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Arsenic in PDB 4hg3: Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate

Protein crystallography data

The structure of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate, PDB code: 4hg3 was solved by H.Liu, X.Qiu, M.Zhang, Y.Gao, L.Niu, M.Teng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.84 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.211, 125.653, 77.964, 90.00, 95.30, 90.00
R / Rfree (%) 19.7 / 22.7

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate (pdb code 4hg3). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 7 binding sites of Arsenic where determined in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate, PDB code: 4hg3:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7;

Arsenic binding site 1 out of 7 in 4hg3

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Arsenic binding site 1 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As409

b:49.1
occ:0.60
 AS A:CAC409 0.0 49.1 0.6
O1 A:CAC409 1.7 48.8 0.6
O2 A:CAC409 1.7 48.9 0.6
C2 A:CAC409 2.0 48.8 0.6
C1 A:CAC409 2.0 48.9 0.6
OE2 A:GLU124 3.9 14.3 1.0
NE2 B:HIS240 4.0 15.7 1.0
O A:HOH626 4.1 23.4 1.0
CD2 B:HIS240 4.5 15.4 1.0
CD2 A:LEU94 4.7 9.1 1.0
CD1 A:ILE121 4.8 8.7 1.0
CD1 A:LEU94 4.8 10.4 1.0

Arsenic binding site 2 out of 7 in 4hg3

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Arsenic binding site 2 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As410

b:24.2
occ:1.00
 AS A:CAC410 0.0 24.2 1.0
O1 A:CAC410 1.7 23.9 1.0
O2 A:CAC410 1.7 24.4 1.0
C2 A:CAC410 2.0 23.8 1.0
C1 A:CAC410 2.0 23.5 1.0
O A:HOH519 3.5 14.6 1.0
O A:HOH597 3.8 14.4 1.0
CD2 A:LEU50 4.1 8.7 1.0
NE2 A:HIS93 4.1 9.7 1.0
NH2 A:ARG250 4.2 24.9 1.0
NH1 A:ARG250 4.2 24.1 1.0
CZ A:ARG250 4.7 24.7 1.0
OE2 A:GLU143 4.7 11.0 1.0
ND2 A:ASN110 4.8 4.2 1.0
OE2 A:GLU45 5.0 7.2 1.0
CE1 A:HIS93 5.0 8.7 1.0

Arsenic binding site 3 out of 7 in 4hg3

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Arsenic binding site 3 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As407

b:54.6
occ:0.50
 AS B:CAC407 0.0 54.6 0.5
O2 B:CAC407 1.7 54.3 0.5
O1 B:CAC407 1.7 54.4 0.5
C1 B:CAC407 2.0 54.4 0.5
C2 B:CAC407 2.0 54.4 0.5
O B:HOH616 4.0 22.5 1.0
O B:HOH614 4.0 29.2 1.0
OE2 B:GLU124 4.3 16.9 1.0
O B:HOH599 4.5 24.9 1.0
CD2 B:LEU94 4.6 10.2 1.0
CD1 B:ILE121 5.0 9.0 1.0
CD1 B:LEU94 5.0 9.3 1.0

Arsenic binding site 4 out of 7 in 4hg3

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Arsenic binding site 4 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As408

b:18.7
occ:0.70
 AS B:CAC408 0.0 18.7 0.7
O1 B:CAC408 1.7 18.4 0.7
O2 B:CAC408 1.7 18.2 0.7
C1 B:CAC408 2.0 18.6 0.7
C2 B:CAC408 2.0 18.4 0.7
O B:HOH524 3.6 14.1 1.0
O B:HOH589 3.8 15.7 1.0
CD2 B:LEU50 4.2 8.4 1.0
NE2 B:HIS93 4.2 10.3 1.0
NH2 B:ARG250 4.2 24.9 1.0
NH1 B:ARG250 4.6 24.3 1.0
OE2 B:GLU143 4.7 13.2 1.0
ND2 B:ASN110 4.8 6.8 1.0
CZ B:ARG250 4.9 24.5 1.0

