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Chlorine in PDB 5l6h: UBA1 in Complex with Ub-ABPA3 Covalent Adduct

Enzymatic activity of UBA1 in Complex with Ub-ABPA3 Covalent Adduct

All present enzymatic activity of UBA1 in Complex with Ub-ABPA3 Covalent Adduct:
6.2.1.45;

Protein crystallography data

The structure of UBA1 in Complex with Ub-ABPA3 Covalent Adduct, PDB code: 5l6h was solved by M.Misra, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.048, 194.098, 230.172, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.8

Other elements in 5l6h:

The structure of UBA1 in Complex with Ub-ABPA3 Covalent Adduct also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct (pdb code 5l6h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct, PDB code: 5l6h:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5l6h

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Chlorine binding site 1 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1102

b:60.8
occ:1.00
 OG1 A:THR571 3.1 30.5 1.0
N A:THR571 3.5 31.4 1.0
CE A:LYS572 3.7 51.9 1.0
O A:HOH1349 4.0 41.9 1.0
CB A:THR571 4.2 33.6 1.0
O A:LEU569 4.2 30.0 1.0
CA A:GLY570 4.2 31.9 1.0
CG2 A:THR571 4.3 35.2 1.0
C A:GLY570 4.4 33.3 1.0
CA A:THR571 4.4 32.8 1.0
NZ A:LYS572 4.5 57.2 1.0
CG A:LYS572 4.6 40.7 1.0
N A:LYS572 4.7 34.4 1.0
O A:THR177 4.7 42.6 1.0
CD A:LYS572 4.8 45.9 1.0
CG1 A:VAL25 4.8 34.8 1.0
OE2 A:GLU179 4.9 51.1 1.0
OD1 A:ASN900 5.0 34.4 1.0
C A:THR571 5.0 32.1 1.0

Chlorine binding site 2 out of 8 in 5l6h

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Chlorine binding site 2 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1103

b:77.8
occ:1.00
 NH2 B:ARG74 2.9 49.7 0.5
NH1 A:ARG861 3.2 78.3 1.0
CZ B:ARG74 3.5 45.2 0.5
NH1 B:ARG74 3.7 43.9 0.5
NE A:ARG861 4.0 66.0 1.0
CZ A:ARG861 4.1 73.5 1.0
O B:HOH217 4.2 41.3 1.0
NE B:ARG74 4.5 44.5 0.5
O A:HOH1501 4.9 53.9 1.0
O A:HOH1623 4.9 53.9 1.0

Chlorine binding site 3 out of 8 in 5l6h

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Chlorine binding site 3 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1104

b:68.9
occ:1.00
 NH1 A:ARG96 3.2 60.6 1.0
O A:HOH1354 3.6 53.9 1.0
CB A:ALA97 4.0 55.2 1.0
CZ A:ARG96 4.4 59.2 1.0
CD A:ARG96 4.5 56.5 1.0
NE A:ARG96 4.8 58.9 1.0
CA A:ALA97 5.0 54.7 1.0

Chlorine binding site 4 out of 8 in 5l6h

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Chlorine binding site 4 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1105

b:91.3
occ:1.00
 CG1 A:VAL117 3.7 61.4 1.0
O A:LEU114 3.8 69.8 1.0
OD1 A:ASP136 4.6 63.4 1.0
O A:ASP115 4.7 69.7 1.0
OH C:TYR723 4.8 68.6 1.0
CG A:ASP136 4.8 57.2 1.0
CG1 A:ILE140 4.9 46.9 1.0
C A:LEU114 4.9 67.4 1.0
CG A:LEU114 4.9 68.4 1.0
CB A:VAL117 4.9 61.0 1.0

Chlorine binding site 5 out of 8 in 5l6h

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Chlorine binding site 5 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1102

b:65.9
occ:1.00
 O C:HOH1442 2.1 74.4 1.0
OG1 C:THR571 3.1 36.5 1.0
O C:HOH1470 3.1 43.1 1.0
N C:THR571 3.4 35.1 1.0
CE C:LYS572 3.8 50.5 1.0
CA C:GLY570 4.0 36.2 1.0
O C:LEU569 4.0 36.1 1.0
CB C:THR571 4.0 35.7 1.0
C C:GLY570 4.2 34.4 1.0
CG2 C:THR571 4.2 36.1 1.0
CA C:THR571 4.3 34.8 1.0
O C:HOH1261 4.3 35.8 1.0
N C:LYS572 4.6 37.6 1.0
NZ C:LYS572 4.7 54.2 1.0
CG1 C:VAL25 4.7 33.4 1.0
CG C:LYS572 4.7 43.4 1.0
C C:THR571 4.8 37.1 1.0
C C:LEU569 4.8 36.9 1.0
CD C:LYS572 4.9 46.6 1.0
N C:GLY570 4.9 36.1 1.0
O C:THR177 5.0 40.1 1.0

Chlorine binding site 6 out of 8 in 5l6h

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Chlorine binding site 6 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1103

b:85.6
occ:1.00
 ND2 C:ASN514 3.6 55.4 1.0
CB C:ASN514 4.2 53.0 1.0
CG2 C:VAL467 4.2 45.6 1.0
CD1 C:TYR465 4.3 44.9 1.0
CG C:ASN514 4.4 57.1 1.0
CE1 C:TYR465 4.4 46.8 1.0
CG C:TYR465 4.4 44.5 1.0
CZ C:TYR465 4.6 48.2 1.0
CD2 C:TYR465 4.6 46.7 1.0
CE2 C:TYR465 4.6 48.3 1.0

Chlorine binding site 7 out of 8 in 5l6h

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Chlorine binding site 7 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1104

b:75.6
occ:1.00
 NH1 C:ARG861 2.6 76.6 1.0
NH2 D:ARG74 2.6 54.1 0.6
CZ D:ARG74 3.5 49.6 0.6
NH1 D:ARG74 3.9 46.2 0.6
CZ C:ARG861 4.0 74.4 1.0
NE D:ARG74 4.5 49.0 0.6
O D:HOH223 4.7 58.6 1.0
NE C:ARG861 4.8 70.7 1.0
CD C:ARG861 4.8 60.9 1.0
O C:HOH1413 4.8 41.9 1.0
NH2 C:ARG861 4.8 71.8 1.0

Chlorine binding site 8 out of 8 in 5l6h

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Chlorine binding site 8 out of 8 in the UBA1 in Complex with Ub-ABPA3 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of UBA1 in Complex with Ub-ABPA3 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1105

b:88.9
occ:1.00
 CA C:GLY960 4.0 54.6 1.0
CZ C:TYR959 4.2 59.6 1.0
CE1 C:TYR959 4.3 57.2 1.0
N C:GLY960 4.3 52.2 1.0
OH C:TYR959 4.4 60.2 1.0
CE2 C:TYR959 4.6 60.1 1.0
CD1 C:TYR959 4.8 56.5 1.0
O C:HOH1404 4.8 47.8 1.0
CD2 C:TYR959 5.0 56.8 1.0

Reference:

M.Misra, M.Kuhn, M.Lobel, H.An, A.V.Statsyuk, C.Sotriffer, H.Schindelin. Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Structure V. 25 1120 2017.
ISSN: ISSN 1878-4186
PubMed: 28578874
DOI: 10.1016/J.STR.2017.05.001
Page generated: Fri Jul 26 11:12:30 2024

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