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Iodine in PDB 2q2l: Crystal Structure of Superoxide Dismutase From P. Atrosanguina

Enzymatic activity of Crystal Structure of Superoxide Dismutase From P. Atrosanguina

All present enzymatic activity of Crystal Structure of Superoxide Dismutase From P. Atrosanguina:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Superoxide Dismutase From P. Atrosanguina, PDB code: 2q2l was solved by Y.Manickam, J.Gill, P.C.Mishra, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.140, 64.120, 63.620, 90.00, 124.33, 90.00
R / Rfree (%) 16.7 / 23.4

Other elements in 2q2l:

The structure of Crystal Structure of Superoxide Dismutase From P. Atrosanguina also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina (pdb code 2q2l). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina, PDB code: 2q2l:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 2q2l

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Iodine binding site 1 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2002

b:22.0
occ:0.50
O A:HOH2077 3.8 35.9 1.0
CA A:SER58 3.9 18.9 1.0
OD1 A:ASN54 4.0 34.8 1.0
N A:SER58 4.1 20.1 1.0
CB A:SER58 4.1 18.6 1.0
O A:MET57 4.1 23.8 1.0
C A:MET57 4.2 21.8 1.0
CB A:ASN54 4.2 24.5 1.0
O A:HOH2069 4.3 19.9 1.0
CB A:MET57 4.5 21.7 1.0
CG A:ASN54 4.5 31.2 1.0
O A:HOH2026 4.7 26.5 1.0

Iodine binding site 2 out of 10 in 2q2l

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Iodine binding site 2 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2003

b:29.6
occ:0.45
O A:HOH2050 2.9 22.4 1.0
N A:ASN64 3.5 14.4 1.0
C A:ASN64 3.7 16.6 1.0
N A:PRO65 4.0 16.9 1.0
O A:ASN64 4.0 17.8 1.0
CD1 A:PHE63 4.0 14.6 1.0
CA A:ASN64 4.1 15.1 1.0
CB A:ALA48 4.1 16.1 1.0
CE1 A:PHE63 4.3 16.1 1.0
CA A:PRO65 4.4 16.4 1.0
C A:PHE63 4.5 14.8 1.0
CB A:ASN64 4.5 14.9 1.0
CD A:PRO65 4.6 16.4 1.0
CA A:PHE63 4.6 14.5 1.0
NH2 A:ARG114 4.7 11.7 1.0
CA A:ALA48 4.9 16.8 1.0
O A:HIS62 5.0 15.8 1.0

Iodine binding site 3 out of 10 in 2q2l

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Iodine binding site 3 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2004

b:26.6
occ:0.48
O A:ARG142 3.5 25.6 1.0
O A:HOH2035 3.7 12.7 1.0
O A:ILE143 3.7 24.0 1.0
C A:ILE143 3.7 23.0 1.0
N A:SER11 3.8 32.2 1.0
CA A:SER10 3.9 30.7 1.0
SG A:CYS56 4.0 21.5 1.0
OG A:SER11 4.0 28.9 1.0
N A:ALA144 4.1 21.6 1.0
CA A:ILE143 4.1 22.0 1.0
C A:ARG142 4.2 24.1 1.0
OG A:SER10 4.3 32.2 1.0
N A:ILE143 4.3 23.2 1.0
C A:SER10 4.3 31.6 1.0
CA A:ALA144 4.3 20.8 1.0
I A:IOD2008 4.4 30.6 0.2
CB A:SER10 4.7 29.5 1.0
CB A:CYS56 4.7 19.2 1.0
CB A:SER11 4.8 33.4 1.0
O A:SER9 4.9 28.5 1.0
CA A:SER11 4.9 33.6 1.0
N A:SER10 4.9 29.4 1.0

Iodine binding site 4 out of 10 in 2q2l

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Iodine binding site 4 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2005

b:27.7
occ:0.35
N A:THR97 3.6 19.4 1.0
O A:THR97 3.9 20.8 1.0
CA A:PHE96 3.9 20.9 1.0
CE1 B:HIS130 4.0 28.3 1.0
NE2 B:HIS130 4.0 24.5 1.0
O A:HOH2075 4.1 26.5 1.0
C A:PHE96 4.2 21.3 1.0
CD1 B:LEU132 4.3 18.7 1.0
CB A:PHE96 4.4 19.9 1.0
CA A:THR97 4.5 18.9 1.0
CB A:THR97 4.5 18.4 1.0
O A:CYS95 4.6 24.3 1.0
C A:THR97 4.6 19.8 1.0
O A:HOH2110 4.7 27.8 1.0

Iodine binding site 5 out of 10 in 2q2l

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Iodine binding site 5 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2007

b:39.1
occ:0.30
CD A:PRO61 3.8 17.6 1.0
CB A:ALA48 3.8 16.1 1.0
CD1 A:LEU49 4.1 13.1 1.0
CG A:PRO61 4.3 16.5 1.0
CG A:LEU49 4.3 14.5 1.0
CD2 A:LEU49 4.3 10.9 1.0
CA A:GLY60 5.0 17.5 1.0

