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Calcium in PDB 4ii3: Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg

Enzymatic activity of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg

All present enzymatic activity of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg, PDB code: 4ii3 was solved by S.K.Olsen, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.500, 113.300, 126.600, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.3

Other elements in 4ii3:

The structure of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg (pdb code 4ii3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg, PDB code: 4ii3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4ii3

Go back to Calcium Binding Sites List in 4ii3
Calcium binding site 1 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:46.1
occ:1.00
 O A:HOH1202 2.8 31.2 1.0
OD2 A:ASP918 2.9 39.0 1.0
OD1 A:ASP918 3.2 42.4 1.0
CG A:ASP918 3.5 40.3 1.0
O A:GLU912 4.4 41.3 1.0
ND1 A:HIS574 4.7 39.7 1.0
CB A:ASP918 5.0 39.0 1.0

Calcium binding site 2 out of 10 in 4ii3

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Calcium binding site 2 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:60.2
occ:1.00
 O A:HOH1230 3.0 10.5 1.0
OE2 A:GLU205 3.4 56.4 1.0
O A:HOH1261 3.5 40.0 1.0
O A:GLY203 3.7 43.4 1.0
CD1 A:LEU181 4.0 47.3 1.0
CG A:GLU205 4.0 52.6 1.0
CD A:GLU205 4.2 54.6 1.0
OD2 A:ASP208 4.3 47.7 1.0
NE2 A:GLN256 4.4 60.3 1.0
CG B:LYS11 4.9 42.8 1.0
CG A:LEU181 4.9 46.6 1.0
CD B:LYS11 4.9 42.6 1.0
C A:GLY203 4.9 44.0 1.0
CB B:LYS11 4.9 44.8 1.0
N A:GLU205 4.9 45.7 1.0
CB A:GLU205 4.9 49.6 1.0

Calcium binding site 3 out of 10 in 4ii3

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Calcium binding site 3 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1106

b:60.9
occ:1.00
 O A:HOH1231 3.1 28.6 1.0
OE2 A:GLU665 3.3 86.9 1.0
O A:LYS659 4.1 82.8 1.0
CD A:GLU665 4.1 86.8 1.0
O A:THR657 4.2 80.2 1.0
CA A:GLU658 4.7 83.2 1.0
OE1 A:GLU665 4.7 87.0 1.0
C A:GLU658 4.8 83.2 1.0
N A:LYS659 4.8 83.2 1.0
O A:VAL656 4.8 77.2 1.0
C A:LYS659 4.9 82.5 1.0
C A:THR657 4.9 80.6 1.0
CG A:GLU665 5.0 85.9 1.0

Calcium binding site 4 out of 10 in 4ii3

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Calcium binding site 4 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1107

b:73.2
occ:1.00
 OE1 A:GLU938 3.0 45.6 1.0
OH A:TYR920 3.6 38.9 1.0
O A:GLU938 3.8 38.9 1.0
CG2 A:VAL908 4.2 35.6 1.0
CD A:GLU938 4.2 45.0 1.0
CD1 A:LEU940 4.2 37.3 1.0
CG1 A:VAL908 4.2 33.8 1.0
O A:VAL908 4.3 31.6 1.0
CB A:GLU938 4.3 41.7 1.0
ND2 A:ASN909 4.4 37.8 1.0
CA A:GLU938 4.6 40.6 1.0
C A:GLU938 4.6 39.6 1.0
CG A:LEU940 4.6 37.8 1.0
CD A:LYS911 4.7 56.8 1.0
CG A:GLU938 4.7 43.4 1.0
CZ A:TYR920 4.7 39.0 1.0
CB A:VAL908 4.8 33.6 1.0
CE1 A:TYR920 4.8 40.0 1.0
CB A:ASN909 4.9 34.1 1.0

Calcium binding site 5 out of 10 in 4ii3

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Calcium binding site 5 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1104

b:57.3
occ:1.00
 OG1 A:THR261 2.8 68.4 1.0
OD2 C:ASP996 2.9 50.6 1.0
O C:HOH1240 2.9 20.4 1.0
OD1 C:ASP996 3.3 51.4 1.0
CG C:ASP996 3.4 49.9 1.0
O C:GLY1000 3.7 45.6 1.0
O A:LYS262 3.8 64.0 1.0
CB A:THR261 4.1 66.7 1.0
CG2 A:THR261 4.3 67.4 1.0
CB C:ASP996 4.7 47.6 1.0
C A:LYS262 4.8 64.5 1.0
C C:GLY1000 4.9 45.7 1.0

