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Sodium in PDB 6lvs: USP14 Catalytic Domain Mutant C114S

Enzymatic activity of USP14 Catalytic Domain Mutant C114S

All present enzymatic activity of USP14 Catalytic Domain Mutant C114S:
3.4.19.12;

Protein crystallography data

The structure of USP14 Catalytic Domain Mutant C114S, PDB code: 6lvs was solved by H.C.Lin, T.H.Lin, C.Y.Chou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.49 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.506, 160.422, 90.311, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 27.7

Sodium Binding Sites:

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 - 41;

Binding sites:

The binding sites of Sodium atom in the USP14 Catalytic Domain Mutant C114S (pdb code 6lvs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 41 binding sites of Sodium where determined in the USP14 Catalytic Domain Mutant C114S, PDB code: 6lvs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 41 in 6lvs

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Sodium binding site 1 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:36.8
occ:1.00
 O A:TYR323 2.7 24.6 1.0
O A:PHE247 2.8 32.7 1.0
N A:THR325 3.0 28.8 1.0
O A:LEU273 3.1 34.5 1.0
OG1 A:THR325 3.5 31.9 1.0
CA A:LEU324 3.6 28.6 1.0
C A:TYR323 3.6 26.9 1.0
O1 A:FMT511 3.7 69.5 1.0
CB A:THR325 3.7 29.2 1.0
C A:PHE247 3.7 32.6 1.0
CA A:PHE247 3.7 31.9 1.0
C A:LEU324 3.7 28.4 1.0
CB A:PHE247 3.8 31.4 1.0
CD1 A:PHE247 3.9 29.6 1.0
C A:LEU273 3.9 34.0 1.0
CA A:THR325 3.9 29.4 1.0
N A:LEU324 4.0 27.4 1.0
CG A:PRO321 4.1 23.2 1.0
CG A:PHE247 4.3 30.6 1.0
C A:FMT511 4.4 76.6 1.0
N A:GLN274 4.4 35.2 1.0
O A:THR325 4.5 29.8 1.0
CA A:GLN274 4.6 36.4 1.0
CD1 A:LEU324 4.7 29.2 1.0
CB A:PRO321 4.7 23.7 1.0
C A:THR325 4.8 29.9 1.0
CG2 A:VAL249 4.8 37.2 1.0
CA A:LEU273 4.8 34.6 1.0
O A:LEU324 4.9 28.7 1.0
CB A:LEU324 4.9 29.4 1.0
N A:GLY248 5.0 33.5 1.0
CA A:TYR323 5.0 28.1 1.0
CE1 A:PHE247 5.0 30.3 1.0

Sodium binding site 2 out of 41 in 6lvs

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Sodium binding site 2 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:46.4
occ:1.00
 NH1 A:ARG330 2.7 37.5 1.0
O A:SER467 3.0 41.4 1.0
O A:VAL347 3.1 39.2 1.0
CB A:ALA475 3.6 28.0 1.0
CA A:SER467 3.7 38.6 1.0
SD A:MET328 3.7 43.6 1.0
C A:SER467 3.7 40.4 1.0
O A:ALA475 3.8 27.1 1.0
CD2 A:PHE349 3.9 30.2 1.0
CZ A:ARG330 4.0 37.4 1.0
N A:ALA475 4.1 28.5 1.0
O A:LEU466 4.1 33.1 1.0
CG A:MET328 4.1 39.2 1.0
CE2 A:PHE349 4.2 30.4 1.0
CA A:ALA475 4.2 28.6 1.0
C A:VAL347 4.2 38.1 1.0
CG2 A:ILE474 4.3 31.2 1.0
C A:ALA475 4.4 28.0 1.0
CB A:VAL347 4.4 38.6 1.0
CB A:SER467 4.4 38.5 1.0
NE A:ARG330 4.5 36.3 1.0
N A:VAL347 4.6 36.5 1.0
CA A:VAL347 4.6 37.7 1.0
N A:SER467 4.7 35.5 1.0
C A:LEU466 4.8 34.2 1.0
NH2 A:ARG330 5.0 38.0 1.0
N A:GLY468 5.0 44.7 1.0

