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Chlorine in PDB 3m13: Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase

Enzymatic activity of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase

All present enzymatic activity of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase:
1.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase, PDB code: 3m13 was solved by F.S.Mathews, Z.-W.Chen, M.S.Jorns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.20 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.296, 69.298, 111.427, 90.00, 93.40, 90.00
R / Rfree (%) 18.7 / 24.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase (pdb code 3m13). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase, PDB code: 3m13:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3m13

Go back to Chlorine Binding Sites List in 3m13
Chlorine binding site 1 out of 4 in the Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:24.0
occ:1.00
 O3' A:FAD400 2.9 20.6 1.0
N A:GLY344 3.1 24.1 1.0
O A:HOH397 3.1 16.9 1.0
N A:THR318 3.5 23.5 1.0
C3' A:FAD400 3.5 19.6 1.0
N A:SER343 3.5 21.5 1.0
CA A:TYR317 3.6 19.3 1.0
C A:PHE342 3.7 23.3 1.0
CA A:GLY344 3.8 21.3 1.0
CB A:PHE342 4.0 21.9 1.0
C A:TYR317 4.0 21.8 1.0
O A:HOH581 4.0 16.6 1.0
C A:SER343 4.1 22.9 1.0
O A:PHE342 4.1 23.6 1.0
CA A:PHE342 4.1 21.4 1.0
C5' A:FAD400 4.1 16.6 1.0
CA A:SER343 4.2 21.9 1.0
O A:MET316 4.2 20.4 1.0
C1' A:FAD400 4.2 15.5 1.0
CB A:TYR317 4.3 20.1 1.0
N A:PHE342 4.3 22.6 1.0
O A:THR318 4.4 25.3 1.0
C4' A:FAD400 4.4 18.1 1.0
OG A:SER43 4.5 19.3 1.0
CA A:THR318 4.6 21.4 1.0
C2' A:FAD400 4.6 17.7 1.0
C A:GLY344 4.6 21.2 1.0
CB A:THR318 4.6 22.4 1.0
CD1 A:TYR317 4.7 17.5 1.0
N A:TYR317 4.7 18.6 1.0
N A:HIS345 4.7 20.7 1.0
OG1 A:THR318 4.7 22.2 1.0
CG A:TYR317 4.8 17.8 1.0
CB A:SER43 4.8 19.6 1.0
C A:THR318 4.8 24.1 1.0
C A:MET316 4.9 22.4 1.0

Chlorine binding site 2 out of 4 in 3m13

Go back to Chlorine Binding Sites List in 3m13
Chlorine binding site 2 out of 4 in the Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:35.1
occ:1.00
 O3' B:FAD400 2.8 29.4 1.0
O B:HOH395 2.9 25.1 1.0
N B:GLY344 3.1 31.6 1.0
N B:THR318 3.4 32.7 1.0
C3' B:FAD400 3.4 25.7 1.0
N B:SER343 3.5 34.7 1.0
C B:PHE342 3.6 36.0 1.0
CA B:TYR317 3.7 30.5 1.0
CA B:GLY344 3.8 30.8 1.0
CB B:PHE342 4.0 36.2 1.0
O B:PHE342 4.0 35.0 1.0
C B:TYR317 4.0 31.6 1.0
CA B:PHE342 4.1 36.9 1.0
C B:SER343 4.1 33.2 1.0
O B:HOH404 4.1 26.1 1.0
O B:MET316 4.2 29.7 1.0
C5' B:FAD400 4.2 23.4 1.0
CA B:SER343 4.2 34.2 1.0
CB B:TYR317 4.3 30.2 1.0
C1' B:FAD400 4.3 28.3 1.0
N B:PHE342 4.4 37.5 1.0
C4' B:FAD400 4.4 24.8 1.0
O B:THR318 4.5 34.5 1.0
CA B:THR318 4.5 32.8 1.0
OG B:SER43 4.6 31.4 1.0
C2' B:FAD400 4.6 27.7 1.0
N B:HIS345 4.6 30.4 1.0
C B:GLY344 4.6 30.9 1.0
CD1 B:TYR317 4.7 29.6 1.0
CB B:THR318 4.7 32.9 1.0
OG1 B:THR318 4.7 34.2 1.0
CG B:TYR317 4.8 28.7 1.0
N B:TYR317 4.8 29.4 1.0
C B:THR318 4.8 33.3 1.0
C B:MET316 4.9 30.4 1.0
CB B:SER43 5.0 29.9 1.0

