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Iodine in PDB 2p4m: High pH Structure of RTMS5 H146S Variant

Protein crystallography data

The structure of High pH Structure of RTMS5 H146S Variant, PDB code: 2p4m was solved by J.M.Battad, P.G.Wilmann, S.Olsen, E.Byres, S.C.Smith, S.G.Dove, K.N.Turcic, R.J.Devenish, J.Rossjohn, M.Prescott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 153.750, 186.319, 185.564, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.9

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iodine atom in the High pH Structure of RTMS5 H146S Variant (pdb code 2p4m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 24 binding sites of Iodine where determined in the High pH Structure of RTMS5 H146S Variant, PDB code: 2p4m:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 1 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2001

b:24.2
occ:1.00
 O A:HOH2112 3.8 25.4 1.0
CB A:ASN203 4.0 27.1 1.0
N A:HIS204 4.0 27.4 1.0
CA A:HIS204 4.1 27.4 1.0
O A:SER210 4.1 28.0 1.0
C A:ASN203 4.1 27.4 1.0
C A:SER210 4.1 28.4 1.0
N A:GLU212 4.1 29.6 1.0
CB A:SER210 4.1 28.3 1.0
CG A:ASN203 4.1 26.8 1.0
C A:VAL211 4.2 29.2 1.0
O A:ASN203 4.2 27.6 1.0
N A:VAL211 4.2 28.6 1.0
CB A:GLU212 4.2 30.2 1.0
CA A:VAL211 4.4 28.9 1.0
OD1 A:ASN203 4.4 26.2 1.0
C A:HIS204 4.5 27.2 1.0
ND2 A:ASN203 4.6 25.1 1.0
O A:VAL211 4.6 29.1 1.0
CA A:ASN203 4.7 27.5 1.0
N A:ASN205 4.7 27.3 1.0
CA A:SER210 4.8 28.4 1.0
CA A:GLU212 4.8 30.2 1.0

Iodine binding site 2 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 2 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2004

b:24.1
occ:1.00
 ND2 A:ASN205 3.8 25.4 1.0
CB A:ASN205 4.1 27.2 1.0
CG A:ASN205 4.5 26.2 1.0

Iodine binding site 3 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 3 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2012

b:58.2
occ:1.00
 O A:PHE129 3.6 29.9 1.0
NZ C:LYS182 3.7 30.5 1.0
CA A:ASN128 3.8 29.4 1.0
C A:ASN128 3.8 29.5 1.0
O C:HOH2034 3.8 24.2 1.0
CE C:LYS182 3.9 31.3 1.0
O A:ASN128 4.0 29.6 1.0
C A:PHE129 4.0 29.8 1.0
CA A:PRO130 4.2 30.0 1.0
SD C:MET156 4.2 32.1 1.0
N A:PRO130 4.2 29.9 1.0
N A:PHE129 4.3 29.6 1.0
CE C:MET156 4.3 32.0 1.0
CD A:PRO131 4.4 30.3 1.0
O A:HOH2069 4.4 25.2 1.0
CB A:ASN128 4.5 29.5 1.0
OD1 A:ASN128 4.6 30.1 1.0
OE1 C:GLU94 4.6 30.3 1.0
CG A:ASN128 4.8 29.7 1.0
N A:ASN128 4.8 29.2 1.0
CG2 C:THR180 4.8 30.4 1.0
CA A:PHE129 4.8 29.6 1.0

Iodine binding site 4 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 4 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2014

b:71.2
occ:1.00
 N A:GLY155 3.3 30.3 1.0
N A:GLY154 3.7 30.2 1.0
O A:HOH2146 3.8 30.6 1.0
CG A:MET189 3.9 30.7 1.0
CA A:GLY155 4.0 30.4 1.0
C A:ARG153 4.0 30.0 1.0
N A:ARG153 4.1 29.9 1.0
CE A:MET189 4.1 31.1 1.0
CA A:ARG153 4.1 30.1 1.0
CB A:ALA152 4.2 29.6 1.0
C A:GLY154 4.3 30.4 1.0
C A:ALA152 4.3 29.8 1.0
CA A:GLY154 4.3 30.3 1.0
CB A:MET189 4.6 30.3 1.0
SD A:MET189 4.6 31.6 1.0
O A:ALA152 4.6 30.0 1.0
O A:ARG153 4.8 29.9 1.0
CA A:ALA152 4.8 29.8 1.0
C A:GLY155 4.9 30.4 1.0
N A:MET156 5.0 30.5 1.0