Sodium binding site 3 out of 41 in 6lvs

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Sodium binding site 3 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:49.8
occ:1.00
 OD1 A:ASN117 2.5 22.9 1.0
OG1 A:THR113 2.5 31.9 1.0
O A:THR108 2.8 28.3 1.0
ND2 A:ASN117 3.1 23.1 1.0
CG A:ASN117 3.1 24.0 1.0
CB A:THR113 3.3 30.7 1.0
N A:LEU110 3.7 29.8 1.0
CG A:PRO172 3.7 31.2 1.0
O A:THR113 3.8 32.2 1.0
CE A:MET116 3.8 31.3 1.0
CD A:PRO172 3.9 32.6 1.0
C A:THR108 3.9 28.4 1.0
CG A:LEU110 4.0 29.1 1.0
CA A:ASN109 4.0 28.1 1.0
CD1 A:LEU110 4.1 29.9 1.0
CG2 A:THR113 4.1 29.9 1.0
CB A:LEU110 4.2 29.4 1.0
C A:ASN109 4.3 28.9 1.0
C A:THR113 4.3 30.9 1.0
N A:ASN109 4.4 28.2 1.0
CA A:THR113 4.4 31.0 1.0
CB A:ASN117 4.6 24.6 1.0
CA A:LEU110 4.6 30.1 1.0
N A:ASN117 5.0 26.4 1.0

Sodium binding site 4 out of 41 in 6lvs

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Sodium binding site 4 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:53.6
occ:1.00
 O1 A:FMT512 2.4 61.7 1.0
O A:TYR436 2.9 22.3 1.0
OD1 A:ASP452 2.9 40.7 1.0
C A:FMT512 3.4 63.4 1.0
N A:ASP452 3.4 36.9 1.0
O A:SER114 3.6 29.1 1.0
O A:PHE450 3.7 33.5 1.0
CB A:SER114 3.7 29.7 1.0
C A:TYR436 3.8 23.2 1.0
CG A:ASP452 3.8 38.6 1.0
CA A:ASP452 3.9 37.3 1.0
CB A:ASN117 3.9 24.6 1.0
CA A:SER114 4.0 29.6 1.0
CA A:VAL437 4.0 24.9 1.0
N A:ALA118 4.0 24.3 1.0
O2 A:FMT512 4.0 63.5 1.0
N A:VAL437 4.2 23.7 1.0
C A:SER114 4.2 29.1 1.0
CB A:ALA118 4.3 24.6 1.0
C A:ASP451 4.3 36.7 1.0
NE2 A:HIS435 4.3 24.0 1.0
CA A:ALA118 4.4 24.5 1.0
CE1 A:HIS435 4.4 24.6 1.0
CB A:ASP452 4.5 37.0 1.0
CA A:ASP451 4.6 35.5 1.0
C A:ASN117 4.6 25.0 1.0
OD2 A:ASP452 4.6 39.0 1.0
N A:SER438 4.7 26.1 1.0
C A:PHE450 4.7 32.9 1.0
C A:VAL437 4.7 26.2 1.0
OG A:SER114 4.8 29.8 1.0
CA A:ASN117 4.9 25.3 1.0
CG2 A:VAL437 4.9 24.3 1.0
CA A:TYR436 4.9 23.2 1.0
ND2 A:ASN117 4.9 23.1 1.0