Chlorine binding site 3 out of 4 in 3m13

Go back to Chlorine Binding Sites List in 3m13
Chlorine binding site 3 out of 4 in the Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:31.9
occ:1.00
 O3' C:FAD400 3.0 28.5 1.0
O C:HOH458 3.0 28.6 1.0
N C:GLY344 3.2 29.1 1.0
N C:THR318 3.2 32.8 1.0
N C:SER343 3.4 31.5 1.0
CA C:TYR317 3.6 30.6 1.0
C3' C:FAD400 3.6 29.6 1.0
C C:PHE342 3.6 30.5 1.0
C C:TYR317 3.8 31.6 1.0
CA C:GLY344 3.9 27.0 1.0
CB C:PHE342 4.0 30.2 1.0
O C:HOH412 4.0 29.7 1.0
CA C:PHE342 4.0 30.4 1.0
O C:MET316 4.1 28.8 1.0
O C:PHE342 4.1 30.6 1.0
C C:SER343 4.1 29.6 1.0
CA C:SER343 4.2 29.7 1.0
O C:THR318 4.2 34.5 1.0
C5' C:FAD400 4.2 27.7 1.0
N C:PHE342 4.2 31.3 1.0
CA C:THR318 4.3 33.5 1.0
CB C:TYR317 4.3 32.7 1.0
C1' C:FAD400 4.5 30.0 1.0
C4' C:FAD400 4.6 28.7 1.0
C C:THR318 4.6 34.3 1.0
CB C:THR318 4.7 35.1 1.0
OG1 C:THR318 4.7 32.1 1.0
N C:TYR317 4.7 29.4 1.0
OG C:SER43 4.7 31.5 1.0
C2' C:FAD400 4.7 28.9 1.0
C C:GLY344 4.7 28.1 1.0
N C:HIS345 4.8 27.9 1.0
C C:MET316 4.8 31.7 1.0
CD1 C:TYR317 4.9 35.4 1.0
CB C:SER43 4.9 32.3 1.0
CG C:TYR317 4.9 30.7 1.0
O C:TYR317 5.0 31.7 1.0

Chlorine binding site 4 out of 4 in 3m13

Go back to Chlorine Binding Sites List in 3m13
Chlorine binding site 4 out of 4 in the Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the LYS265ARG Peg-Crystallized Mutant of Monomeric Sarcosine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:26.4
occ:1.00
 O3' D:FAD400 2.8 21.7 1.0
O D:HOH401 3.1 20.7 1.0
N D:GLY344 3.1 27.0 1.0
N D:THR318 3.3 26.8 1.0
N D:SER343 3.4 26.0 1.0
C3' D:FAD400 3.5 23.3 1.0
CA D:TYR317 3.6 24.5 1.0
C D:PHE342 3.7 27.7 1.0
CA D:GLY344 3.8 25.2 1.0
C D:TYR317 3.9 27.2 1.0
O D:HOH435 3.9 27.0 1.0
CB D:PHE342 3.9 26.0 1.0
CA D:PHE342 4.1 25.3 1.0
C D:SER343 4.1 26.6 1.0
CA D:SER343 4.1 26.8 1.0
O D:MET316 4.2 25.2 1.0
O D:PHE342 4.2 28.1 1.0
C5' D:FAD400 4.2 24.8 1.0
N D:PHE342 4.3 25.9 1.0
CB D:TYR317 4.3 23.9 1.0
C1' D:FAD400 4.3 22.8 1.0
O D:THR318 4.4 29.9 1.0
CA D:THR318 4.4 28.5 1.0
C4' D:FAD400 4.4 23.9 1.0
C2' D:FAD400 4.6 23.2 1.0
CB D:THR318 4.6 28.8 1.0
OG1 D:THR318 4.6 31.1 1.0
OG D:SER43 4.7 29.0 1.0
CD1 D:TYR317 4.7 27.0 1.0
N D:TYR317 4.7 24.2 1.0
C D:THR318 4.7 28.9 1.0
C D:GLY344 4.7 25.5 1.0
CB D:SER43 4.8 25.8 1.0
CG D:TYR317 4.8 24.5 1.0
N D:HIS345 4.8 25.2 1.0
C D:MET316 4.9 27.1 1.0

Reference:

M.S.Jorns, Z.W.Chen, F.S.Mathews. Structural Characterization of Mutations at the Oxygen Activation Site in Monomeric Sarcosine Oxidase. Biochemistry V. 49 3631 2010.
ISSN: ISSN 0006-2960
PubMed: 20353187
DOI: 10.1021/BI100160J
Page generated: Sat Jul 20 23:54:06 2024

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