Iodine binding site 5 out of 24 in 2p4m

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Iodine binding site 5 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2006

b:28.1
occ:1.00
 O B:HOH2056 3.7 30.7 1.0
ND2 B:ASN205 3.8 27.8 1.0
CB B:ASN205 4.1 28.6 1.0
CG B:ASN205 4.5 28.3 1.0

Iodine binding site 6 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 6 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2008

b:27.7
occ:1.00
 O B:HOH2164 3.6 40.9 1.0
N B:HIS204 4.0 28.5 1.0
CA B:HIS204 4.0 28.6 1.0
CB B:ASN203 4.0 28.6 1.0
C B:ASN203 4.1 28.6 1.0
N B:GLU212 4.1 30.3 1.0
CG B:ASN203 4.1 28.2 1.0
C B:SER210 4.2 29.3 1.0
C B:VAL211 4.2 29.8 1.0
O B:SER210 4.2 29.2 1.0
N B:VAL211 4.2 29.4 1.0
CB B:SER210 4.2 29.2 1.0
CB B:GLU212 4.2 30.8 1.0
O B:ASN203 4.3 28.7 1.0
CA B:VAL211 4.3 29.6 1.0
OD1 B:ASN203 4.4 27.9 1.0
C B:HIS204 4.4 28.5 1.0
ND2 B:ASN203 4.6 26.9 1.0
O B:VAL211 4.6 29.8 1.0
N B:ASN205 4.7 28.7 1.0
CA B:ASN203 4.7 28.7 1.0
CA B:GLU212 4.8 30.7 1.0
CA B:SER210 4.8 29.2 1.0
O B:HIS204 5.0 28.3 1.0

Iodine binding site 7 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 7 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2013

b:74.6
occ:1.00
 NZ D:LYS182 3.6 31.2 1.0
O B:PHE129 3.7 29.4 1.0
CA B:ASN128 3.8 28.8 1.0
C B:ASN128 3.9 28.9 1.0
O D:HOH2042 3.9 28.6 1.0
CE D:LYS182 3.9 31.9 1.0
C B:PHE129 4.0 29.3 1.0
O B:ASN128 4.1 29.0 1.0
SD D:MET156 4.2 33.9 1.0
CE D:MET156 4.3 33.4 1.0
N B:PRO130 4.3 29.6 1.0
CA B:PRO130 4.3 29.8 1.0
N B:PHE129 4.3 28.9 1.0
CD B:PRO131 4.4 30.5 1.0
O B:HOH2121 4.5 27.5 1.0
OD1 B:ASN128 4.6 30.2 1.0
CB B:ASN128 4.6 28.8 1.0
OE1 D:GLU94 4.7 32.6 1.0
CG B:ASN128 4.8 29.3 1.0
CG2 D:THR180 4.8 31.1 1.0
N B:ASN128 4.8 28.4 1.0
CA B:PHE129 4.9 29.0 1.0

Iodine binding site 8 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 8 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2015

b:64.7
occ:1.00
 N B:GLY155 3.3 30.5 1.0
N B:GLY154 3.7 30.1 1.0
O B:HOH2063 3.7 25.8 1.0
CG B:MET189 3.9 29.1 1.0
N B:ARG153 4.0 29.8 1.0
CA B:GLY155 4.0 30.6 1.0
C B:ARG153 4.0 30.1 1.0
CA B:ARG153 4.1 29.9 1.0
CB B:ALA152 4.1 29.4 1.0
CE B:MET189 4.2 29.3 1.0
C B:ALA152 4.2 29.6 1.0
C B:GLY154 4.3 30.5 1.0
CA B:GLY154 4.4 30.3 1.0
O B:ALA152 4.6 29.7 1.0
CB B:MET189 4.6 29.2 1.0
SD B:MET189 4.7 29.9 1.0
CA B:ALA152 4.8 29.5 1.0
O B:ARG153 4.8 29.9 1.0
C B:GLY155 4.9 30.7 1.0