Calcium binding site 6 out of 10 in 4ii3

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Calcium binding site 6 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1105

b:56.5
occ:1.00
 O C:HOH1242 2.9 10.3 1.0
O C:HOH1241 3.0 49.8 1.0
OD2 C:ASP918 3.1 48.5 1.0
OD1 C:ASP918 3.5 49.1 1.0
CG C:ASP918 3.7 47.0 1.0
ND1 C:HIS574 4.3 41.7 1.0
O C:GLU912 4.5 45.8 1.0
CE1 C:HIS574 4.8 40.1 1.0

Calcium binding site 7 out of 10 in 4ii3

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Calcium binding site 7 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1106

b:81.1
occ:1.00
 OD1 C:ASP611 3.3 68.5 1.0
OD2 C:ASP611 3.4 65.8 1.0
NE2 C:GLN619 3.6 78.9 1.0
CG C:ASP611 3.8 66.5 1.0
OE1 C:GLN619 3.9 79.8 1.0
CD C:GLN619 4.2 78.8 1.0

Calcium binding site 8 out of 10 in 4ii3

Go back to Calcium Binding Sites List in 4ii3
Calcium binding site 8 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1107

b:53.0
occ:1.00
 OE1 C:GLU938 3.2 49.1 1.0
O C:GLU938 3.5 38.6 1.0
OH C:TYR920 3.9 43.9 1.0
ND2 C:ASN909 4.0 35.7 1.0
CG2 C:VAL908 4.1 32.5 1.0
O C:VAL908 4.1 37.8 1.0
CB C:GLU938 4.2 42.6 1.0
CD1 C:LEU940 4.2 37.7 1.0
CG1 C:VAL908 4.2 37.4 1.0
CD C:GLU938 4.3 48.0 1.0
C C:GLU938 4.4 39.8 1.0
CA C:GLU938 4.5 41.1 1.0
CG C:LEU940 4.6 37.6 1.0
CB C:ASN909 4.6 33.7 1.0
CD C:LYS911 4.7 49.9 1.0
CG C:GLU938 4.7 45.1 1.0
CB C:VAL908 4.8 35.6 1.0
CG C:ASN909 4.8 34.2 1.0
C C:VAL908 4.8 36.9 1.0
CD2 C:LEU940 4.9 37.4 1.0
CB C:LYS911 5.0 44.5 1.0

Calcium binding site 9 out of 10 in 4ii3

Go back to Calcium Binding Sites List in 4ii3
Calcium binding site 9 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1108

b:46.0
occ:1.00
 O C:HOH1211 3.2 22.8 1.0
CE1 C:TYR920 3.7 44.8 1.0
NZ C:LYS911 4.0 54.2 1.0
CD1 C:TYR920 4.0 44.0 1.0
O C:ARG919 4.3 43.7 1.0
CZ C:TYR920 4.4 44.7 1.0
CB C:ASP918 4.7 44.1 1.0
O C:HOH1247 4.7 28.1 1.0
OE1 C:GLU938 4.7 49.1 1.0
CG C:ASP918 4.8 47.0 1.0
OH C:TYR920 4.8 43.9 1.0
CE C:LYS911 4.8 51.0 1.0
OD1 C:ASP918 4.8 49.1 1.0
C C:ARG919 4.9 42.5 1.0
CG C:TYR920 5.0 43.5 1.0

Calcium binding site 10 out of 10 in 4ii3

Go back to Calcium Binding Sites List in 4ii3
Calcium binding site 10 out of 10 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1109

b:72.1
occ:1.00
 O C:THR657 2.9 92.5 1.0
C C:THR657 3.9 92.5 1.0
OE2 C:GLU658 4.1 92.7 1.0
O C:VAL656 4.3 91.0 1.0
CA C:THR657 4.7 91.9 1.0
N C:GLU658 4.7 92.9 1.0
CA C:GLU658 4.8 93.5 1.0
CD C:GLU658 5.0 93.3 1.0

Reference:

S.K.Olsen, C.D.Lima. Structure of A Ubiquitin E1-E2 Complex: Insights to E1-E2 Thioester Transfer. Mol.Cell V. 49 884 2013.
ISSN: ISSN 1097-2765
PubMed: 23416107
DOI: 10.1016/J.MOLCEL.2013.01.013
Page generated: Sun Jul 14 08:09:28 2024

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