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Iodine in PDB 4wyh: Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus

Protein crystallography data

The structure of Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus, PDB code: 4wyh was solved by S.Ouyang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.42 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.258, 36.232, 83.758, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus (pdb code 4wyh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus, PDB code: 4wyh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 4wyh

Go back to Iodine Binding Sites List in 4wyh
Iodine binding site 1 out of 5 in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus


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 Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:11.8
occ:0.98
 N A:LYS141 3.7 5.5 1.0
N A:GLU142 3.9 6.6 1.0
CA A:ASP140 4.2 6.8 1.0
C A:ASP140 4.3 6.6 1.0
CA A:LYS141 4.4 7.6 1.0
O A:ARG139 4.4 11.2 1.0
CB A:LYS141 4.4 6.7 1.0
OD1 A:ASP140 4.5 8.5 1.0
CB A:GLU142 4.6 5.3 1.0
C A:LYS141 4.6 6.6 1.0
CA A:GLU142 4.9 7.9 1.0
N A:ASP140 4.9 6.1 1.0

Iodine binding site 2 out of 5 in 4wyh

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Iodine binding site 2 out of 5 in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus


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 Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:15.0
occ:0.95
 CD2 A:LEU77 3.9 6.0 1.0
CZ2 A:TRP115 4.1 9.6 1.0
C A:LYS73 4.3 6.6 1.0
CG A:ARG74 4.3 7.4 1.0
N A:ARG74 4.3 6.1 1.0
CB A:LYS73 4.3 9.5 1.0
O A:LYS73 4.4 5.4 1.0
CA A:ARG74 4.4 6.7 1.0
CB A:LEU77 4.6 5.1 1.0
CH2 A:TRP115 4.8 8.0 1.0
CA A:LYS73 4.9 7.9 1.0
CG A:LEU77 4.9 8.2 1.0
CB A:ARG74 5.0 6.4 1.0

Iodine binding site 3 out of 5 in 4wyh

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Iodine binding site 3 out of 5 in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus


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 Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:14.2
occ:0.28
 O A:HOH348 2.4 26.0 1.0
O A:HOH315 2.9 21.8 1.0
O A:HOH357 3.5 11.5 1.0
N A:LYS73 3.5 6.1 1.0
O A:HOH345 3.6 29.2 1.0
O A:ASP70 3.6 7.2 1.0
N A:ARG72 3.8 7.6 1.0
CB A:ARG72 3.9 7.5 1.0
CG A:LYS73 3.9 12.3 1.0
CB A:LYS73 4.0 9.5 1.0
C A:ASP70 4.1 7.7 1.0
CA A:ARG72 4.2 7.0 1.0
NE A:ARG72 4.2 8.4 1.0
O A:GLN69 4.2 12.5 1.0
CD A:LYS73 4.2 17.2 1.0
CE1 A:TYR103 4.3 8.8 1.0
C A:ARG72 4.3 7.5 1.0
NH2 A:ARG72 4.4 13.1 1.0
CA A:LYS73 4.4 7.9 1.0
C A:SER71 4.6 5.3 1.0
CE A:LYS73 4.6 23.4 1.0
CZ A:ARG72 4.6 11.8 1.0
N A:SER71 4.7 7.8 1.0
CA A:ASP70 4.7 8.4 1.0
OH A:TYR103 4.7 15.6 1.0
CG A:ARG72 4.9 7.8 1.0
CA A:SER71 4.9 6.9 1.0
CZ A:TYR103 5.0 11.1 1.0

Iodine binding site 4 out of 5 in 4wyh

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Iodine binding site 4 out of 5 in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus


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 Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:22.8
occ:0.25
 NZ A:LYS73 3.4 33.2 1.0
CE A:LYS73 3.7 23.4 1.0
CD2 A:TYR112 3.8 35.1 1.0
CG A:TRP115 3.8 11.6 1.0
N A:TYR112 3.9 17.3 1.0
CB A:TRP115 4.0 8.8 1.0
CG2 A:VAL111 4.0 10.5 1.0
CD2 A:TRP115 4.0 6.6 1.0
CD A:LYS73 4.1 17.2 1.0
CD1 A:TRP115 4.2 9.7 1.0
CA A:VAL111 4.3 12.8 1.0
O A:HOH307 4.3 27.0 1.0
CE3 A:TRP115 4.4 9.1 1.0
CE2 A:TRP115 4.5 10.9 1.0
CB A:TYR112 4.6 19.7 1.0
O A:LYS110 4.6 14.9 1.0
NE1 A:TRP115 4.6 13.0 1.0
CE2 A:TYR112 4.6 34.4 1.0
CG A:TYR112 4.6 30.5 1.0
C A:VAL111 4.7 11.0 1.0
CB A:VAL111 4.7 11.9 1.0
CA A:TYR112 4.9 20.2 1.0

Iodine binding site 5 out of 5 in 4wyh

Go back to Iodine Binding Sites List in 4wyh
Iodine binding site 5 out of 5 in the Crystal Structure of Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus


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 Prix From the Hyperthermophilic Archaeon Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:30.4
occ:0.29
 O A:ARG139 3.9 11.2 1.0
CH2 A:TRP131 4.3 9.2 1.0
CB A:ARG139 4.4 11.4 1.0
C A:ARG139 4.7 9.8 1.0
O A:HOH319 4.7 12.1 1.0
CD A:ARG139 4.9 15.0 1.0
CA A:ARG139 5.0 7.5 1.0

Reference:

B.Liu, S.Ouyang, K.S.Makarova, Q.Xia, Y.Zhu, Z.Li, L.Guo, E.V.Koonin, Z.J.Liu, L.Huang. A Primase Subunit Essential For Efficient Primer Synthesis By An Archaeal Eukaryotic-Type Primase. Nat Commun V. 6 7300 2015.
ISSN: ESSN 2041-1723
PubMed: 26095544
DOI: 10.1038/NCOMMS8300
Page generated: Sun Aug 11 20:10:43 2024

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