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Iodine in PDB 5jgp: Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions

Enzymatic activity of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions

All present enzymatic activity of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions, PDB code: 5jgp was solved by I.Melnikov, V.Polovinkin, A.Popov, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.11 / 2.70
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.241, 73.663, 236.428, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 26.3

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions (pdb code 5jgp). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions, PDB code: 5jgp:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 5jgp

Go back to Iodine Binding Sites List in 5jgp
Iodine binding site 1 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:39.2
occ:0.40
 NH2 A:ARG145 1.3 31.4 0.5
CZ A:ARG145 1.8 31.4 0.5
NE A:ARG145 2.0 33.9 0.5
O A:HOH410 2.8 17.6 1.0
NH1 A:ARG145 3.0 30.6 0.5
CD A:ARG145 3.4 35.4 0.5
CA A:TYR142 3.8 33.3 1.0
CD A:ARG145 3.9 44.7 0.5
CG A:PRO92 4.0 45.6 1.0
CB A:TYR142 4.0 33.1 1.0
NE A:ARG145 4.1 46.5 0.5
N A:TYR142 4.1 33.2 1.0
O A:HOH514 4.2 57.6 1.0
CD1 A:TYR142 4.3 36.0 1.0
CG A:ARG145 4.4 43.1 0.5
CG A:ARG145 4.4 36.1 0.5
C A:HIS141 4.6 32.0 1.0
CG A:TYR142 4.6 34.6 1.0
CB A:PRO92 4.6 46.8 1.0
CB A:ARG145 4.7 36.0 0.5
CB A:ARG145 4.8 40.1 0.5
O A:HIS141 4.8 30.7 1.0
CB A:HIS141 5.0 35.9 1.0

Iodine binding site 2 out of 12 in 5jgp

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Iodine binding site 2 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:97.0
occ:0.92
 O A:HOH528 3.1 46.4 1.0
O A:HOH517 3.7 47.5 1.0
N A:ILE2 3.7 44.1 1.0
O A:ILE2 3.7 36.4 1.0
CA A:MET1 3.9 59.0 1.0
O A:HOH407 4.0 17.7 1.0
NZ A:LYS213 4.0 44.7 1.0
CB A:MET1 4.2 63.1 1.0
CG1 A:ILE2 4.3 39.6 1.0
C A:MET1 4.4 50.7 1.0
O A:HOH438 4.4 35.1 1.0
CE A:LYS4 4.4 71.8 1.0
C A:ILE2 4.6 38.2 1.0
NZ A:LYS4 4.6 74.6 1.0
CA A:ILE2 4.7 39.6 1.0

Iodine binding site 3 out of 12 in 5jgp

Go back to Iodine Binding Sites List in 5jgp
Iodine binding site 3 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:51.4
occ:0.55
 O A:HOH428 3.8 60.8 1.0
CA A:ARG171 4.0 39.5 1.0
NE A:ARG170 4.1 66.1 1.0
CB A:HIS174 4.1 30.7 0.4
ND1 A:HIS174 4.1 27.1 0.4
CB A:HIS174 4.3 40.3 0.6
CG A:HIS174 4.3 28.0 0.4
CB A:ARG171 4.4 42.4 1.0
CG A:ARG171 4.5 49.1 1.0
N A:ARG171 4.5 40.2 1.0
NH1 A:ARG170 4.6 71.4 1.0
CG A:HIS174 4.6 44.8 0.6
O A:ARG170 4.6 40.2 1.0
CZ A:ARG170 4.8 68.3 1.0
C A:ARG170 4.8 39.8 1.0
CD A:ARG170 4.9 62.2 1.0
ND1 A:HIS174 4.9 47.5 0.6
O A:ARG171 4.9 46.2 1.0
CE1 A:HIS174 4.9 25.9 0.4
C A:ARG171 5.0 41.5 1.0

Iodine binding site 4 out of 12 in 5jgp

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Iodine binding site 4 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:63.2
occ:0.56
 ND2 A:ASN110 3.6 34.9 1.0
O A:ARG71 3.8 27.7 1.0
OE1 A:GLN75 3.9 51.2 1.0
O A:HOH485 4.0 31.9 1.0
CG A:GLN72 4.0 50.4 1.0
CA A:GLN72 4.0 38.6 1.0
C A:ARG71 4.0 32.3 1.0
N A:GLN72 4.1 34.7 1.0
OD1 A:ASN110 4.4 32.5 1.0
CG A:ASN110 4.4 32.4 1.0
CB A:GLN75 4.5 40.9 1.0
CB A:ARG71 4.5 34.2 1.0
CB A:GLN72 4.6 45.1 1.0
CD A:GLN75 4.8 45.8 1.0
CZ2 A:TRP106 4.8 34.0 1.0
CG A:GLN75 4.9 43.4 1.0
CA A:ARG71 5.0 31.7 1.0

Iodine binding site 5 out of 12 in 5jgp

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Iodine binding site 5 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:0.6
occ:0.92
 CG2 A:THR202 4.0 49.4 1.0
CB A:ASN216 4.0 43.2 1.0
ND2 A:ASN216 4.1 42.9 1.0
CG A:LYS213 4.4 40.9 1.0
CA A:LYS213 4.4 35.9 1.0
O A:LYS213 4.6 32.6 1.0
CG A:ASN216 4.6 44.6 1.0
CB A:LYS213 4.6 37.8 1.0
OG1 A:THR202 4.8 48.1 1.0
CB A:THR202 4.9 48.6 1.0
C A:LYS213 5.0 35.9 1.0

