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Iodine in PDB 2hib: Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization

Protein crystallography data

The structure of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization, PDB code: 2hib was solved by M.G.Rudolph, D.Roeser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.83 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.890, 109.110, 43.492, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 23.8

Other elements in 2hib:

The structure of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization (pdb code 2hib). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization, PDB code: 2hib:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 2hib

Go back to Iodine Binding Sites List in 2hib
Iodine binding site 1 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1003

b:31.9
occ:0.50
 N X:LYS249 3.7 32.0 1.0
CB X:LYS249 3.8 32.9 1.0
CB X:PRO252 4.0 30.7 1.0
N X:ASN248 4.0 30.3 1.0
O X:TRP246 4.1 29.2 1.0
O X:HOH1107 4.1 34.9 1.0
CG X:LYS249 4.1 35.7 1.0
CA X:GLY247 4.1 28.8 1.0
CG X:PRO252 4.3 30.7 1.0
CA X:LYS249 4.3 32.6 1.0
O X:LYS249 4.4 31.2 1.0
CD1 X:TRP246 4.4 26.8 1.0
C X:GLY247 4.4 29.3 1.0
C X:TRP246 4.7 28.0 1.0
C X:ASN248 4.8 31.7 1.0
CA X:PRO252 4.8 30.7 1.0
N X:GLY247 4.9 28.3 1.0
C X:LYS249 4.9 31.9 1.0
CA X:ASN248 4.9 31.5 1.0

Iodine binding site 2 out of 11 in 2hib

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Iodine binding site 2 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1004

b:36.4
occ:0.50
 N X:LEU225 3.6 26.9 1.0
O X:HOH1271 3.6 32.2 1.0
CB X:ARG224 3.9 26.2 1.0
CG1 X:VAL215 4.0 28.7 1.0
CA X:ARG224 4.1 26.8 1.0
CG2 X:VAL215 4.2 27.9 1.0
CB X:LEU225 4.3 26.2 1.0
C X:ARG224 4.4 26.4 1.0
CA X:LEU225 4.5 26.4 1.0
CG2 X:THR219 4.5 27.4 1.0
CB X:VAL215 4.5 28.6 1.0
CG X:LEU225 4.6 26.8 1.0
CA X:VAL215 4.8 27.7 1.0
O X:LEU225 4.9 26.3 1.0
CD1 X:LEU225 4.9 26.9 1.0

Iodine binding site 3 out of 11 in 2hib

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Iodine binding site 3 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1005

b:38.1
occ:0.50
 O X:HOH1118 3.4 36.6 1.0
CD X:LYS109 3.9 43.6 1.0
CG X:LYS109 4.1 39.7 1.0
CB X:LYS109 4.1 36.4 1.0
CB X:ALA114 4.2 32.4 1.0
O X:LYS109 4.5 33.9 1.0
CG X:PRO106 4.5 37.2 1.0
CA X:LYS109 4.7 35.9 1.0
CE X:LYS109 5.0 45.8 1.0
C X:LYS109 5.0 34.6 1.0

Iodine binding site 4 out of 11 in 2hib

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Iodine binding site 4 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1006

b:40.3
occ:0.50
 SG X:CYS341 3.0 42.8 1.0
OG X:SER336 3.3 30.0 1.0
NE1 X:TRP299 3.4 26.8 1.0
OG X:SER333 3.4 26.9 1.0
O X:HOH1145 3.5 39.0 1.0
OH X:TYR340 3.6 47.1 1.0
CB X:CYS341 3.8 39.3 1.0
N X:SER336 3.9 29.0 1.0
CB X:MET335 4.1 28.1 1.0
CA X:SER336 4.1 29.0 1.0
ND2 X:ASN360 4.2 25.1 1.0
CE2 X:TRP299 4.2 27.7 1.0
C X:MET335 4.2 28.5 1.0
O X:HOH1016 4.2 20.5 0.5
CB X:SER336 4.2 29.3 1.0
CZ2 X:TRP299 4.3 27.3 1.0
CB X:SER333 4.3 28.1 1.0
CD1 X:TRP299 4.4 27.5 1.0
N X:SER333 4.4 27.2 1.0
CZ X:TYR340 4.5 45.7 1.0
CA X:MET335 4.6 28.6 1.0
O X:MET335 4.7 29.0 1.0
CA X:SER333 4.9 27.2 1.0
N X:MET335 5.0 27.9 1.0