Iodine binding site 9 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 9 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I2005

b:25.4
occ:1.00
 N C:HIS204 3.9 27.6 1.0
ND2 G:ASN205 3.9 29.3 1.0
CA C:HIS204 4.0 27.7 1.0
CB C:ASN203 4.0 27.4 1.0
C C:ASN203 4.0 27.6 1.0
CB G:ASN205 4.0 28.9 1.0
CG C:ASN203 4.1 27.0 1.0
O C:SER210 4.1 29.6 1.0
N C:GLU212 4.2 30.8 1.0
O C:ASN203 4.2 27.5 1.0
C C:SER210 4.2 29.7 1.0
CB C:SER210 4.2 29.5 1.0
C C:VAL211 4.3 30.6 1.0
N C:VAL211 4.3 30.0 1.0
CB C:GLU212 4.3 31.3 1.0
C C:HIS204 4.4 27.8 1.0
OD1 C:ASN203 4.4 26.1 1.0
CA C:VAL211 4.4 30.3 1.0
ND2 C:ASN203 4.5 26.4 1.0
CG G:ASN205 4.5 28.8 1.0
N C:ASN205 4.6 27.9 1.0
CA C:ASN203 4.7 27.6 1.0
O C:VAL211 4.8 30.4 1.0
CA C:SER210 4.9 29.6 1.0
CA C:GLU212 4.9 31.3 1.0
O C:HIS204 5.0 27.7 1.0

Iodine binding site 10 out of 24 in 2p4m

Go back to Iodine Binding Sites List in 2p4m
Iodine binding site 10 out of 24 in the High pH Structure of RTMS5 H146S Variant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of High pH Structure of RTMS5 H146S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I2010

b:60.8
occ:1.00
 O C:HOH2118 2.9 36.2 1.0
NZ A:LYS182 3.7 31.5 1.0
O C:PHE129 3.8 28.9 1.0
CA C:ASN128 3.8 28.4 1.0
C C:ASN128 3.8 28.4 1.0
O A:HOH2118 4.0 28.1 1.0
CE A:LYS182 4.0 32.1 1.0
C C:PHE129 4.0 28.9 1.0
O C:ASN128 4.0 28.4 1.0
CA C:PRO130 4.1 29.2 1.0
N C:PRO130 4.2 29.1 1.0
SD A:MET156 4.2 31.8 1.0
CD C:PRO131 4.2 29.7 1.0
CE A:MET156 4.3 31.2 1.0
N C:PHE129 4.3 28.7 1.0
O C:HOH2053 4.4 21.6 1.0
CB C:ASN128 4.6 28.2 1.0
OE1 A:GLU94 4.7 29.1 1.0
CG2 A:THR180 4.7 29.3 1.0
OD1 C:ASN128 4.8 30.0 1.0
N C:ASN128 4.8 28.2 1.0
CA C:PHE129 4.8 28.7 1.0
CG C:ASN128 4.9 28.6 1.0

Reference:

J.M.Battad, P.G.Wilmann, S.Olsen, E.Byres, S.C.Smith, S.G.Dove, K.N.Turcic, R.J.Devenish, J.Rossjohn, M.Prescott. A Structural Basis For the pH-Dependent Increase in Fluorescence Efficiency of Chromoproteins J.Mol.Biol. V. 368 998 2007.
ISSN: ISSN 0022-2836
PubMed: 17376484
DOI: 10.1016/J.JMB.2007.02.007
Page generated: Sun Aug 11 14:14:04 2024

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