Iodine binding site 6 out of 10 in 2q2l

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Iodine binding site 6 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2008

b:30.6
occ:0.25
O A:HOH2035 2.4 12.7 1.0
CB A:CYS56 3.7 19.2 1.0
N A:MET57 3.8 20.4 1.0
CG A:MET57 3.8 31.2 1.0
O A:ARG142 3.9 25.6 1.0
O A:HOH2079 4.0 21.2 1.0
N A:CYS56 4.1 21.8 1.0
CB A:ARG142 4.1 23.0 1.0
CA A:CYS56 4.2 20.7 1.0
C A:CYS56 4.2 20.1 1.0
CB A:MET57 4.3 21.7 1.0
I A:IOD2004 4.4 26.6 0.5
SD A:MET57 4.4 40.1 1.0
CA A:MET57 4.5 22.4 1.0
O A:HOH2111 4.6 36.7 1.0
C A:ARG142 4.7 24.1 1.0
SG A:CYS56 4.8 21.5 1.0
CD A:ARG142 4.9 17.9 1.0
CA A:ARG142 5.0 24.5 1.0
CG A:ARG142 5.0 20.5 1.0

Iodine binding site 7 out of 10 in 2q2l

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Iodine binding site 7 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2001

b:28.5
occ:0.80
CA B:SER58 3.9 21.5 1.0
OD1 B:ASN54 3.9 19.8 1.0
CD2 A:LEU19 4.0 26.2 1.0
CB B:SER58 4.0 19.8 1.0
N B:SER58 4.0 21.2 1.0
O B:MET57 4.1 25.1 1.0
C B:MET57 4.1 23.9 1.0
CB B:ASN54 4.3 24.4 1.0
NE2 A:GLN151 4.4 24.5 1.0
CB B:MET57 4.4 25.6 1.0
CD1 A:LEU19 4.4 23.7 1.0
O B:HOH2056 4.5 28.2 1.0
CG B:ASN54 4.6 24.2 1.0
O A:HOH2033 4.6 31.7 1.0
OG1 A:THR17 4.7 25.0 1.0
SD B:MET57 4.8 37.9 1.0
CG A:LEU19 4.8 24.7 1.0
CA B:MET57 4.9 25.2 1.0

Iodine binding site 8 out of 10 in 2q2l

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Iodine binding site 8 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2006

b:25.4
occ:0.25
O B:HOH2050 2.8 25.9 1.0
N B:ASN64 3.5 22.0 1.0
C B:ASN64 3.6 23.5 1.0
O B:ASN64 3.7 24.8 1.0
N B:PRO65 3.8 23.7 1.0
CA B:ASN64 4.0 22.6 1.0
CD1 B:PHE63 4.1 16.9 1.0
CA B:PRO65 4.2 23.9 1.0
CB B:ALA48 4.4 15.0 1.0
CD B:PRO65 4.5 24.1 1.0
C B:PHE63 4.5 20.2 1.0
CE1 B:PHE63 4.5 16.2 1.0
CA B:PHE63 4.6 18.8 1.0
CB B:ASN64 4.7 20.9 1.0
O B:HIS62 4.9 22.1 1.0
NH2 B:ARG114 4.9 17.2 1.0
O B:HOH2099 5.0 34.5 1.0

Iodine binding site 9 out of 10 in 2q2l

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Iodine binding site 9 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2009

b:25.2
occ:0.25
CA B:ASP91 3.7 31.5 1.0
CB B:ASP91 4.0 32.0 1.0
O B:ASP91 4.1 29.8 1.0
C B:ASP91 4.2 29.8 1.0
O B:ASP90 4.3 33.9 1.0
N B:ASP91 4.7 32.0 1.0
C B:ASP90 4.9 34.1 1.0

Iodine binding site 10 out of 10 in 2q2l

Go back to Iodine Binding Sites List in 2q2l
Iodine binding site 10 out of 10 in the Crystal Structure of Superoxide Dismutase From P. Atrosanguina


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 Superoxide Dismutase From P. Atrosanguina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2010

b:36.3
occ:0.30
CD B:PRO61 3.8 17.8 1.0
CD1 B:LEU49 3.9 8.7 1.0
CD2 B:LEU49 4.0 14.8 1.0
CB B:ALA48 4.1 15.0 1.0
CG B:LEU49 4.1 14.2 1.0
CG B:PRO61 4.7 19.1 1.0
CA B:GLY60 4.9 19.4 1.0

Reference:

M.Yogavel, J.Gill, P.C.Mishra, A.Sharma. Sad Phasing of A Structure Based on Cocrystallized Iodides Using An in-House Cu Kalpha X-Ray Source: Effects of Data Redundancy and Completeness on Structure Solution Acta Crystallogr.,Sect.D V. 63 931 2007.
ISSN: ISSN 0907-4449
PubMed: 17642520
DOI: 10.1107/S0907444907029174
Page generated: Sun Jan 24 17:24:20 2021

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