Iodine binding site 5 out of 11 in 2hib

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Iodine binding site 5 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1007

b:38.9
occ:0.50
 O X:HOH1209 3.2 45.6 1.0
O X:HOH1265 3.4 57.0 1.0
OD2 X:ASP368 3.6 31.9 0.3
N X:ASP368 3.6 31.7 1.0
CD X:ARG224 3.9 26.9 1.0
CA X:ALA367 4.0 27.6 1.0
NE X:ARG224 4.0 27.5 1.0
CG X:ARG224 4.1 26.7 1.0
O X:HOH1219 4.1 47.4 1.0
CG X:ASP368 4.2 33.0 0.7
C X:ALA367 4.3 29.1 1.0
O X:GLY222 4.3 27.1 1.0
OD2 X:ASP368 4.3 35.1 0.7
CB X:ASP368 4.3 33.1 0.3
CB X:ASP368 4.3 32.8 0.7
CB X:ALA367 4.4 27.1 1.0
CG X:ASP368 4.4 32.8 0.3
C X:LYS223 4.4 27.1 1.0
CA X:LYS223 4.5 27.3 1.0
CB X:ARG224 4.6 26.2 1.0
OD1 X:ASP368 4.6 30.2 0.7
CA X:ASP368 4.6 33.1 1.0
O X:LYS223 4.6 27.4 1.0
N X:ARG224 4.8 27.0 1.0
O X:ALA366 4.8 23.8 1.0

Iodine binding site 6 out of 11 in 2hib

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Iodine binding site 6 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1008

b:27.6
occ:0.50
 OD1 X:ASP203 1.5 31.2 0.5
CG X:ASP203 2.5 29.3 0.5
OD2 X:ASP203 2.9 30.2 0.5
O X:HOH1173 3.6 41.9 1.0
N X:ASP203 3.8 28.1 1.0
CB X:ASP203 3.8 28.1 0.5
CD2 X:HIS204 3.8 27.0 1.0
CD X:PRO202 3.9 29.2 1.0
CB X:ASP203 3.9 28.4 0.5
CA X:ARG201 4.0 29.3 1.0
O X:HIS200 4.1 30.3 1.0
N X:PRO202 4.1 28.7 1.0
NE2 X:HIS204 4.1 26.3 1.0
CG X:PRO202 4.2 29.2 1.0
C X:ARG201 4.2 29.0 1.0
CA X:ASP203 4.3 27.9 0.5
CA X:ASP203 4.3 27.7 0.5
CG X:ASP203 4.5 28.4 0.5
O X:HOH1085 4.5 32.4 1.0
O X:HOH1148 4.5 39.6 1.0
OD2 X:ASP203 4.6 28.6 0.5
CG X:PRO280 4.6 23.6 1.0
C X:ASP203 4.8 27.7 1.0
N X:HIS204 4.8 26.1 1.0
C X:HIS200 4.8 29.4 1.0
N X:ARG201 4.8 29.6 1.0
C X:PRO202 4.9 28.5 1.0
CB X:ARG201 4.9 28.7 1.0
O X:ARG201 4.9 28.5 1.0

Iodine binding site 7 out of 11 in 2hib

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Iodine binding site 7 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1009

b:46.1
occ:0.40
 O X:HOH1014 1.6 12.8 0.6
O X:HOH1048 1.7 30.2 0.6
ND2 X:ASN269 3.8 25.8 1.0
O X:GLN276 3.8 29.2 1.0
CG X:MET161 3.8 47.1 1.0
SD X:MET161 4.0 50.6 1.0
CE2 X:PHE158 4.1 32.5 1.0
C X:GLN276 4.1 29.2 1.0
CB X:GLN276 4.1 29.9 1.0
CZ3 X:TRP261 4.2 29.3 1.0
CB X:ASN269 4.2 30.1 1.0
CG X:ASN269 4.5 28.8 1.0
CD2 X:PHE158 4.5 32.6 1.0
CA X:GLN276 4.6 29.4 1.0
CH2 X:TRP261 4.6 28.4 1.0
N X:GLY277 4.7 29.2 1.0
CE X:MET161 4.7 48.5 1.0
O X:GLY160 4.8 42.0 1.0
CE1 X:TYR334 4.8 30.4 1.0
C X:GLY160 4.9 42.2 1.0
CE3 X:TRP261 5.0 29.1 1.0
CG X:GLN276 5.0 33.1 1.0