Arsenic binding site 5 out of 7 in 4hg3

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Arsenic binding site 5 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As404

b:48.9
occ:0.60
 AS C:CAC404 0.0 48.9 0.6
O2 C:CAC404 1.7 48.8 0.6
O1 C:CAC404 1.7 48.5 0.6
C2 C:CAC404 2.0 48.7 0.6
C1 C:CAC404 2.0 48.8 0.6
C1 C:CAC405 4.1 32.3 0.6
O C:HOH657 4.2 21.0 1.0
OG C:SER51 4.3 11.1 1.0
C C:ASN53 4.5 14.0 1.0
CA C:ASN53 4.5 14.1 1.0
OG C:SER146 4.6 17.5 1.0
N C:PRO54 4.7 14.2 1.0
O C:SER51 4.7 11.7 1.0
CD C:PRO54 4.8 14.0 1.0
O C:ASN53 4.8 14.0 1.0
N C:ASN53 4.8 13.7 1.0
O C:HOH586 4.9 22.8 1.0
O C:GLN52 4.9 13.6 1.0

Arsenic binding site 6 out of 7 in 4hg3

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Arsenic binding site 6 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As405

b:32.6
occ:0.60
 AS C:CAC405 0.0 32.6 0.6
O1 C:CAC405 1.7 32.1 0.6
O2 C:CAC405 1.7 32.3 0.6
C2 C:CAC405 2.0 32.1 0.6
C1 C:CAC405 2.0 32.3 0.6
O C:HOH657 3.5 21.0 1.0
NE2 C:HIS93 4.1 10.6 1.0
CD2 C:LEU50 4.3 9.5 1.0
OE2 C:GLU143 4.3 18.0 1.0
O C:HOH586 4.3 22.8 1.0
ND2 C:ASN110 4.5 10.3 1.0
C2 C:CAC404 4.7 48.7 0.6
OE2 C:GLU45 4.7 6.7 1.0
O C:HOH619 4.9 24.8 1.0
CE1 C:HIS93 4.9 10.1 1.0
NH1 C:ARG250 4.9 24.4 1.0
CD C:GLU143 4.9 18.2 1.0
O2 C:CAC404 4.9 48.8 0.6

Arsenic binding site 7 out of 7 in 4hg3

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Arsenic binding site 7 out of 7 in the Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Structural Insights Into Yeast NIT2: Wild-Type Yeast NIT2 in Complex with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As404

b:20.1
occ:0.60
 AS D:CAC404 0.0 20.1 0.6
O1 D:CAC404 1.7 20.1 0.6
O2 D:CAC404 1.7 19.7 0.6
C1 D:CAC404 2.0 19.9 0.6
C2 D:CAC404 2.0 19.9 0.6
O D:HOH576 3.5 26.5 1.0
O D:HOH598 3.8 23.2 1.0
NE2 D:HIS93 3.8 16.9 1.0
CD2 D:LEU50 4.0 18.5 1.0
NH2 D:ARG250 4.4 29.7 1.0
NH1 D:ARG250 4.4 28.6 1.0
CE1 D:HIS93 4.6 17.1 1.0
ND2 D:ASN110 4.6 15.1 1.0
OE2 D:GLU143 4.8 21.4 1.0
CZ D:ARG250 4.8 28.8 1.0
CD2 D:HIS93 4.9 16.8 1.0
CB D:ALA46 5.0 13.8 1.0

Reference:

H.Liu, Y.Gao, M.Zhang, X.Qiu, A.J.L.Cooper, L.Niu, M.Teng. Structures of Enzyme-Intermediate Complexes of Yeast NIT2: Insights Into Its Catalytic Mechanism and Different Substrate Specificity Compared with Mammalian NIT2 Acta Crystallogr.,Sect.D V. 69 1470 2013.
ISSN: ISSN 0907-4449
PubMed: 23897470
DOI: 10.1107/S0907444913009347
Page generated: Wed Jul 10 12:09:59 2024

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