Sodium binding site 5 out of 41 in 6lvs

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Sodium binding site 5 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:95.8
occ:1.00
 O A:SER433 2.1 36.3 1.0
NE2 A:HIS426 2.8 23.3 1.0
O A:SER430 3.1 30.9 1.0
C A:SER433 3.1 30.9 1.0
O A:SER431 3.1 30.7 1.0
CD2 A:HIS426 3.3 23.5 1.0
C A:SER431 3.3 30.2 1.0
N A:SER433 3.7 29.0 1.0
CE1 A:TYR436 3.7 21.8 1.0
NE2 A:GLN197 3.7 39.8 1.0
OH A:TYR436 3.7 21.7 1.0
CA A:SER431 3.8 30.3 1.0
CB A:GLN197 3.9 37.6 1.0
N A:SER432 3.9 28.3 1.0
CD A:GLN197 3.9 41.3 1.0
CG A:GLN197 3.9 41.3 1.0
CE1 A:HIS426 3.9 23.2 1.0
CZ A:TYR436 3.9 21.9 1.0
C A:GLY434 4.0 25.1 1.0
N A:GLY434 4.0 27.2 1.0
CA A:SER433 4.0 30.5 1.0
CA A:GLY434 4.0 25.8 1.0
C A:SER430 4.1 30.5 1.0
C A:SER432 4.2 29.1 1.0
N A:HIS435 4.2 24.4 1.0
O A:GLY434 4.3 24.3 1.0
CA A:SER432 4.4 28.0 1.0
N A:SER431 4.4 30.5 1.0
CD1 A:TYR436 4.5 21.9 1.0
CG A:HIS426 4.6 23.9 1.0
O A:GLN198 4.6 27.5 1.0
OE1 A:GLN197 4.7 38.2 1.0
CZ A:PHE331 4.8 32.9 1.0
ND1 A:HIS426 4.9 23.5 1.0
CB A:SER433 4.9 31.2 1.0
CE2 A:TYR436 5.0 22.1 1.0

Sodium binding site 6 out of 41 in 6lvs

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Sodium binding site 6 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:54.9
occ:1.00
 OE2 A:GLU202 2.8 45.3 1.0
OE1 A:GLN185 2.8 45.3 1.0
OE1 A:GLN206 2.9 37.7 1.0
CG A:GLU202 3.4 39.2 1.0
CD A:GLU202 3.5 44.2 1.0
CD A:GLN206 3.5 38.0 1.0
CG A:GLN206 3.7 37.8 1.0
CD A:GLN185 3.9 43.6 1.0
CG A:GLN185 4.6 42.1 1.0
OE1 A:GLU202 4.6 48.0 1.0
NE2 A:GLN206 4.7 38.2 1.0
CB A:GLU202 4.9 35.8 1.0
O A:GLU202 5.0 33.2 1.0

Sodium binding site 7 out of 41 in 6lvs

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Sodium binding site 7 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:78.4
occ:1.00
 O A:GLY434 2.9 24.3 1.0
CG A:GLN197 3.2 41.3 1.0
OD1 A:ASN112 3.3 41.1 1.0
C A:SER433 3.6 30.9 1.0
O A:SER433 3.7 36.3 1.0
N A:GLY434 3.7 27.2 1.0
CB A:GLN197 3.9 37.6 1.0
CG A:ASN112 3.9 38.8 1.0
C A:GLY434 4.0 25.1 1.0
CA A:SER433 4.2 30.5 1.0
ND2 A:ASN112 4.3 39.2 1.0
C3 A:GOL502 4.3 61.2 1.0
O A:SER432 4.4 30.1 1.0
CA A:GLY434 4.4 25.8 1.0
CD A:GLN197 4.4 41.3 1.0
O A:HOH601 4.5 41.6 1.0
NE2 A:GLN197 4.6 39.8 1.0
CB A:ASN112 4.8 37.1 1.0
C A:SER432 4.8 29.1 1.0
N A:SER433 4.9 29.0 1.0
N A:GLN197 4.9 36.6 1.0
CA A:GLN197 4.9 36.1 1.0

Sodium binding site 8 out of 41 in 6lvs

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Sodium binding site 8 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:52.5
occ:1.00
 OG1 B:THR113 2.6 31.9 1.0
OD1 B:ASN117 2.8 22.7 1.0
O B:THR108 2.9 25.3 1.0
ND2 B:ASN117 3.1 24.4 1.0
CG B:ASN117 3.2 23.9 1.0
CB B:THR113 3.4 30.9 1.0
N B:LEU110 3.7 29.5 1.0
CG B:PRO172 3.7 33.0 1.0
CG B:LEU110 3.8 28.7 1.0
CD1 B:LEU110 3.8 29.3 1.0
CD B:PRO172 3.9 33.9 1.0
O B:THR113 3.9 32.2 1.0
CE B:MET116 4.0 28.2 1.0
C B:THR108 4.0 26.8 1.0
CB B:LEU110 4.0 28.9 1.0
CA B:ASN109 4.1 27.4 1.0
CG2 B:THR113 4.3 29.9 1.0
C B:ASN109 4.3 28.5 1.0
C B:THR113 4.5 30.5 1.0
N B:ASN109 4.5 27.7 1.0
CA B:LEU110 4.5 29.8 1.0
CA B:THR113 4.5 30.9 1.0
CB B:ASN117 4.7 25.0 1.0