Iodine binding site 8 out of 11 in 2hib

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Iodine binding site 8 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1010

b:35.0
occ:0.30
 O X:ARG242 3.3 31.8 1.0
O X:HOH1057 3.4 28.8 1.0
NH1 X:ARG236 3.6 26.8 1.0
O X:HOH1221 3.6 47.0 1.0
O X:HOH1096 3.6 34.2 1.0
NH2 X:ARG236 3.6 26.6 1.0
C X:ARG242 3.8 31.8 1.0
C X:ASN241 3.8 33.5 1.0
O X:ASN241 4.0 33.0 1.0
CB X:THR103 4.0 35.5 1.0
CA X:ASN241 4.1 34.3 1.0
CZ X:ARG236 4.1 24.8 1.0
N X:ARG242 4.1 32.6 1.0
OG1 X:THR103 4.1 34.1 1.0
O X:HOH1227 4.3 48.9 1.0
CB X:ALA347 4.4 28.1 1.0
O X:GLY102 4.4 33.8 1.0
N X:LEU243 4.5 30.7 1.0
CA X:ARG242 4.5 32.5 1.0
O X:HOH1245 4.7 51.4 1.0
CA X:LEU243 4.7 30.3 1.0
CB X:ASN241 4.8 35.2 1.0
CG2 X:THR103 4.9 35.8 1.0

Iodine binding site 9 out of 11 in 2hib

Go back to Iodine Binding Sites List in 2hib
Iodine binding site 9 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1011

b:49.0
occ:0.30
 O X:HOH1145 2.8 39.0 1.0
O X:HOH1146 3.3 38.8 1.0
NE1 X:TRP180 3.4 31.9 1.0
NE1 X:TRP179 3.7 33.7 1.0
O X:HOH1136 3.8 36.2 0.5
CE2 X:TYR340 3.9 45.2 1.0
O X:HOH1016 3.9 20.5 0.5
CD1 X:TRP180 4.0 31.6 1.0
CZ2 X:TRP179 4.2 33.9 1.0
CE2 X:TRP179 4.3 34.3 1.0
CE2 X:TRP180 4.6 31.0 1.0
OH X:TYR340 4.6 47.1 1.0
CB X:ALA177 4.7 38.1 1.0
CD2 X:TYR340 4.7 44.8 1.0
CZ X:TYR340 4.8 45.7 1.0
CD1 X:TRP179 4.9 33.9 1.0

Iodine binding site 10 out of 11 in 2hib

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Iodine binding site 10 out of 11 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I1012

b:38.2
occ:0.30
 O X:HOH1018 2.0 24.1 0.7
N X:LYS253 3.3 29.7 1.0
CD X:LYS249 3.9 38.4 1.0
O X:HOH1054 4.0 28.2 1.0
CA X:PRO252 4.0 30.7 1.0
O X:GLN251 4.1 31.7 1.0
C X:PRO252 4.1 30.1 1.0
CA X:LYS253 4.2 30.4 1.0
CG X:LYS249 4.2 35.7 1.0
CB X:LYS249 4.5 32.9 1.0
N X:GLY254 4.7 29.9 1.0
C X:GLN251 4.8 31.8 1.0
CE X:LYS249 4.8 41.2 1.0
N X:PRO252 4.9 31.1 1.0
C X:LYS253 5.0 30.4 1.0

Reference:

D.Roeser, B.Schmidt, A.Preusser-Kunze, M.G.Rudolph. Probing the Oxygen-Binding Site of the Human Formylglycine-Generating Enzyme Using Halide Ions. Acta Crystallogr.,Sect.D V. 63 621 2007.
ISSN: ISSN 0907-4449
PubMed: 17452787
DOI: 10.1107/S0907444907009961
Page generated: Sun Aug 11 13:56:30 2024

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