Iodine binding site 6 out of 12 in 5jgp

Go back to Iodine Binding Sites List in 5jgp
Iodine binding site 6 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:46.7
occ:0.34
 CG1 A:VAL177 3.6 34.8 1.0
O A:HOH457 3.9 51.8 1.0
CD A:ARG173 4.0 58.4 1.0
N A:ALA178 4.1 30.9 1.0
CB A:ARG173 4.2 44.6 1.0
O A:ARG173 4.3 34.4 1.0
NE A:ARG173 4.3 63.4 1.0
CB A:VAL177 4.3 33.5 1.0
CA A:ALA178 4.4 30.6 1.0
CB A:ALA178 4.4 29.9 1.0
C A:VAL177 4.7 32.7 1.0
CG A:ARG173 4.7 51.2 1.0
CA A:ARG173 4.7 40.6 1.0
C A:ARG173 4.8 36.8 1.0
CZ A:ARG173 4.9 65.7 1.0

Iodine binding site 7 out of 12 in 5jgp

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Iodine binding site 7 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:57.1
occ:0.46
 O A:HOH496 2.4 14.0 1.0
OE1 A:GLU108 3.7 68.8 1.0
OD1 A:ASN105 3.8 35.9 1.0
CH2 A:TRP120 3.9 29.6 1.0
O A:ASN105 3.9 27.8 1.0
CD1 A:TYR128 4.1 24.8 1.0
CB A:ASN105 4.1 32.5 1.0
CG A:ASN105 4.1 33.0 1.0
CZ2 A:TRP120 4.1 28.4 1.0
CA A:ASN105 4.1 31.4 1.0
O A:HOH425 4.2 46.9 1.0
CB A:GLU108 4.3 45.7 1.0
CG A:GLU108 4.4 54.3 1.0
C A:ASN105 4.4 29.6 1.0
CD A:GLU108 4.5 64.6 1.0
CE1 A:TYR128 4.5 25.6 1.0
ND2 A:ASN105 5.0 33.8 1.0

Iodine binding site 8 out of 12 in 5jgp

Go back to Iodine Binding Sites List in 5jgp
Iodine binding site 8 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:57.1
occ:0.37
 O A:ASN203 2.4 45.3 1.0
C A:ASN203 3.6 41.9 1.0
CD A:PRO205 3.7 25.9 1.0
N A:PRO205 3.8 26.4 1.0
O A:HOH495 3.8 46.3 1.0
CB A:PRO205 4.0 24.9 1.0
C A:LEU204 4.1 29.7 1.0
CG A:PRO205 4.2 25.3 1.0
CA A:PRO205 4.3 27.0 1.0
CA A:LEU204 4.4 34.9 1.0
N A:LEU204 4.4 37.2 1.0
CA A:ASN203 4.5 47.8 1.0
O A:LEU204 4.8 29.1 1.0
CB A:ASN203 4.8 53.1 1.0
O A:HOH530 4.9 44.2 1.0
O A:HOH464 5.0 50.8 1.0

Iodine binding site 9 out of 12 in 5jgp

Go back to Iodine Binding Sites List in 5jgp
Iodine binding site 9 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I310

b:68.3
occ:0.54
 ND2 A:ASN111 3.2 39.0 1.0
OE2 A:GLU108 3.7 64.8 1.0
CG A:GLU108 3.8 54.3 1.0
CD A:GLU108 4.1 64.6 1.0
CA A:GLU108 4.1 40.4 1.0
CG A:ASN111 4.2 39.8 1.0
CB A:GLU108 4.2 45.7 1.0
CB A:ASN111 4.3 36.9 1.0
O A:GLU108 4.4 36.4 1.0
NE A:ARG112 4.5 36.6 1.0
C A:GLU108 4.8 36.0 1.0
CG A:ARG112 4.9 35.1 1.0

Iodine binding site 10 out of 12 in 5jgp

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Iodine binding site 10 out of 12 in the Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Nitrate/Nitrite Sensor Narq Fragment Bound with Iodide Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I311

b:36.5
occ:0.67
 O A:HOH455 3.2 18.2 1.0
CB A:SER10 3.7 36.4 1.0
CG1 A:ILE172 4.0 30.9 1.0
NE A:ARG171 4.1 69.3 1.0
CG A:ARG171 4.2 49.1 1.0
OG A:SER10 4.3 38.2 1.0
CA A:ILE172 4.3 35.3 1.0
CD2 A:LEU11 4.4 50.2 1.0
CG2 A:VAL176 4.4 29.9 1.0
N A:ILE172 4.4 37.1 1.0
CG A:LEU11 4.5 53.2 1.0
CD A:ARG171 4.5 57.7 1.0
OE1 A:GLN175 4.6 58.8 1.0
O A:ARG171 4.7 46.2 1.0
C A:ARG171 4.7 41.5 1.0
CG1 A:VAL7 4.8 41.6 1.0
O A:HOH431 4.8 37.1 1.0
CB A:ILE172 4.8 33.9 1.0
CZ A:ARG171 4.8 82.5 1.0
N A:LEU11 4.9 38.7 1.0
NH1 A:ARG171 4.9 87.3 1.0
O A:VAL7 4.9 38.3 1.0
CG2 A:VAL7 5.0 38.9 1.0
C A:SER10 5.0 36.5 1.0
CB A:ARG171 5.0 42.4 1.0

Reference:

I.Melnikov, V.Polovinkin, K.Kovalev, I.Gushchin, M.Shevtsov, V.Shevchenko, A.Mishin, A.Alekseev, F.Rodriguez-Valera, V.Borshchevskiy, V.Cherezov, G.A.Leonard, V.Gordeliy, A.Popov. Fast Iodide-Sad Phasing For High-Throughput Membrane Protein Structure Determination. Sci Adv V. 3 02952 2017.
ISSN: ESSN 2375-2548
PubMed: 28508075
DOI: 10.1126/SCIADV.1602952
Page generated: Sun Aug 11 21:06:59 2024

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