Sodium binding site 9 out of 41 in 6lvs

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Sodium binding site 9 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:55.2
occ:1.00
 NH1 B:ARG330 2.7 37.2 1.0
O B:VAL347 3.0 34.2 1.0
O B:SER467 3.1 38.5 1.0
CB B:ALA475 3.7 30.4 1.0
CA B:SER467 3.7 36.8 1.0
C B:SER467 3.7 38.1 1.0
O B:ALA475 3.8 27.7 1.0
SD B:MET328 3.8 44.8 1.0
CD2 B:PHE349 3.9 29.2 1.0
CZ B:ARG330 3.9 36.2 1.0
CG B:MET328 4.1 38.4 1.0
C B:VAL347 4.1 34.4 1.0
CB B:VAL347 4.2 33.9 1.0
O B:LEU466 4.2 33.7 1.0
CE2 B:PHE349 4.3 29.7 1.0
N B:ALA475 4.3 31.3 1.0
CA B:ALA475 4.3 30.9 1.0
N B:VAL347 4.4 33.5 1.0
C B:ALA475 4.5 30.1 1.0
CA B:VAL347 4.5 34.2 1.0
CB B:SER467 4.5 37.4 1.0
CG2 B:ILE474 4.5 32.9 1.0
NE B:ARG330 4.5 34.9 1.0
N B:SER467 4.7 35.3 1.0
C B:LEU466 4.9 33.9 1.0
CG1 B:VAL347 4.9 34.0 1.0
NH2 B:ARG330 4.9 36.6 1.0
N B:GLY468 5.0 41.8 1.0

Sodium binding site 10 out of 41 in 6lvs

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Sodium binding site 10 out of 41 in the USP14 Catalytic Domain Mutant C114S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of USP14 Catalytic Domain Mutant C114S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:91.5
occ:1.00
 O1 B:FMT515 1.7 72.3 1.0
O2 B:FMT512 1.9 47.6 1.0
OG B:SER114 2.1 27.1 1.0
O B:HOH606 2.6 32.8 1.0
C B:FMT512 2.6 52.7 1.0
C B:FMT515 2.8 80.2 1.0
CB B:SER114 3.3 28.1 1.0
O1 B:FMT512 3.6 57.6 1.0
CA B:HIS435 3.7 24.9 1.0
N B:SER114 3.8 29.7 1.0
O2 B:FMT515 3.8 84.1 1.0
O B:GLY434 3.9 26.9 1.0
O B:ASN112 4.0 33.7 1.0
CA B:SER114 4.0 29.0 1.0
C B:ASN112 4.0 33.2 1.0
NE2 B:GLN197 4.0 51.4 1.0
CD1 B:TYR436 4.1 23.5 1.0
CA B:ASN112 4.1 35.3 1.0
N B:TYR436 4.2 24.4 1.0
CD B:GLN197 4.2 48.9 1.0
ND1 B:HIS435 4.3 24.8 1.0
N B:TYR115 4.3 28.6 1.0
CB B:GLN197 4.4 41.6 1.0
N B:HIS435 4.4 26.0 1.0
CB B:HIS435 4.4 24.7 1.0
C B:GLY434 4.5 27.2 1.0
C B:HIS435 4.5 24.5 1.0
C B:SER114 4.5 29.7 1.0
N B:THR113 4.6 31.3 1.0
CE1 B:TYR436 4.6 23.2 1.0
OE1 B:GLN197 4.6 49.4 1.0
CB B:ASN112 4.6 37.1 1.0
CG B:GLN197 4.6 45.9 1.0
CG B:HIS435 4.7 24.6 1.0
C B:THR113 4.9 30.5 1.0
ND2 B:ASN109 4.9 26.7 1.0
CA B:GLN197 5.0 39.3 1.0

Reference:

H.C.Lin, H.C.Lin, T.H.Lin, C.Y.Chou. N/A N/A.
Page generated: Tue Dec 15 12:34:01 2020

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