dec 14 22:47:47 2020

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